HRT-UML: a design method for hard real-time systems based on the UML notation

NASA Astrophysics Data System (ADS)

D'Alessandro, Massimo; Mazzini, Silvia; di Natale, Marco; Lipari, Giuseppe

2002-07-01

The Hard Real-Time-Unified Modelling Language (HRT-UML) method aims at providing a comprehensive solution to the modeling of Hard Real Time systems. The experience shows that the design of Hard Real-Time systems needs methodologies suitable for the modeling and analysis of aspects related to time, schedulability and performance. In the context of the European Aerospace community a reference method for design is Hierarchical Object Oriented Design (HOOD) and in particular its extension for the modeling of hard real time systems, Hard Real-Time-Hierarchical Object Oriented Design (HRT-HOOD), recommended by the European Space Agency (ESA) for the development of on-board systems. On the other hand in recent years the Unified Modelling Language (UML) has been gaining a very large acceptance in a wide range of domains, all over the world, becoming a de-facto international standard. Tool vendors are very active in this potentially big market. In the Aerospace domain the common opinion is that UML, as a general notation, is not suitable for Hard Real Time systems, even if its importance is recognized as a standard and as a technological trend in the near future. These considerations suggest the possibility of replacing the HRT-HOOD method with a customized version of UML, that incorporates the advantages of both standards and complements the weak points. This approach has the clear advantage of making HRT-HOOD converge on a more powerful and expressive modeling notation. The paper identifies a mapping of the HRT-HOOD semantics into the UML one, and proposes a UML extension profile, that we call HRT-UML, based on the UML standard extension mechanisms, to fully represent HRT-HOOD design concepts. Finally it discusses the relationships between our profile and the UML profile for schedulability, performance and time, adopted by OMG in November 2001.

A Formal Modelling Language Extending SysML for Simulation of Continuous and Discrete System

DTIC Science & Technology

2012-11-01

UNCLASSIFIED DSTO-GD-0734 16. A Formal Modelling Language Extending SysML for Simulation of Continuous and Discrete System – Mark Hodson1 and...be conceptual at some level because a one to one mapping with the real system will never exist. SysML is an extension and modification of UML that...simulation, which can provide great insights into the behaviour of complex systems. Although UML and SysML primarily support conceptual modelling they

Indexing Anatomical Phrases in Neuro-Radiology Reports to the UMLS 2005AA

PubMed Central

Bashyam, Vijayaraghavan; Taira, Ricky K.

2005-01-01

This work describes a methodology to index anatomical phrases to the 2005AA release of the Unified Medical Language System (UMLS). A phrase chunking tool based on Natural Language Processing (NLP) was developed to identify semantically coherent phrases within medical reports. Using this phrase chunker, a set of 2,551 unique anatomical phrases was extracted from brain radiology reports. These phrases were mapped to the 2005AA release of the UMLS using a vector space model. Precision for the task of indexing unique phrases was 0.87. PMID:16778995

Using the Unified Modelling Language (UML) to guide the systemic description of biological processes and systems.

PubMed

Roux-Rouquié, Magali; Caritey, Nicolas; Gaubert, Laurent; Rosenthal-Sabroux, Camille

2004-07-01

One of the main issues in Systems Biology is to deal with semantic data integration. Previously, we examined the requirements for a reference conceptual model to guide semantic integration based on the systemic principles. In the present paper, we examine the usefulness of the Unified Modelling Language (UML) to describe and specify biological systems and processes. This makes unambiguous representations of biological systems, which would be suitable for translation into mathematical and computational formalisms, enabling analysis, simulation and prediction of these systems behaviours.

Toward a Model-Based Approach for Flight System Fault Protection

NASA Technical Reports Server (NTRS)

Day, John; Meakin, Peter; Murray, Alex

2012-01-01

Use SysML/UML to describe the physical structure of the system This part of the model would be shared with other teams - FS Systems Engineering, Planning & Execution, V&V, Operations, etc., in an integrated model-based engineering environment Use the UML Profile mechanism, defining Stereotypes to precisely express the concepts of the FP domain This extends the UML/SysML languages to contain our FP concepts Use UML/SysML, along with our profile, to capture FP concepts and relationships in the model Generate typical FP engineering products (the FMECA, Fault Tree, MRD, V&V Matrices)

Modeling a Nursing Guideline with Standard Terminology and Unified Modeling Language for a Nursing Decision Support System: A Case Study.

PubMed

Choi, Jeeyae; Jansen, Kay; Coenen, Amy

In recent years, Decision Support Systems (DSSs) have been developed and used to achieve "meaningful use". One approach to developing DSSs is to translate clinical guidelines into a computer-interpretable format. However, there is no specific guideline modeling approach to translate nursing guidelines to computer-interpretable guidelines. This results in limited use of DSSs in nursing. Unified modeling language (UML) is a software writing language known to accurately represent the end-users' perspective, due to its expressive characteristics. Furthermore, standard terminology enabled DSSs have been shown to smoothly integrate into existing health information systems. In order to facilitate development of nursing DSSs, the UML was used to represent a guideline for medication management for older adults encode with the International Classification for Nursing Practice (ICNP®). The UML was found to be a useful and sufficient tool to model a nursing guideline for a DSS.

Modeling a Nursing Guideline with Standard Terminology and Unified Modeling Language for a Nursing Decision Support System: A Case Study

PubMed Central

Choi, Jeeyae; Jansen, Kay; Coenen, Amy

2015-01-01

In recent years, Decision Support Systems (DSSs) have been developed and used to achieve “meaningful use”. One approach to developing DSSs is to translate clinical guidelines into a computer-interpretable format. However, there is no specific guideline modeling approach to translate nursing guidelines to computer-interpretable guidelines. This results in limited use of DSSs in nursing. Unified modeling language (UML) is a software writing language known to accurately represent the end-users’ perspective, due to its expressive characteristics. Furthermore, standard terminology enabled DSSs have been shown to smoothly integrate into existing health information systems. In order to facilitate development of nursing DSSs, the UML was used to represent a guideline for medication management for older adults encode with the International Classification for Nursing Practice (ICNP®). The UML was found to be a useful and sufficient tool to model a nursing guideline for a DSS. PMID:26958174

Standardizing clinical trials workflow representation in UML for international site comparison.

PubMed

de Carvalho, Elias Cesar Araujo; Jayanti, Madhav Kishore; Batilana, Adelia Portero; Kozan, Andreia M O; Rodrigues, Maria J; Shah, Jatin; Loures, Marco R; Patil, Sunita; Payne, Philip; Pietrobon, Ricardo

2010-11-09

With the globalization of clinical trials, a growing emphasis has been placed on the standardization of the workflow in order to ensure the reproducibility and reliability of the overall trial. Despite the importance of workflow evaluation, to our knowledge no previous studies have attempted to adapt existing modeling languages to standardize the representation of clinical trials. Unified Modeling Language (UML) is a computational language that can be used to model operational workflow, and a UML profile can be developed to standardize UML models within a given domain. This paper's objective is to develop a UML profile to extend the UML Activity Diagram schema into the clinical trials domain, defining a standard representation for clinical trial workflow diagrams in UML. Two Brazilian clinical trial sites in rheumatology and oncology were examined to model their workflow and collect time-motion data. UML modeling was conducted in Eclipse, and a UML profile was developed to incorporate information used in discrete event simulation software. Ethnographic observation revealed bottlenecks in workflow: these included tasks requiring full commitment of CRCs, transferring notes from paper to computers, deviations from standard operating procedures, and conflicts between different IT systems. Time-motion analysis revealed that nurses' activities took up the most time in the workflow and contained a high frequency of shorter duration activities. Administrative assistants performed more activities near the beginning and end of the workflow. Overall, clinical trial tasks had a greater frequency than clinic routines or other general activities. This paper describes a method for modeling clinical trial workflow in UML and standardizing these workflow diagrams through a UML profile. In the increasingly global environment of clinical trials, the standardization of workflow modeling is a necessary precursor to conducting a comparative analysis of international clinical trials workflows.

Standardizing Clinical Trials Workflow Representation in UML for International Site Comparison

PubMed Central

de Carvalho, Elias Cesar Araujo; Jayanti, Madhav Kishore; Batilana, Adelia Portero; Kozan, Andreia M. O.; Rodrigues, Maria J.; Shah, Jatin; Loures, Marco R.; Patil, Sunita; Payne, Philip; Pietrobon, Ricardo

2010-01-01

Background With the globalization of clinical trials, a growing emphasis has been placed on the standardization of the workflow in order to ensure the reproducibility and reliability of the overall trial. Despite the importance of workflow evaluation, to our knowledge no previous studies have attempted to adapt existing modeling languages to standardize the representation of clinical trials. Unified Modeling Language (UML) is a computational language that can be used to model operational workflow, and a UML profile can be developed to standardize UML models within a given domain. This paper's objective is to develop a UML profile to extend the UML Activity Diagram schema into the clinical trials domain, defining a standard representation for clinical trial workflow diagrams in UML. Methods Two Brazilian clinical trial sites in rheumatology and oncology were examined to model their workflow and collect time-motion data. UML modeling was conducted in Eclipse, and a UML profile was developed to incorporate information used in discrete event simulation software. Results Ethnographic observation revealed bottlenecks in workflow: these included tasks requiring full commitment of CRCs, transferring notes from paper to computers, deviations from standard operating procedures, and conflicts between different IT systems. Time-motion analysis revealed that nurses' activities took up the most time in the workflow and contained a high frequency of shorter duration activities. Administrative assistants performed more activities near the beginning and end of the workflow. Overall, clinical trial tasks had a greater frequency than clinic routines or other general activities. Conclusions This paper describes a method for modeling clinical trial workflow in UML and standardizing these workflow diagrams through a UML profile. In the increasingly global environment of clinical trials, the standardization of workflow modeling is a necessary precursor to conducting a comparative analysis of international clinical trials workflows. PMID:21085484

Automated encoding of clinical documents based on natural language processing.

PubMed

Friedman, Carol; Shagina, Lyudmila; Lussier, Yves; Hripcsak, George

2004-01-01

The aim of this study was to develop a method based on natural language processing (NLP) that automatically maps an entire clinical document to codes with modifiers and to quantitatively evaluate the method. An existing NLP system, MedLEE, was adapted to automatically generate codes. The method involves matching of structured output generated by MedLEE consisting of findings and modifiers to obtain the most specific code. Recall and precision applied to Unified Medical Language System (UMLS) coding were evaluated in two separate studies. Recall was measured using a test set of 150 randomly selected sentences, which were processed using MedLEE. Results were compared with a reference standard determined manually by seven experts. Precision was measured using a second test set of 150 randomly selected sentences from which UMLS codes were automatically generated by the method and then validated by experts. Recall of the system for UMLS coding of all terms was .77 (95% CI.72-.81), and for coding terms that had corresponding UMLS codes recall was .83 (.79-.87). Recall of the system for extracting all terms was .84 (.81-.88). Recall of the experts ranged from .69 to .91 for extracting terms. The precision of the system was .89 (.87-.91), and precision of the experts ranged from .61 to .91. Extraction of relevant clinical information and UMLS coding were accomplished using a method based on NLP. The method appeared to be comparable to or better than six experts. The advantage of the method is that it maps text to codes along with other related information, rendering the coded output suitable for effective retrieval.

Unified modeling language and design of a case-based retrieval system in medical imaging.

PubMed Central

LeBozec, C.; Jaulent, M. C.; Zapletal, E.; Degoulet, P.

1998-01-01

One goal of artificial intelligence research into case-based reasoning (CBR) systems is to develop approaches for designing useful and practical interactive case-based environments. Explaining each step of the design of the case-base and of the retrieval process is critical for the application of case-based systems to the real world. We describe herein our approach to the design of IDEM--Images and Diagnosis from Examples in Medicine--a medical image case-based retrieval system for pathologists. Our approach is based on the expressiveness of an object-oriented modeling language standard: the Unified Modeling Language (UML). We created a set of diagrams in UML notation illustrating the steps of the CBR methodology we used. The key aspect of this approach was selecting the relevant objects of the system according to user requirements and making visualization of cases and of the components of the case retrieval process. Further evaluation of the expressiveness of the design document is required but UML seems to be a promising formalism, improving the communication between the developers and users. Images Figure 6 Figure 7 PMID:9929346

Unified modeling language and design of a case-based retrieval system in medical imaging.

PubMed

LeBozec, C; Jaulent, M C; Zapletal, E; Degoulet, P

1998-01-01

One goal of artificial intelligence research into case-based reasoning (CBR) systems is to develop approaches for designing useful and practical interactive case-based environments. Explaining each step of the design of the case-base and of the retrieval process is critical for the application of case-based systems to the real world. We describe herein our approach to the design of IDEM--Images and Diagnosis from Examples in Medicine--a medical image case-based retrieval system for pathologists. Our approach is based on the expressiveness of an object-oriented modeling language standard: the Unified Modeling Language (UML). We created a set of diagrams in UML notation illustrating the steps of the CBR methodology we used. The key aspect of this approach was selecting the relevant objects of the system according to user requirements and making visualization of cases and of the components of the case retrieval process. Further evaluation of the expressiveness of the design document is required but UML seems to be a promising formalism, improving the communication between the developers and users.

Vehicle System Management Modeling in UML for Ares I

NASA Technical Reports Server (NTRS)

Pearson, Newton W.; Biehn, Bradley A.; Curry, Tristan D.; Martinez, Mario R.

2011-01-01

The Spacecraft & Vehicle Systems Department of Marshall Space Flight Center is responsible for modeling the Vehicle System Management for the Ares I vehicle which was a part of the now canceled Constellation Program. An approach to generating the requirements for the Vehicle System Management was to use the Unified Modeling Language technique to build and test a model that would fulfill the Vehicle System Management requirements. UML has been used on past projects (flight software) in the design phase of the effort but this was the first attempt to use the UML technique from a top down requirements perspective.

Query Expansion Using SNOMED-CT and Weighing Schemes

DTIC Science & Technology

2014-11-01

For this research, we have used SNOMED-CT along with UMLS Methathesaurus as our ontology in medical domain to expand the queries. General Terms...CT along with UMLS Methathesaurus as our ontology in medical domain to expand the queries. 15. SUBJECT TERMS 16. SECURITY CLASSIFICATION OF: 17...University of the Basque country discuss their finding on query expansion using external sources headlined by Unified Medical Language System ( UMLS

Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts

PubMed Central

He, Zhe; Perl, Yehoshua; Elhanan, Gai; Chen, Yan; Geller, James; Bian, Jiang

2018-01-01

The Unified Medical Language System (UMLS) is an important terminological system. By the policy of its curators, each concept of the UMLS should be assigned the most specific Semantic Types (STs) in the UMLS Semantic Network (SN). Hence, the Semantic Types of most UMLS concepts are assigned at or near the bottom (leaves) of the UMLS Semantic Network. While most ST assignments are correct, some errors do occur. Therefore, Quality Assurance efforts of UMLS curators for ST assignments should concentrate on automatically detected sets of UMLS concepts with higher error rates than random sets. In this paper, we investigate the assignments of top-level semantic types in the UMLS semantic network to concepts, identify potential erroneous assignments, define four categories of errors, and thus provide assistance to curators of the UMLS to avoid these assignments errors. Human experts analyzed samples of concepts assigned 10 of the top-level semantic types and categorized the erroneous ST assignments into these four logical categories. Two thirds of the concepts assigned these 10 top-level semantic types are erroneous. Our results demonstrate that reviewing top-level semantic type assignments to concepts provides an effective way for UMLS quality assurance, comparing to reviewing a random selection of semantic type assignments. PMID:29375930

Auditing the Assignments of Top-Level Semantic Types in the UMLS Semantic Network to UMLS Concepts.

PubMed

He, Zhe; Perl, Yehoshua; Elhanan, Gai; Chen, Yan; Geller, James; Bian, Jiang

2017-11-01

The Unified Medical Language System (UMLS) is an important terminological system. By the policy of its curators, each concept of the UMLS should be assigned the most specific Semantic Types (STs) in the UMLS Semantic Network (SN). Hence, the Semantic Types of most UMLS concepts are assigned at or near the bottom (leaves) of the UMLS Semantic Network. While most ST assignments are correct, some errors do occur. Therefore, Quality Assurance efforts of UMLS curators for ST assignments should concentrate on automatically detected sets of UMLS concepts with higher error rates than random sets. In this paper, we investigate the assignments of top-level semantic types in the UMLS semantic network to concepts, identify potential erroneous assignments, define four categories of errors, and thus provide assistance to curators of the UMLS to avoid these assignments errors. Human experts analyzed samples of concepts assigned 10 of the top-level semantic types and categorized the erroneous ST assignments into these four logical categories. Two thirds of the concepts assigned these 10 top-level semantic types are erroneous. Our results demonstrate that reviewing top-level semantic type assignments to concepts provides an effective way for UMLS quality assurance, comparing to reviewing a random selection of semantic type assignments.

Automatic Synthesis of UML Designs from Requirements in an Iterative Process

NASA Technical Reports Server (NTRS)

Schumann, Johann; Whittle, Jon; Clancy, Daniel (Technical Monitor)

2001-01-01

The Unified Modeling Language (UML) is gaining wide popularity for the design of object-oriented systems. UML combines various object-oriented graphical design notations under one common framework. A major factor for the broad acceptance of UML is that it can be conveniently used in a highly iterative, Use Case (or scenario-based) process (although the process is not a part of UML). Here, the (pre-) requirements for the software are specified rather informally as Use Cases and a set of scenarios. A scenario can be seen as an individual trace of a software artifact. Besides first sketches of a class diagram to illustrate the static system breakdown, scenarios are a favorite way of communication with the customer, because scenarios describe concrete interactions between entities and are thus easy to understand. Scenarios with a high level of detail are often expressed as sequence diagrams. Later in the design and implementation stage (elaboration and implementation phases), a design of the system's behavior is often developed as a set of statecharts. From there (and the full-fledged class diagram), actual code development is started. Current commercial UML tools support this phase by providing code generators for class diagrams and statecharts. In practice, it can be observed that the transition from requirements to design to code is a highly iterative process. In this talk, a set of algorithms is presented which perform reasonable synthesis and transformations between different UML notations (sequence diagrams, Object Constraint Language (OCL) constraints, statecharts). More specifically, we will discuss the following transformations: Statechart synthesis, introduction of hierarchy, consistency of modifications, and "design-debugging".

Towards a Semantic Lexicon for Biological Language Processing

DOE PAGES

Verspoor, Karin

2005-01-01

This paper explores the use of the resources in the National Library of Medicine's Unified Medical Language System (UMLS) for the construction of a lexicon useful for processing texts in the field of molecular biology. A lexicon is constructed from overlapping terms in the UMLS SPECIALIST lexicon and the UMLS Metathesaurus to obtain both morphosyntactic and semantic information for terms, and the coverage of a domain corpus is assessed. Over 77% of tokens in the domain corpus are found in the constructed lexicon, validating the lexicon's coverage of the most frequent terms in the domain and indicating that the constructedmore » lexicon is potentially an important resource for biological text processing.« less

Consistent model driven architecture

NASA Astrophysics Data System (ADS)

Niepostyn, Stanisław J.

2015-09-01

The goal of the MDA is to produce software systems from abstract models in a way where human interaction is restricted to a minimum. These abstract models are based on the UML language. However, the semantics of UML models is defined in a natural language. Subsequently the verification of consistency of these diagrams is needed in order to identify errors in requirements at the early stage of the development process. The verification of consistency is difficult due to a semi-formal nature of UML diagrams. We propose automatic verification of consistency of the series of UML diagrams originating from abstract models implemented with our consistency rules. This Consistent Model Driven Architecture approach enables us to generate automatically complete workflow applications from consistent and complete models developed from abstract models (e.g. Business Context Diagram). Therefore, our method can be used to check practicability (feasibility) of software architecture models.

Connecting Architecture and Implementation

NASA Astrophysics Data System (ADS)

Buchgeher, Georg; Weinreich, Rainer

Software architectures are still typically defined and described independently from implementation. To avoid architectural erosion and drift, architectural representation needs to be continuously updated and synchronized with system implementation. Existing approaches for architecture representation like informal architecture documentation, UML diagrams, and Architecture Description Languages (ADLs) provide only limited support for connecting architecture descriptions and implementations. Architecture management tools like Lattix, SonarJ, and Sotoarc and UML-tools tackle this problem by extracting architecture information directly from code. This approach works for low-level architectural abstractions like classes and interfaces in object-oriented systems but fails to support architectural abstractions not found in programming languages. In this paper we present an approach for linking and continuously synchronizing a formalized architecture representation to an implementation. The approach is a synthesis of functionality provided by code-centric architecture management and UML tools and higher-level architecture analysis approaches like ADLs.

A UML Profile for State Analysis

NASA Technical Reports Server (NTRS)

Murray, Alex; Rasmussen, Robert

2010-01-01

State Analysis is a systems engineering methodology for the specification and design of control systems, developed at the Jet Propulsion Laboratory. The methodology emphasizes an analysis of the system under control in terms of States and their properties and behaviors and their effects on each other, a clear separation of the control system from the controlled system, cognizance in the control system of the controlled system's State, goal-based control built on constraining the controlled system's States, and disciplined techniques for State discovery and characterization. State Analysis (SA) introduces two key diagram types: State Effects and Goal Network diagrams. The team at JPL developed a tool for performing State Analysis. The tool includes a drawing capability, backed by a database that supports the diagram types and the organization of the elements of the SA models. But the tool does not support the usual activities of software engineering and design - a disadvantage, since systems to which State Analysis can be applied tend to be very software-intensive. This motivated the work described in this paper: the development of a preliminary Unified Modeling Language (UML) profile for State Analysis. Having this profile would enable systems engineers to specify a system using the methods and graphical language of State Analysis, which is easily linked with a larger system model in SysML (Systems Modeling Language), while also giving software engineers engaged in implementing the specified control system immediate access to and use of the SA model, in the same language, UML, used for other software design. That is, a State Analysis profile would serve as a shared modeling bridge between system and software models for the behavior aspects of the system. This paper begins with an overview of State Analysis and its underpinnings, followed by an overview of the mapping of SA constructs to the UML metamodel. It then delves into the details of these mappings and the constraints associated with them. Finally, we give an example of the use of the profile for expressing an example SA model.

Modelling biological behaviours with the unified modelling language: an immunological case study and critique.

PubMed

Read, Mark; Andrews, Paul S; Timmis, Jon; Kumar, Vipin

2014-10-06

We present a framework to assist the diagrammatic modelling of complex biological systems using the unified modelling language (UML). The framework comprises three levels of modelling, ranging in scope from the dynamics of individual model entities to system-level emergent properties. By way of an immunological case study of the mouse disease experimental autoimmune encephalomyelitis, we show how the framework can be used to produce models that capture and communicate the biological system, detailing how biological entities, interactions and behaviours lead to higher-level emergent properties observed in the real world. We demonstrate how the UML can be successfully applied within our framework, and provide a critique of UML's ability to capture concepts fundamental to immunology and biology more generally. We show how specialized, well-explained diagrams with less formal semantics can be used where no suitable UML formalism exists. We highlight UML's lack of expressive ability concerning cyclic feedbacks in cellular networks, and the compounding concurrency arising from huge numbers of stochastic, interacting agents. To compensate for this, we propose several additional relationships for expressing these concepts in UML's activity diagram. We also demonstrate the ambiguous nature of class diagrams when applied to complex biology, and question their utility in modelling such dynamic systems. Models created through our framework are non-executable, and expressly free of simulation implementation concerns. They are a valuable complement and precursor to simulation specifications and implementations, focusing purely on thoroughly exploring the biology, recording hypotheses and assumptions, and serve as a communication medium detailing exactly how a simulation relates to the real biology.

Modelling biological behaviours with the unified modelling language: an immunological case study and critique

PubMed Central

Read, Mark; Andrews, Paul S.; Timmis, Jon; Kumar, Vipin

2014-01-01

We present a framework to assist the diagrammatic modelling of complex biological systems using the unified modelling language (UML). The framework comprises three levels of modelling, ranging in scope from the dynamics of individual model entities to system-level emergent properties. By way of an immunological case study of the mouse disease experimental autoimmune encephalomyelitis, we show how the framework can be used to produce models that capture and communicate the biological system, detailing how biological entities, interactions and behaviours lead to higher-level emergent properties observed in the real world. We demonstrate how the UML can be successfully applied within our framework, and provide a critique of UML's ability to capture concepts fundamental to immunology and biology more generally. We show how specialized, well-explained diagrams with less formal semantics can be used where no suitable UML formalism exists. We highlight UML's lack of expressive ability concerning cyclic feedbacks in cellular networks, and the compounding concurrency arising from huge numbers of stochastic, interacting agents. To compensate for this, we propose several additional relationships for expressing these concepts in UML's activity diagram. We also demonstrate the ambiguous nature of class diagrams when applied to complex biology, and question their utility in modelling such dynamic systems. Models created through our framework are non-executable, and expressly free of simulation implementation concerns. They are a valuable complement and precursor to simulation specifications and implementations, focusing purely on thoroughly exploring the biology, recording hypotheses and assumptions, and serve as a communication medium detailing exactly how a simulation relates to the real biology. PMID:25142524

Designing Control System Application Software for Change

NASA Technical Reports Server (NTRS)

Boulanger, Richard

2001-01-01

The Unified Modeling Language (UML) was used to design the Environmental Systems Test Stand (ESTS) control system software. The UML was chosen for its ability to facilitate a clear dialog between software designer and customer, from which requirements are discovered and documented in a manner which transposes directly to program objects. Applying the UML to control system software design has resulted in a baseline set of documents from which change and effort of that change can be accurately measured. As the Environmental Systems Test Stand evolves, accurate estimates of the time and effort required to change the control system software will be made. Accurate quantification of the cost of software change can be before implementation, improving schedule and budget accuracy.

The Impact of an Automated Learning Component against a Traditional Lecturing Environment

ERIC Educational Resources Information Center

Maycock, Keith W.; Keating, J. G.

2017-01-01

This experimental study investigates the effect on the examination performance of a cohort of first-year undergraduate learners undertaking a Unified Modelling Language (UML) course using an adaptive learning system against a control group of learners undertaking the same UML course through a traditional lecturing environment. The adaptive…

Representing clinical guidelines in UMl: a comparative study.

PubMed

Hederman, Lucy; Smutek, Daniel; Wade, Vincent; Knape, Thomas

2002-01-01

Clinical guidelines can be represented using models, such as GLIF, specifically designed for healthcare guidelines. This paper demonstrates that they can also be modelled using a mainstream business modelling language such as UML. The paper presents a guideline in GLIF and as UML activity diagrams, and then presents a mapping of GLIF primitives to UML. The potential benefits of using a mainstream modelling language are outlined. These include availability of advanced modelling tools, transfer between modelling tools, and automation via business workflow technology.

Use of Unified Modeling Language (UML) in Model-Based Development (MBD) For Safety-Critical Applications

DTIC Science & Technology

2014-12-01

appears that UML is becoming the de facto MBD language. OMG® states the following on the MDA® FAQ page: “Although not formally required [for MBD], UML...a known limitation [42], so UML users should plan accordingly, especially for safety-critical programs. For example, “models are not used to...description of the MBD tool chain can be produced. That description could be resident in a Plan for Software Aspects of Certification (PSAC) or Software

Graphical User Interface for an Observing Control System for the UK Infrared Telescope

NASA Astrophysics Data System (ADS)

Tan, M.; Bridger, A.; Wright, G. S.; Adamson, A. J.; Currie, M. J.; Economou, F.

A Graphical user interface for the observing control system of UK Infrared Telescope has been developed as a part of the ORAC (Observatory Reduction and Acquisition Control) Project. We analyzed and designed the system using the Unified Modelling Language (UML) with the CASE tool Rational Rose 98. The system has been implemented in a modular way with Java packages using Swing and RMI. This system is component-based with pluggability. Object orientation concepts and UML notations have been applied throughout the development.

A UML model for the description of different brain-computer interface systems.

PubMed

Quitadamo, Lucia Rita; Abbafati, Manuel; Saggio, Giovanni; Marciani, Maria Grazia; Cardarilli, Gian Carlo; Bianchi, Luigi

2008-01-01

BCI research lacks a universal descriptive language among labs and a unique standard model for the description of BCI systems. This results in a serious problem in comparing performances of different BCI processes and in unifying tools and resources. In such a view we implemented a Unified Modeling Language (UML) model for the description virtually of any BCI protocol and we demonstrated that it can be successfully applied to the most common ones such as P300, mu-rhythms, SCP, SSVEP, fMRI. Finally we illustrated the advantages in utilizing a standard terminology for BCIs and how the same basic structure can be successfully adopted for the implementation of new systems.

UML activity diagrams in requirements specification of logic controllers

NASA Astrophysics Data System (ADS)

Grobelna, Iwona; Grobelny, Michał

2015-12-01

Logic controller specification can be prepared using various techniques. One of them is the wide understandable and user-friendly UML language and its activity diagrams. Using formal methods during the design phase increases the assurance that implemented system meets the project requirements. In the approach we use the model checking technique to formally verify a specification against user-defined behavioral requirements. The properties are usually defined as temporal logic formulas. In the paper we propose to use UML activity diagrams in requirements definition and then to formalize them as temporal logic formulas. As a result, UML activity diagrams can be used both for logic controller specification and for requirements definition, what simplifies the specification and verification process.

Using Unified Modelling Language (UML) as a process-modelling technique for clinical-research process improvement.

PubMed

Kumarapeli, P; De Lusignan, S; Ellis, T; Jones, B

2007-03-01

The Primary Care Data Quality programme (PCDQ) is a quality-improvement programme which processes routinely collected general practice computer data. Patient data collected from a wide range of different brands of clinical computer systems are aggregated, processed, and fed back to practices in an educational context to improve the quality of care. Process modelling is a well-established approach used to gain understanding and systematic appraisal, and identify areas of improvement of a business process. Unified modelling language (UML) is a general purpose modelling technique used for this purpose. We used UML to appraise the PCDQ process to see if the efficiency and predictability of the process could be improved. Activity analysis and thinking-aloud sessions were used to collect data to generate UML diagrams. The UML model highlighted the sequential nature of the current process as a barrier for efficiency gains. It also identified the uneven distribution of process controls, lack of symmetric communication channels, critical dependencies among processing stages, and failure to implement all the lessons learned in the piloting phase. It also suggested that improved structured reporting at each stage - especially from the pilot phase, parallel processing of data and correctly positioned process controls - should improve the efficiency and predictability of research projects. Process modelling provided a rational basis for the critical appraisal of a clinical data processing system; its potential maybe underutilized within health care.

k-neighborhood Decentralization: A Comprehensive Solution to Index the UMLS for Large Scale Knowledge Discovery

PubMed Central

Xiang, Yang; Lu, Kewei; James, Stephen L.; Borlawsky, Tara B.; Huang, Kun; Payne, Philip R.O.

2011-01-01

The Unified Medical Language System (UMLS) is the largest thesaurus in the biomedical informatics domain. Previous works have shown that knowledge constructs comprised of transitively-associated UMLS concepts are effective for discovering potentially novel biomedical hypotheses. However, the extremely large size of the UMLS becomes a major challenge for these applications. To address this problem, we designed a k-neighborhood Decentralization Labeling Scheme (kDLS) for the UMLS, and the corresponding method to effectively evaluate the kDLS indexing results. kDLS provides a comprehensive solution for indexing the UMLS for very efficient large scale knowledge discovery. We demonstrated that it is highly effective to use kDLS paths to prioritize disease-gene relations across the whole genome, with extremely high fold-enrichment values. To our knowledge, this is the first indexing scheme capable of supporting efficient large scale knowledge discovery on the UMLS as a whole. Our expectation is that kDLS will become a vital engine for retrieving information and generating hypotheses from the UMLS for future medical informatics applications. PMID:22154838

k-Neighborhood decentralization: a comprehensive solution to index the UMLS for large scale knowledge discovery.

PubMed

Xiang, Yang; Lu, Kewei; James, Stephen L; Borlawsky, Tara B; Huang, Kun; Payne, Philip R O

2012-04-01

The Unified Medical Language System (UMLS) is the largest thesaurus in the biomedical informatics domain. Previous works have shown that knowledge constructs comprised of transitively-associated UMLS concepts are effective for discovering potentially novel biomedical hypotheses. However, the extremely large size of the UMLS becomes a major challenge for these applications. To address this problem, we designed a k-neighborhood Decentralization Labeling Scheme (kDLS) for the UMLS, and the corresponding method to effectively evaluate the kDLS indexing results. kDLS provides a comprehensive solution for indexing the UMLS for very efficient large scale knowledge discovery. We demonstrated that it is highly effective to use kDLS paths to prioritize disease-gene relations across the whole genome, with extremely high fold-enrichment values. To our knowledge, this is the first indexing scheme capable of supporting efficient large scale knowledge discovery on the UMLS as a whole. Our expectation is that kDLS will become a vital engine for retrieving information and generating hypotheses from the UMLS for future medical informatics applications. Copyright © 2011 Elsevier Inc. All rights reserved.

UMLS content views appropriate for NLP processing of the biomedical literature vs. clinical text.

PubMed

Demner-Fushman, Dina; Mork, James G; Shooshan, Sonya E; Aronson, Alan R

2010-08-01

Identification of medical terms in free text is a first step in such Natural Language Processing (NLP) tasks as automatic indexing of biomedical literature and extraction of patients' problem lists from the text of clinical notes. Many tools developed to perform these tasks use biomedical knowledge encoded in the Unified Medical Language System (UMLS) Metathesaurus. We continue our exploration of automatic approaches to creation of subsets (UMLS content views) which can support NLP processing of either the biomedical literature or clinical text. We found that suppression of highly ambiguous terms in the conservative AutoFilter content view can partially replace manual filtering for literature applications, and suppression of two character mappings in the same content view achieves 89.5% precision at 78.6% recall for clinical applications. Published by Elsevier Inc.

Knowledge acquisition to qualify Unified Medical Language System interconceptual relationships.

PubMed Central

Le Duff, F.; Burgun, A.; Cleret, M.; Pouliquen, B.; Barac'h, V.; Le Beux, P.

2000-01-01

Adding automatically relations between concepts from a database to a knowledge base such as the Unified Medical Language System can be very useful to increase the consistency of the latter one. But the transfer of qualified relationships is more interesting. The most important interest of these new acquisitions is that the UMLS became more compliant and medically pertinent to be used in different medical applications. This paper describes the possibility to inherit automatically medical inter-conceptual relationships qualifiers from a disease description included into a database and to integrate them into the UMLS knowledge base. The paper focuses on the transmission of knowledge from a French medical database to an English one. PMID:11079930

OBO to UML: Support for the development of conceptual models in the biomedical domain.

PubMed

Waldemarin, Ricardo C; de Farias, Cléver R G

2018-04-01

A conceptual model abstractly defines a number of concepts and their relationships for the purposes of understanding and communication. Once a conceptual model is available, it can also be used as a starting point for the development of a software system. The development of conceptual models using the Unified Modeling Language (UML) facilitates the representation of modeled concepts and allows software developers to directly reuse these concepts in the design of a software system. The OBO Foundry represents the most relevant collaborative effort towards the development of ontologies in the biomedical domain. The development of UML conceptual models in the biomedical domain may benefit from the use of domain-specific semantics and notation. Further, the development of these models may also benefit from the reuse of knowledge contained in OBO ontologies. This paper investigates the support for the development of conceptual models in the biomedical domain using UML as a conceptual modeling language and using the support provided by the OBO Foundry for the development of biomedical ontologies, namely entity kind and relationship types definitions provided by the Basic Formal Ontology (BFO) and the OBO Core Relations Ontology (OBO Core), respectively. Further, the paper investigates the support for the reuse of biomedical knowledge currently available in OBOFFF ontologies in the development these conceptual models. The paper describes a UML profile for the OBO Core Relations Ontology, which basically defines a number of stereotypes to represent BFO entity kinds and OBO Core relationship types definitions. The paper also presents a support toolset consisting of a graphical editor named OBO-RO Editor, which directly supports the development of UML models using the extensions defined by our profile, and a command-line tool named OBO2UML, which directly converts an OBOFFF ontology into a UML model. Copyright © 2018 Elsevier Inc. All rights reserved.

CASE tools and UML: state of the ART.

PubMed

Agarwal, S

2001-05-01

With increasing need for automated tools to assist complex systems development, software design methods are becoming popular. This article analyzes the state of art in computer-aided software engineering (CASE) tools and unified modeling language (UML), focusing on their evolution, merits, and industry usage. It identifies managerial issues for the tools' adoption and recommends an action plan to select and implement them. While CASE and UML offer inherent advantages like cheaper, shorter, and efficient development cycles, they suffer from poor user satisfaction. The critical success factors for their implementation include, among others, management and staff commitment, proper corporate infrastructure, and user training.

The UMLS Knowledge Sources: Tools for Building Better User Interfaces

PubMed Central

Lindberg, Donald A. B.; Humphreys, Betsy L.

1990-01-01

The current focus of the National Library of Medicine's Unified Medical Language System (UMLS) project is the development, testing, and evaluation of the first versions of three new knowledge sources: the Metathesaurus, the Semantic Network, and the Information Sources Map. These three knowledge sources can be used by interface programs to conduct an intelligent interaction with the user and to make the conceptual link between the user's question and relevant machine-readable information. NLM is providing experimental copies of the initial versions of the UMLS knowledge sources in exchange for feedback on ways they can and should be improved. The hope is that the results of such experimentation will provide both immediate improvements in biomedical information service and useful suggestions for enhancements to the UMLS.

Feasibility and Utility of Lexical Analysis for Occupational Health Text.

PubMed

Harber, Philip; Leroy, Gondy

2017-06-01

Assess feasibility and potential utility of natural language processing (NLP) for storing and analyzing occupational health data. Basic NLP lexical analysis methods were applied to 89,000 Mine Safety and Health Administration (MSHA) free text records. Steps included tokenization, term and co-occurrence counts, term annotation, and identifying exposure-health effect relationships. Presence of terms in the Unified Medical Language System (UMLS) was assessed. The methods efficiently demonstrated common exposures, health effects, and exposure-injury relationships. Many workplace terms are not present in UMLS or map inaccurately. Use of free text rather than narrowly defined numerically coded fields is feasible, flexible, and efficient. It has potential to encourage workers and clinicians to provide more data and to support automated knowledge creation. The lexical method used is easily generalizable to other areas. The UMLS vocabularies should be enhanced to be relevant to occupational health.

Alignment of the UMLS semantic network with BioTop: methodology and assessment.

PubMed

Schulz, Stefan; Beisswanger, Elena; van den Hoek, László; Bodenreider, Olivier; van Mulligen, Erik M

2009-06-15

For many years, the Unified Medical Language System (UMLS) semantic network (SN) has been used as an upper-level semantic framework for the categorization of terms from terminological resources in biomedicine. BioTop has recently been developed as an upper-level ontology for the biomedical domain. In contrast to the SN, it is founded upon strict ontological principles, using OWL DL as a formal representation language, which has become standard in the semantic Web. In order to make logic-based reasoning available for the resources annotated or categorized with the SN, a mapping ontology was developed aligning the SN with BioTop. The theoretical foundations and the practical realization of the alignment are being described, with a focus on the design decisions taken, the problems encountered and the adaptations of BioTop that became necessary. For evaluation purposes, UMLS concept pairs obtained from MEDLINE abstracts by a named entity recognition system were tested for possible semantic relationships. Furthermore, all semantic-type combinations that occur in the UMLS Metathesaurus were checked for satisfiability. The effort-intensive alignment process required major design changes and enhancements of BioTop and brought up several design errors that could be fixed. A comparison between a human curator and the ontology yielded only a low agreement. Ontology reasoning was also used to successfully identify 133 inconsistent semantic-type combinations. BioTop, the OWL DL representation of the UMLS SN, and the mapping ontology are available at http://www.purl.org/biotop/.

Representation of Nursing Terminologies in UMLS

PubMed Central

Kim, Tae Youn; Coenen, Amy; Hardiker, Nicholas; Bartz, Claudia C.

2011-01-01

There are seven nursing terminologies or classifications that are considered a standard to support nursing practice in the U.S. Harmonizing these terminologies will enhance the interoperability of clinical data documented across nursing practice. As a first step to harmonize the nursing terminologies, the purpose of this study was to examine how nursing problems or diagnostic concepts from select terminologies were cross-mapped in Unified Medical Language System (UMLS). A comparison analysis was conducted by examining whether cross-mappings available in UMLS through concept unique identifiers were consistent with cross-mappings conducted by human experts. Of 423 concepts from three terminologies, 411 (97%) were manually cross-mapped by experts to the International Classification for Nursing Practice. The UMLS semantic mapping among the 411 nursing concepts presented 33.6% accuracy (i.e., 138 of 411 concepts) when compared to expert cross-mappings. Further research and collaboration among experts in this field are needed for future enhancement of UMLS. PMID:22195127

The Use of UML for Software Requirements Expression and Management

NASA Technical Reports Server (NTRS)

Murray, Alex; Clark, Ken

2015-01-01

It is common practice to write English-language "shall" statements to embody detailed software requirements in aerospace software applications. This paper explores the use of the UML language as a replacement for the English language for this purpose. Among the advantages offered by the Unified Modeling Language (UML) is a high degree of clarity and precision in the expression of domain concepts as well as architecture and design. Can this quality of UML be exploited for the definition of software requirements? While expressing logical behavior, interface characteristics, timeliness constraints, and other constraints on software using UML is commonly done and relatively straight-forward, achieving the additional aspects of the expression and management of software requirements that stakeholders expect, especially traceability, is far less so. These other characteristics, concerned with auditing and quality control, include the ability to trace a requirement to a parent requirement (which may well be an English "shall" statement), to trace a requirement to verification activities or scenarios which verify that requirement, and to trace a requirement to elements of the software design which implement that requirement. UML Use Cases, designed for capturing requirements, have not always been satisfactory. Some applications of them simply use the Use Case model element as a repository for English requirement statements. Other applications of Use Cases, in which Use Cases are incorporated into behavioral diagrams that successfully communicate the behaviors and constraints required of the software, do indeed take advantage of UML's clarity, but not in ways that support the traceability features mentioned above. Our approach uses the Stereotype construct of UML to precisely identify elements of UML constructs, especially behaviors such as State Machines and Activities, as requirements, and also to achieve the necessary mapping capabilities. We describe this approach in the context of a space-based software application currently under development at the Jet Propulsion Laboratory.

minimUML: A Minimalist Approach to UML Diagramming for Early Computer Science Education

ERIC Educational Resources Information Center

Turner, Scott A.; Perez-Quinones, Manuel A.; Edwards, Stephen H.

2005-01-01

In introductory computer science courses, the Unified Modeling Language (UML) is commonly used to teach basic object-oriented design. However, there appears to be a lack of suitable software to support this task. Many of the available programs that support UML focus on developing code and not on enhancing learning. Programs designed for…

Meeting medical terminology needs--the Ontology-Enhanced Medical Concept Mapper.

PubMed

Leroy, G; Chen, H

2001-12-01

This paper describes the development and testing of the Medical Concept Mapper, a tool designed to facilitate access to online medical information sources by providing users with appropriate medical search terms for their personal queries. Our system is valuable for patients whose knowledge of medical vocabularies is inadequate to find the desired information, and for medical experts who search for information outside their field of expertise. The Medical Concept Mapper maps synonyms and semantically related concepts to a user's query. The system is unique because it integrates our natural language processing tool, i.e., the Arizona (AZ) Noun Phraser, with human-created ontologies, the Unified Medical Language System (UMLS) and WordNet, and our computer generated Concept Space, into one system. Our unique contribution results from combining the UMLS Semantic Net with Concept Space in our deep semantic parsing (DSP) algorithm. This algorithm establishes a medical query context based on the UMLS Semantic Net, which allows Concept Space terms to be filtered so as to isolate related terms relevant to the query. We performed two user studies in which Medical Concept Mapper terms were compared against human experts' terms. We conclude that the AZ Noun Phraser is well suited to extract medical phrases from user queries, that WordNet is not well suited to provide strictly medical synonyms, that the UMLS Metathesaurus is well suited to provide medical synonyms, and that Concept Space is well suited to provide related medical terms, especially when these terms are limited by our DSP algorithm.

A rule-based approach to model checking of UML state machines

NASA Astrophysics Data System (ADS)

Grobelna, Iwona; Grobelny, Michał; Stefanowicz, Łukasz

2016-12-01

In the paper a new approach to formal verification of control process specification expressed by means of UML state machines in version 2.x is proposed. In contrast to other approaches from the literature, we use the abstract and universal rule-based logical model suitable both for model checking (using the nuXmv model checker), but also for logical synthesis in form of rapid prototyping. Hence, a prototype implementation in hardware description language VHDL can be obtained that fully reflects the primary, already formally verified specification in form of UML state machines. Presented approach allows to increase the assurance that implemented system meets the user-defined requirements.

Comprehensive Aspectual UML approach to support AspectJ.

PubMed

Magableh, Aws; Shukur, Zarina; Ali, Noorazean Mohd

2014-01-01

Unified Modeling Language is the most popular and widely used Object-Oriented modelling language in the IT industry. This study focuses on investigating the ability to expand UML to some extent to model crosscutting concerns (Aspects) to support AspectJ. Through a comprehensive literature review, we identify and extensively examine all the available Aspect-Oriented UML modelling approaches and find that the existing Aspect-Oriented Design Modelling approaches using UML cannot be considered to provide a framework for a comprehensive Aspectual UML modelling approach and also that there is a lack of adequate Aspect-Oriented tool support. This study also proposes a set of Aspectual UML semantic rules and attempts to generate AspectJ pseudocode from UML diagrams. The proposed Aspectual UML modelling approach is formally evaluated using a focus group to test six hypotheses regarding performance; a "good design" criteria-based evaluation to assess the quality of the design; and an AspectJ-based evaluation as a reference measurement-based evaluation. The results of the focus group evaluation confirm all the hypotheses put forward regarding the proposed approach. The proposed approach provides a comprehensive set of Aspectual UML structural and behavioral diagrams, which are designed and implemented based on a comprehensive and detailed set of AspectJ programming constructs.

Comprehensive Aspectual UML Approach to Support AspectJ

PubMed Central

Magableh, Aws; Shukur, Zarina; Mohd. Ali, Noorazean

2014-01-01

Unified Modeling Language is the most popular and widely used Object-Oriented modelling language in the IT industry. This study focuses on investigating the ability to expand UML to some extent to model crosscutting concerns (Aspects) to support AspectJ. Through a comprehensive literature review, we identify and extensively examine all the available Aspect-Oriented UML modelling approaches and find that the existing Aspect-Oriented Design Modelling approaches using UML cannot be considered to provide a framework for a comprehensive Aspectual UML modelling approach and also that there is a lack of adequate Aspect-Oriented tool support. This study also proposes a set of Aspectual UML semantic rules and attempts to generate AspectJ pseudocode from UML diagrams. The proposed Aspectual UML modelling approach is formally evaluated using a focus group to test six hypotheses regarding performance; a “good design” criteria-based evaluation to assess the quality of the design; and an AspectJ-based evaluation as a reference measurement-based evaluation. The results of the focus group evaluation confirm all the hypotheses put forward regarding the proposed approach. The proposed approach provides a comprehensive set of Aspectual UML structural and behavioral diagrams, which are designed and implemented based on a comprehensive and detailed set of AspectJ programming constructs. PMID:25136656

Net-centric ACT-R-Based Cognitive Architecture with DEVS Unified Process

DTIC Science & Technology

2011-04-01

effort has been spent in analyzing various forms of requirement specifications, viz, state-based, Natural Language based, UML-based, Rule- based, BPMN ...requirement specifications in one of the chosen formats such as BPMN , DoDAF, Natural Language Processing (NLP) based, UML- based, DSL or simply

A UMLS-based spell checker for natural language processing in vaccine safety.

PubMed

Tolentino, Herman D; Matters, Michael D; Walop, Wikke; Law, Barbara; Tong, Wesley; Liu, Fang; Fontelo, Paul; Kohl, Katrin; Payne, Daniel C

2007-02-12

The Institute of Medicine has identified patient safety as a key goal for health care in the United States. Detecting vaccine adverse events is an important public health activity that contributes to patient safety. Reports about adverse events following immunization (AEFI) from surveillance systems contain free-text components that can be analyzed using natural language processing. To extract Unified Medical Language System (UMLS) concepts from free text and classify AEFI reports based on concepts they contain, we first needed to clean the text by expanding abbreviations and shortcuts and correcting spelling errors. Our objective in this paper was to create a UMLS-based spelling error correction tool as a first step in the natural language processing (NLP) pipeline for AEFI reports. We developed spell checking algorithms using open source tools. We used de-identified AEFI surveillance reports to create free-text data sets for analysis. After expansion of abbreviated clinical terms and shortcuts, we performed spelling correction in four steps: (1) error detection, (2) word list generation, (3) word list disambiguation and (4) error correction. We then measured the performance of the resulting spell checker by comparing it to manual correction. We used 12,056 words to train the spell checker and tested its performance on 8,131 words. During testing, sensitivity, specificity, and positive predictive value (PPV) for the spell checker were 74% (95% CI: 74-75), 100% (95% CI: 100-100), and 47% (95% CI: 46%-48%), respectively. We created a prototype spell checker that can be used to process AEFI reports. We used the UMLS Specialist Lexicon as the primary source of dictionary terms and the WordNet lexicon as a secondary source. We used the UMLS as a domain-specific source of dictionary terms to compare potentially misspelled words in the corpus. The prototype sensitivity was comparable to currently available tools, but the specificity was much superior. The slow processing speed may be improved by trimming it down to the most useful component algorithms. Other investigators may find the methods we developed useful for cleaning text using lexicons specific to their area of interest.

A UMLS-based spell checker for natural language processing in vaccine safety

PubMed Central

Tolentino, Herman D; Matters, Michael D; Walop, Wikke; Law, Barbara; Tong, Wesley; Liu, Fang; Fontelo, Paul; Kohl, Katrin; Payne, Daniel C

2007-01-01

Background The Institute of Medicine has identified patient safety as a key goal for health care in the United States. Detecting vaccine adverse events is an important public health activity that contributes to patient safety. Reports about adverse events following immunization (AEFI) from surveillance systems contain free-text components that can be analyzed using natural language processing. To extract Unified Medical Language System (UMLS) concepts from free text and classify AEFI reports based on concepts they contain, we first needed to clean the text by expanding abbreviations and shortcuts and correcting spelling errors. Our objective in this paper was to create a UMLS-based spelling error correction tool as a first step in the natural language processing (NLP) pipeline for AEFI reports. Methods We developed spell checking algorithms using open source tools. We used de-identified AEFI surveillance reports to create free-text data sets for analysis. After expansion of abbreviated clinical terms and shortcuts, we performed spelling correction in four steps: (1) error detection, (2) word list generation, (3) word list disambiguation and (4) error correction. We then measured the performance of the resulting spell checker by comparing it to manual correction. Results We used 12,056 words to train the spell checker and tested its performance on 8,131 words. During testing, sensitivity, specificity, and positive predictive value (PPV) for the spell checker were 74% (95% CI: 74–75), 100% (95% CI: 100–100), and 47% (95% CI: 46%–48%), respectively. Conclusion We created a prototype spell checker that can be used to process AEFI reports. We used the UMLS Specialist Lexicon as the primary source of dictionary terms and the WordNet lexicon as a secondary source. We used the UMLS as a domain-specific source of dictionary terms to compare potentially misspelled words in the corpus. The prototype sensitivity was comparable to currently available tools, but the specificity was much superior. The slow processing speed may be improved by trimming it down to the most useful component algorithms. Other investigators may find the methods we developed useful for cleaning text using lexicons specific to their area of interest. PMID:17295907

Evaluation of emergency medical text processor, a system for cleaning chief complaint text data.

PubMed

Travers, Debbie A; Haas, Stephanie W

2004-11-01

Emergency Medical Text Processor (EMT-P) version 1, a natural language processing system that cleans emergency department text (e.g., chst pn, chest pai), was developed to maximize extraction of standard terms (e.g., chest pain). The authors compared the number of standard terms extracted from raw chief complaint (CC) data with that for CC data cleaned with EMT-P and evaluated the accuracy of EMT-P. This cross-sectional observation study included CC text entries for all emergency department visits to three tertiary care centers in 2001. Terms were extracted from CC entries before and after cleaning with EMT-P. Descriptive statistics included number and percentage of all entries (tokens) and all unique entries (types) that matched a standard term from the Unified Medical Language System (UMLS). An expert panel rated the accuracy of the CC-UMLS term matches; inter-rater reliability was measured with kappa. The authors collected 203,509 CC entry tokens, of which 63,946 were unique entry types. For the raw data, 89,337 tokens (44%) and 5,081 types (8%) matched a standard term. After EMT-P cleaning, 168,050 tokens (83%) and 44,430 types (69%) matched a standard term. The expert panel reached consensus on 201 of the 222 CC-UMLS term matches reviewed (kappa=0.69-0.72). Ninety-six percent of the 201 matches were rated equivalent or related. Thirty-eight percent of the nonmatches were found to match UMLS concepts. EMT-P version 1 is relatively accurate, and cleaning with EMT-P improved the CC-UMLS term match rate over raw data. The authors identified areas for improvement in future EMT-P versions and issues to be resolved in developing a standard CC terminology.

Analysis and design of hospital management information system based on UML

NASA Astrophysics Data System (ADS)

Ma, Lin; Zhao, Huifang; You, Shi Jun; Ge, Wenyong

2018-05-01

With the rapid development of computer technology, computer information management system has been utilized in many industries. Hospital Information System (HIS) is in favor of providing data for directors, lightening the workload for the medical workers, and improving the workers efficiency. According to the HIS demand analysis and system design, this paper focus on utilizing unified modeling language (UML) models to establish the use case diagram, class diagram, sequence chart and collaboration diagram, and satisfying the demands of the daily patient visit, inpatient, drug management and other relevant operations. At last, the paper summarizes the problems of the system and puts forward an outlook of the HIS system.

Semantic Mappings and Locality of Nursing Diagnostic Concepts in UMLS

PubMed Central

Kim, Tae Youn; Coenen, Amy; Hardiker, Nicholas

2011-01-01

One solution for enhancing the interoperability between nursing information systems, given the availability of multiple nursing terminologies, is to cross-map existing nursing concepts. The Unified Medical Language System (UMLS) developed and distributed by the National Library of Medicine (NLM) is a knowledge resource containing cross-mappings of various terminologies in a unified framework. While the knowledge resource has been available for the last two decades, little research on the representation of nursing terminologies in UMLS has been conducted. As a first step, UMLS semantic mappings and concept locality were examined for nursing diagnostic concepts or problems selected from three terminologies (i.e., CCC, ICNP, and NANDA-I) along with corresponding SNOMED CT concepts. The evaluation of UMLS semantic mappings was conducted by measuring the proportion of concordance between UMLS and human expert mappings. The semantic locality of nursing diagnostic concepts was assessed by examining the associations of select concepts and the placement of the nursing concepts on the Semantic Network and Group. The study found that the UMLS mappings of CCC and NANDA-I concepts to SNOMED CT were highly concordant to expert mappings. The level of concordance in mappings of ICNP to SNOMED CT, CCC and NANDA-I within UMLS was relatively low, indicating the need for further research and development. Likewise, the semantic locality of ICNP concepts could be further improved. Various stakeholders need to collaborate to enhance the NLM knowledge resource and the interoperability of nursing data within the discipline as well as across health-related disciplines. PMID:21951759

Modeling the Car Crash Crisis Management System Using HiLA

NASA Astrophysics Data System (ADS)

Hölzl, Matthias; Knapp, Alexander; Zhang, Gefei

An aspect-oriented modeling approach to the Car Crash Crisis Management System (CCCMS) using the High-Level Aspect (HiLA) language is described. HiLA is a language for expressing aspects for UML static structures and UML state machines. In particular, HiLA supports both a static graph transformational and a dynamic approach of applying aspects. Furthermore, it facilitates methodologically turning use case descriptions into state machines: for each main success scenario, a base state machine is developed; all extensions to this main success scenario are covered by aspects. Overall, the static structure of the CCCMS is modeled in 43 classes, the main success scenarios in 13 base machines, the use case extensions in 47 static and 31 dynamic aspects, most of which are instantiations of simple aspect templates.

Exploring the possibility of modeling a genetic counseling guideline using agile methodology.

PubMed

Choi, Jeeyae

2013-01-01

Increased demand of genetic counseling services heightened the necessity of a computerized genetic counseling decision support system. In order to develop an effective and efficient computerized system, modeling of genetic counseling guideline is an essential step. Throughout this pilot study, Agile methodology with United Modeling Language (UML) was utilized to model a guideline. 13 tasks and 14 associated elements were extracted. Successfully constructed conceptual class and activity diagrams revealed that Agile methodology with UML was a suitable tool to modeling a genetic counseling guideline.

Extraction of UMLS® Concepts Using Apache cTAKES™ for German Language.

PubMed

Becker, Matthias; Böckmann, Britta

2016-01-01

Automatic information extraction of medical concepts and classification with semantic standards from medical reports is useful for standardization and for clinical research. This paper presents an approach for an UMLS concept extraction with a customized natural language processing pipeline for German clinical notes using Apache cTAKES. The objectives are, to test the natural language processing tool for German language if it is suitable to identify UMLS concepts and map these with SNOMED-CT. The German UMLS database and German OpenNLP models extended the natural language processing pipeline, so the pipeline can normalize to domain ontologies such as SNOMED-CT using the German concepts. For testing, the ShARe/CLEF eHealth 2013 training dataset translated into German was used. The implemented algorithms are tested with a set of 199 German reports, obtaining a result of average 0.36 F1 measure without German stemming, pre- and post-processing of the reports.

The UMLS Knowledge Source Server: an experience in Web 2.0 technologies.

PubMed

Thorn, Karen E; Bangalore, Anantha K; Browne, Allen C

2007-10-11

The UMLS Knowledge Source Server (UMLSKS), developed at the National Library of Medicine (NLM), makes the knowledge sources of the Unified Medical Language System (UMLS) available to the research community over the Internet. In 2003, the UMLSKS was redesigned utilizing state-of-the-art technologies available at that time. That design offered a significant improvement over the prior version but presented a set of technology-dependent issues that limited its functionality and usability. Four areas of desired improvement were identified: software interfaces, web interface content, system maintenance/deployment, and user authentication. By employing next generation web technologies, newer authentication paradigms and further refinements in modular design methods, these areas could be addressed and corrected to meet the ever increasing needs of UMLSKS developers. In this paper we detail the issues present with the existing system and describe the new system's design using new technologies considered entrants in the Web 2.0 development era.

ADEpedia 2.0: Integration of Normalized Adverse Drug Events (ADEs) Knowledge from the UMLS.

PubMed

Jiang, Guoqian; Liu, Hongfang; Solbrig, Harold R; Chute, Christopher G

2013-01-01

A standardized Adverse Drug Events (ADEs) knowledge base that encodes known ADE knowledge can be very useful in improving ADE detection for drug safety surveillance. In our previous study, we developed the ADEpedia that is a standardized knowledge base of ADEs based on drug product labels. The objectives of the present study are 1) to integrate normalized ADE knowledge from the Unified Medical Language System (UMLS) into the ADEpedia; and 2) to enrich the knowledge base with the drug-disorder co-occurrence data from a 51-million-document electronic medical records (EMRs) system. We extracted 266,832 drug-disorder concept pairs from the UMLS, covering 14,256 (1.69%) distinct drug concepts and 19,006 (3.53%) distinct disorder concepts. Of them, 71,626 (26.8%) concept pairs from UMLS co-occurred in the EMRs. We performed a preliminary evaluation on the utility of the UMLS ADE data. In conclusion, we have built an ADEpedia 2.0 framework that intends to integrate known ADE knowledge from disparate sources. The UMLS is a useful source for providing standardized ADE knowledge relevant to indications, contraindications and adverse effects, and complementary to the ADE data from drug product labels. The statistics from EMRs would enable the meaningful use of ADE data for drug safety surveillance.

A remote sensing computer-assisted learning tool developed using the unified modeling language

NASA Astrophysics Data System (ADS)

Friedrich, J.; Karslioglu, M. O.

The goal of this work has been to create an easy-to-use and simple-to-make learning tool for remote sensing at an introductory level. Many students struggle to comprehend what seems to be a very basic knowledge of digital images, image processing and image arithmetic, for example. Because professional programs are generally too complex and overwhelming for beginners and often not tailored to the specific needs of a course regarding functionality, a computer-assisted learning (CAL) program was developed based on the unified modeling language (UML), the present standard for object-oriented (OO) system development. A major advantage of this approach is an easier transition from modeling to coding of such an application, if modern UML tools are being used. After introducing the constructed UML model, its implementation is briefly described followed by a series of learning exercises. They illustrate how the resulting CAL tool supports students taking an introductory course in remote sensing at the author's institution.

Comparison of BrainTool to other UML modeling and model transformation tools

NASA Astrophysics Data System (ADS)

Nikiforova, Oksana; Gusarovs, Konstantins

2017-07-01

In the last 30 years there were numerous model generated software systems offered targeting problems with the development productivity and the resulting software quality. CASE tools developed due today's date are being advertised as having "complete code-generation capabilities". Nowadays the Object Management Group (OMG) is calling similar arguments in regards to the Unified Modeling Language (UML) models at different levels of abstraction. It is being said that software development automation using CASE tools enables significant level of automation. Actual today's CASE tools are usually offering a combination of several features starting with a model editor and a model repository for a traditional ones and ending with code generator (that could be using a scripting or domain-specific (DSL) language), transformation tool to produce the new artifacts from the manually created and transformation definition editor to define new transformations for the most advanced ones. Present paper contains the results of CASE tool (mainly UML editors) comparison against the level of the automation they are offering.

Graph-based word sense disambiguation of biomedical documents.

PubMed

Agirre, Eneko; Soroa, Aitor; Stevenson, Mark

2010-11-15

Word Sense Disambiguation (WSD), automatically identifying the meaning of ambiguous words in context, is an important stage of text processing. This article presents a graph-based approach to WSD in the biomedical domain. The method is unsupervised and does not require any labeled training data. It makes use of knowledge from the Unified Medical Language System (UMLS) Metathesaurus which is represented as a graph. A state-of-the-art algorithm, Personalized PageRank, is used to perform WSD. When evaluated on the NLM-WSD dataset, the algorithm outperforms other methods that rely on the UMLS Metathesaurus alone. The WSD system is open source licensed and available from http://ixa2.si.ehu.es/ukb/. The UMLS, MetaMap program and NLM-WSD corpus are available from the National Library of Medicine https://www.nlm.nih.gov/research/umls/, http://mmtx.nlm.nih.gov and http://wsd.nlm.nih.gov. Software to convert the NLM-WSD corpus into a format that can be used by our WSD system is available from http://www.dcs.shef.ac.uk/∼marks/biomedical_wsd under open source license.

SysML: A Language for Space System Engineering

NASA Astrophysics Data System (ADS)

Mazzini, S.; Strangapede, A.

2008-08-01

This paper presents the results of an ESA/ESTEC internal study, performed with the support of INTECS, about modeling languages to support Space System Engineering activities and processes, with special emphasis on system requirements identification and analysis. The study was focused on the assessment of dedicated UML profiles, their positioning alongside the system and software life cycles and associated methodologies. Requirements for a Space System Requirements Language were identified considering the ECSS-E-10 and ECSS-E_40 processes. The study has identified SysML as a very promising language, having as theoretical background the reference system processes defined by the ISO15288, as well as industrial practices.

A UML profile for the OBO relation ontology

PubMed Central

2012-01-01

Background Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain. Results We have studied the OBO Relation Ontology, the UML metamodel and the UML profiling mechanism. Based on these studies, we have proposed an extension to the UML metamodel in conformance with the OBO Relation Ontology and we have defined a profile that implements the extended metamodel. Finally, we have applied the proposed UML profile in the development of a number of fragments from different ontologies. Particularly, we have considered the Gene Ontology (GO), the PRotein Ontology (PRO) and the Xenopus Anatomy and Development Ontology (XAO). Conclusions The use of an established and well-known graphical language in the development of biomedical ontologies provides a more intuitive form of capturing and representing knowledge than using only text-based notations. The use of the profile requires the domain expert to reason about the underlying semantics of the concepts and relationships being modeled, which helps preventing the introduction of inconsistencies in an ontology under development and facilitates the identification and correction of errors in an already defined ontology. PMID:23095840

Towards a semantic lexicon for biological language processing

DOE Office of Scientific and Technical Information (OSTI.GOV)

Verspoor, K.

It is well understood that natural language processing (NLP) applications require sophisticated lexical resources to support their processing goals. In the biomedical domain, we are privileged to have access to extensive terminological resources in the form of controlled vocabularies and ontologies, which have been integrated into the framework of the National Library of Medicine's Unified Medical Language System's (UMLS) Metathesaurus. However, the existence of such terminological resources does not guarantee their utility for NLP. In particular, we have two core requirements for lexical resources for NLP in addition to the basic enumeration of important domain terms: representation of morphosyntactic informationmore » about those terms, specifically part of speech information and inflectional patterns to support parsing and lemma assignment, and representation of semantic information indicating general categorical information about terms, and significant relations between terms to support text understanding and inference (Hahn et at, 1999). Biomedical vocabularies by and large commonly leave out morphosyntactic information, and where they address semantic considerations, they often do so in an unprincipled manner, for instance by indicating a relation between two concepts without indicating the type of that relation. But all is not lost. The UMLS knowledge sources include two additional resources which are relevant - the SPECIALIST lexicon, a lexicon addressing our morphosyntactic requirements, and the Semantic Network, a representation of core conceptual categories in the biomedical domain. The coverage of these two knowledge sources with respect to the full coverage of the Metathesaurus is, however, not entirely clear. Furthermore, when our goals are specifically to process biological text - and often more specifically, text in the molecular biology domain - it is difficult to say whether the coverage of these resources is meaningful. The utility of the UMLS knowledge sources for medical language processing (MLP) has been explored (Johnson, 1999; Friedman et al 2001); the time has now come to repeat these experiments with respect to biological language processing (BLP). To that end, this paper presents an analysis of ihe UMLS resources, specifically with an eye towards constructing lexical resources suitable for BLP. We follow the paradigm presented in Johnson (1999) for medical language, exploring overlap between the UMLS Metathesaurus and SPECIALIST lexicon to construct a morphosyntactic and semantically-specified lexicon, and then further explore the overlap with a relevant domain corpus for molecular biology.« less

An Evaluation of the UMLS in Representing Corpus Derived Clinical Concepts

PubMed Central

Friedlin, Jeff; Overhage, Marc

2011-01-01

We performed an evaluation of the Unified Medical Language System (UMLS) in representing concepts derived from medical narrative documents from three domains: chest x-ray reports, discharge summaries and admission notes. We detected concepts in these documents by identifying noun phrases (NPs) and N-grams, including unigrams (single words), bigrams (word pairs) and trigrams (word triples). After removing NPs and N-grams that did not represent discrete clinical concepts, we processed the remaining with the UMLS MetaMap program. We manually reviewed the results of MetaMap processing to determine whether MetaMap found full, partial or no representation of the concept. For full representations, we determined whether post-coordination was required. Our results showed that a large portion of concepts found in clinical narrative documents are either unrepresented or poorly represented in the current version of the UMLS Metathesaurus and that post-coordination was often required in order to fully represent a concept. PMID:22195097

Structuration and acquisition of medical knowledge. Using UMLS in the conceptual graph formalism.

PubMed Central

Volot, F.; Zweigenbaum, P.; Bachimont, B.; Ben Said, M.; Bouaud, J.; Fieschi, M.; Boisvieux, J. F.

1993-01-01

The use of a taxonomy, such as the concept type lattice (CTL) of Conceptual Graphs, is a central structuring piece in a knowledge-based system. The knowledge it contains is constantly used by the system, and its structure provides a guide for the acquisition of other pieces of knowledge. We show how UMLS can be used as a knowledge resource to build a CTL and how the CTL can help the process of acquisition for other kinds of knowledge. We illustrate this method in the context of the MENELAS natural language understanding project. PMID:8130568

Using UMLS to map from a library to a clinical classification: Improving the functionality of a digital library.

PubMed

Robinson, Judas; de Lusignan, Simon; Kostkova, Patty; Madge, Bruce

2006-01-01

The Metathesaurus of the Unified Medical Language System (UMLS) offers the possibility of mapping between various medical vocabularies. The Primary Care Electronic Library (PCEL) contains a database of over six thousand Medical Subject Headings (MeSH terms) describing the resources of the electronic library. We were interested to know if it was possible to map from MeSH to the Systemized Nomenclature of Medicine Clinical Terms (SNOMED CT). Such a mapping would aid healthcare professionals to retrieve relevant data from our digital library as it would enable links between clinical systems and indexed material.

Dynamic generation of a table of contents with consumer-friendly labels.

PubMed

Miller, Trudi; Leroy, Gondy; Wood, Elizabeth

2006-01-01

Consumers increasingly look to the Internet for health information, but available resources are too difficult for the majority to understand. Interactive tables of contents (TOC) can help consumers access health information by providing an easy to understand structure. Using natural language processing and the Unified Medical Language System (UMLS), we have automatically generated TOCs for consumer health information. The TOC are categorized according to consumer-friendly labels for the UMLS semantic types and semantic groups. Categorizing phrases by semantic types is significantly more correct and relevant. Greater correctness and relevance was achieved with documents that are difficult to read than those at an easier reading level. Pruning TOCs to use categories that consumers favor further increases relevancy and correctness while reducing structural complexity.

Enabling online studies of conceptual relationships between medical terms: developing an efficient web platform.

PubMed

Albin, Aaron; Ji, Xiaonan; Borlawsky, Tara B; Ye, Zhan; Lin, Simon; Payne, Philip Ro; Huang, Kun; Xiang, Yang

2014-10-07

The Unified Medical Language System (UMLS) contains many important ontologies in which terms are connected by semantic relations. For many studies on the relationships between biomedical concepts, the use of transitively associated information from ontologies and the UMLS has been shown to be effective. Although there are a few tools and methods available for extracting transitive relationships from the UMLS, they usually have major restrictions on the length of transitive relations or on the number of data sources. Our goal was to design an efficient online platform that enables efficient studies on the conceptual relationships between any medical terms. To overcome the restrictions of available methods and to facilitate studies on the conceptual relationships between medical terms, we developed a Web platform, onGrid, that supports efficient transitive queries and conceptual relationship studies using the UMLS. This framework uses the latest technique in converting natural language queries into UMLS concepts, performs efficient transitive queries, and visualizes the result paths. It also dynamically builds a relationship matrix for two sets of input biomedical terms. We are thus able to perform effective studies on conceptual relationships between medical terms based on their relationship matrix. The advantage of onGrid is that it can be applied to study any two sets of biomedical concept relations and the relations within one set of biomedical concepts. We use onGrid to study the disease-disease relationships in the Online Mendelian Inheritance in Man (OMIM). By crossvalidating our results with an external database, the Comparative Toxicogenomics Database (CTD), we demonstrated that onGrid is effective for the study of conceptual relationships between medical terms. onGrid is an efficient tool for querying the UMLS for transitive relations, studying the relationship between medical terms, and generating hypotheses.

A UML profile for the OBO relation ontology.

PubMed

Guardia, Gabriela D A; Vêncio, Ricardo Z N; de Farias, Cléver R G

2012-01-01

Ontologies have increasingly been used in the biomedical domain, which has prompted the emergence of different initiatives to facilitate their development and integration. The Open Biological and Biomedical Ontologies (OBO) Foundry consortium provides a repository of life-science ontologies, which are developed according to a set of shared principles. This consortium has developed an ontology called OBO Relation Ontology aiming at standardizing the different types of biological entity classes and associated relationships. Since ontologies are primarily intended to be used by humans, the use of graphical notations for ontology development facilitates the capture, comprehension and communication of knowledge between its users. However, OBO Foundry ontologies are captured and represented basically using text-based notations. The Unified Modeling Language (UML) provides a standard and widely-used graphical notation for modeling computer systems. UML provides a well-defined set of modeling elements, which can be extended using a built-in extension mechanism named Profile. Thus, this work aims at developing a UML profile for the OBO Relation Ontology to provide a domain-specific set of modeling elements that can be used to create standard UML-based ontologies in the biomedical domain.

Quality Assurance of UMLS Semantic Type Assignments Using SNOMED CT Hierarchies.

PubMed

Gu, H; Chen, Y; He, Z; Halper, M; Chen, L

2016-01-01

The Unified Medical Language System (UMLS) is one of the largest biomedical terminological systems, with over 2.5 million concepts in its Metathesaurus repository. The UMLS's Semantic Network (SN) with its collection of 133 high-level semantic types serves as an abstraction layer on top of the Metathesaurus. In particular, the SN elaborates an aspect of the Metathesaurus's concepts via the assignment of one or more types to each concept. Due to the scope and complexity of the Metathesaurus, errors are all but inevitable in this semantic-type assignment process. To develop a semi-automated methodology to help assure the quality of semantic-type assignments within the UMLS. The methodology uses a cross-validation strategy involving SNOMED CT's hierarchies in combination with UMLS semantic types. Semantically uniform, disjoint concept groups are generated programmatically by partitioning the collection of all concepts in the same SNOMED CT hierarchy according to their respective semantic-type assignments in the UMLS. Domain experts are then called upon to review the concepts in any group having a small number of concepts. It is our hypothesis that a semantic-type assignment combination applicable only to a very small number of concepts in a SNOMED CT hierarchy is an indicator of potential problems. The methodology was applied to the UMLS 2013AA release along with the SNOMED CT from January 2013. An overall error rate of 33% was found for concepts proposed by the quality-assurance methodology. Supporting our hypothesis, that number was four times higher than the error rate found in control samples. The results show that the quality-assurance methodology can aid in effective and efficient identification of UMLS semantic-type assignment errors.

Physician nurse care: A new use of UMLS to measure professional contribution: Are we talking about the same patient a new graph matching algorithm?

PubMed

Boyd, Andrew D; Dunn Lopez, Karen; Lugaresi, Camillo; Macieira, Tamara; Sousa, Vanessa; Acharya, Sabita; Balasubramanian, Abhinaya; Roussi, Khawllah; Keenan, Gail M; Lussier, Yves A; Li, Jianrong 'John'; Burton, Michel; Di Eugenio, Barbara

2018-05-01

Physician and nurses have worked together for generations; however, their language and training are vastly different; comparing and contrasting their work and their joint impact on patient outcomes is difficult in light of this difference. At the same time, the EHR only includes the physician perspective via the physician-authored discharge summary, but not nurse documentation. Prior research in this area has focused on collaboration and the usage of similar terminology. The objective of the study is to gain insight into interprofessional care by developing a computational metric to identify similarities, related concepts and differences in physician and nurse work. 58 physician discharge summaries and the corresponding nurse plans of care were transformed into Unified Medical Language System (UMLS) Concept Unique Identifiers (CUIs). MedLEE, a Natural Language Processing (NLP) program, extracted "physician terms" from free-text physician summaries. The nursing plans of care were constructed using the HANDS © nursing documentation software. HANDS © utilizes structured terminologies: nursing diagnosis (NANDA-I), outcomes (NOC), and interventions (NIC) to create "nursing terms". The physician's and nurse's terms were compared using the UMLS network for relatedness, overlaying the physician and nurse terms for comparison. Our overarching goal is to provide insight into the care, by innovatively applying graph algorithms to the UMLS network. We reveal the relationships between the care provided by each professional that is specific to the patient level. We found that only 26% of patients had synonyms (identical UMLS CUIs) between the two professions' documentation. On average, physicians' discharge summaries contain 27 terms and nurses' documentation, 18. Traversing the UMLS network, we found an average of 4 terms related (distance less than 2) between the professions, leaving most concepts as unrelated between nurse and physician care. Our hypothesis that physician's and nurse's practice domains are markedly different is supported by the preliminary, quantitative evidence we found. Leveraging the UMLS network and graph traversal algorithms, allows us to compare and contrast nursing and physician care on a single patient, enabling a more complete picture of patient care. We can differentiate professional contributions to patient outcomes and related and divergent concepts by each profession. Copyright © 2018 The Author(s). Published by Elsevier B.V. All rights reserved.

Physician nurse care: A new use of UMLS to measure professional contribution

PubMed Central

Boyd, Andrew D.; Lopez, Karen Dunn; Lugaresi, Camillo; Macieira, Tamara; Sousa, Vanessa; Acharya, Sabita; Balasubramanian, Abhinaya; Roussi, Khawllah; Keenan, Gail M.; Lussier, Yves A.; ‘John’ Li, Jianrong; Burton, Michel; Di Eugenio, Barbara

2018-01-01

Background Physician and nurses have worked together for generations; however, their language and training are vastly different; comparing and contrasting their work and their joint impact on patient outcomes is difficult in light of this difference. At the same time, the EHR only includes the physician perspective via the physician-authored discharge summary, but not nurse documentation. Prior research in this area has focused on collaboration and the usage of similar terminology. Objective The objective of the study is to gain insight into interprofessional care by developing a computational metric to identify similarities, related concepts and differences in physician and nurse work. Methods 58 physician discharge summaries and the corresponding nurse plans of care were transformed into Unified Medical Language System (UMLS) Concept Unique Identifiers (CUIs). MedLEE, a Natural Language Processing (NLP) program, extracted “physician terms” from free-text physician summaries. The nursing plans of care were constructed using the HANDS© nursing documentation software. HANDS© utilizes structured terminologies: nursing diagnosis (NANDA-I), outcomes (NOC), and interventions (NIC) to create “nursing terms”. The physician’s and nurse’s terms were compared using the UMLS network for relatedness, overlaying the physician and nurse terms for comparison. Our overarching goal is to provide insight into the care, by innovatively applying graph algorithms to the UMLS network. We reveal the relationships between the care provided by each professional that is specific to the patient level. Results We found that only 26% of patients had synonyms (identical UMLS CUIs) between the two professions’ documentation. On average, physicians’ discharge summaries contain 27 terms and nurses’ documentation, 18. Traversing the UMLS network, we found an average of 4 terms related (distance less than 2) between the professions, leaving most concepts as unrelated between nurse and physician care. Conclusion Our hypothesis that physician’s and nurse’s practice domains are markedly different is supported by the preliminary, quantitative evidence we found. Leveraging the UMLS network and graph traversal algorithms, allows us to compare and contrast nursing and physician care on a single patient, enabling a more complete picture of patient care. We can differentiate professional contributions to patient outcomes and related and divergent concepts by each profession. PMID:29602435

BGen: A UML Behavior Network Generator Tool

NASA Technical Reports Server (NTRS)

Huntsberger, Terry; Reder, Leonard J.; Balian, Harry

2010-01-01

BGen software was designed for autogeneration of code based on a graphical representation of a behavior network used for controlling automatic vehicles. A common format used for describing a behavior network, such as that used in the JPL-developed behavior-based control system, CARACaS ["Control Architecture for Robotic Agent Command and Sensing" (NPO-43635), NASA Tech Briefs, Vol. 32, No. 10 (October 2008), page 40] includes a graph with sensory inputs flowing through the behaviors in order to generate the signals for the actuators that drive and steer the vehicle. A computer program to translate Unified Modeling Language (UML) Freeform Implementation Diagrams into a legacy C implementation of Behavior Network has been developed in order to simplify the development of C-code for behavior-based control systems. UML is a popular standard developed by the Object Management Group (OMG) to model software architectures graphically. The C implementation of a Behavior Network is functioning as a decision tree.

Architectural Design of a LMS with LTSA-Conformance

ERIC Educational Resources Information Center

Sengupta, Souvik; Dasgupta, Ranjan

2017-01-01

This paper illustrates an approach for architectural design of a Learning Management System (LMS), which is verifiable against the Learning Technology System Architecture (LTSA) conformance rules. We introduce a new method for software architectural design that extends the Unified Modeling Language (UML) component diagram with the formal…

The feasibility of using UML to compare the impact of different brands of computer system on the clinical consultation.

PubMed

Kumarapeli, Pushpa; de Lusignan, Simon; Koczan, Phil; Jones, Beryl; Sheeler, Ian

2007-01-01

UK general practice is universally computerised, with computers used in the consulting room at the point of care. Practices use a range of different brands of computer system, which have developed organically to meet the needs of general practitioners and health service managers. Unified Modelling Language (UML) is a standard modelling and specification notation widely used in software engineering. To examine the feasibility of UML notation to compare the impact of different brands of general practice computer system on the clinical consultation. Multi-channel video recordings of simulated consultation sessions were recorded on three different clinical computer systems in common use (EMIS, iSOFT Synergy and IPS Vision). User action recorder software recorded time logs of keyboard and mouse use, and pattern recognition software captured non-verbal communication. The outputs of these were used to create UML class and sequence diagrams for each consultation. We compared 'definition of the presenting problem' and 'prescribing', as these tasks were present in all the consultations analysed. Class diagrams identified the entities involved in the clinical consultation. Sequence diagrams identified common elements of the consultation (such as prescribing) and enabled comparisons to be made between the different brands of computer system. The clinician and computer system interaction varied greatly between the different brands. UML sequence diagrams are useful in identifying common tasks in the clinical consultation, and for contrasting the impact of the different brands of computer system on the clinical consultation. Further research is needed to see if patterns demonstrated in this pilot study are consistently displayed.

Program Synthesizes UML Sequence Diagrams

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

A computer program called "Rational Sequence" generates Universal Modeling Language (UML) sequence diagrams of a target Java program running on a Java virtual machine (JVM). Rational Sequence thereby performs a reverse engineering function that aids in the design documentation of the target Java program. Whereas previously, the construction of sequence diagrams was a tedious manual process, Rational Sequence generates UML sequence diagrams automatically from the running Java code.

Semantically-Rigorous Systems Engineering Modeling Using Sysml and OWL

NASA Technical Reports Server (NTRS)

Jenkins, J. Steven; Rouquette, Nicolas F.

2012-01-01

The Systems Modeling Language (SysML) has found wide acceptance as a standard graphical notation for the domain of systems engineering. SysML subsets and extends the Unified Modeling Language (UML) to define conventions for expressing structural, behavioral, and analytical elements, and relationships among them. SysML-enabled modeling tools are available from multiple providers, and have been used for diverse projects in military aerospace, scientific exploration, and civil engineering. The Web Ontology Language (OWL) has found wide acceptance as a standard notation for knowledge representation. OWL-enabled modeling tools are available from multiple providers, as well as auxiliary assets such as reasoners and application programming interface libraries, etc. OWL has been applied to diverse projects in a wide array of fields. While the emphasis in SysML is on notation, SysML inherits (from UML) a semantic foundation that provides for limited reasoning and analysis. UML's partial formalization (FUML), however, does not cover the full semantics of SysML, which is a substantial impediment to developing high confidence in the soundness of any conclusions drawn therefrom. OWL, by contrast, was developed from the beginning on formal logical principles, and consequently provides strong support for verification of consistency and satisfiability, extraction of entailments, conjunctive query answering, etc. This emphasis on formal logic is counterbalanced by the absence of any graphical notation conventions in the OWL standards. Consequently, OWL has had only limited adoption in systems engineering. The complementary strengths and weaknesses of SysML and OWL motivate an interest in combining them in such a way that we can benefit from the attractive graphical notation of SysML and the formal reasoning of OWL. This paper describes an approach to achieving that combination.

Software system architecture for corporate user support

NASA Astrophysics Data System (ADS)

Sukhopluyeva, V. S.; Kuznetsov, D. Y.

2017-01-01

In this article, several existing ready-to-use solutions for the HelpDesk are reviewed. Advantages and disadvantages of these systems are identified. Architecture of software solution for a corporate user support system is presented in a form of the use case, state, and component diagrams described by using a unified modeling language (UML).

Building an automated problem list based on natural language processing: lessons learned in the early phase of development.

PubMed

Solti, Imre; Aaronson, Barry; Fletcher, Grant; Solti, Magdolna; Gennari, John H; Cooper, Melissa; Payne, Tom

2008-11-06

Detailed problem lists that comply with JCAHO requirements are important components of electronic health records. Besides improving continuity of care electronic problem lists could serve as foundation infrastructure for clinical trial recruitment, research, biosurveillance and billing informatics modules. However, physicians rarely maintain problem lists. Our team is building a system using MetaMap and UMLS to automatically populate the problem list. We report our early results evaluating the application. Three physicians generated gold standard problem lists for 100 cardiology ambulatory progress notes. Our application had 88% sensitivity and 66% precision using a non-modified UMLS dataset. The systemâs misses concentrated in the group of ambiguous problem list entries (Chi-square=27.12 p<0.0001). In addition to the explicit entries, the notes included 10% implicit entry candidates. MetaMap and UMLS are readily applicable to automate the problem list. Ambiguity in medical documents has consequences for performance evaluation of automated systems.

Towards refactoring the Molecular Function Ontology with a UML profile for function modeling.

PubMed

Burek, Patryk; Loebe, Frank; Herre, Heinrich

2017-10-04

Gene Ontology (GO) is the largest resource for cataloging gene products. This resource grows steadily and, naturally, this growth raises issues regarding the structure of the ontology. Moreover, modeling and refactoring large ontologies such as GO is generally far from being simple, as a whole as well as when focusing on certain aspects or fragments. It seems that human-friendly graphical modeling languages such as the Unified Modeling Language (UML) could be helpful in connection with these tasks. We investigate the use of UML for making the structural organization of the Molecular Function Ontology (MFO), a sub-ontology of GO, more explicit. More precisely, we present a UML dialect, called the Function Modeling Language (FueL), which is suited for capturing functions in an ontologically founded way. FueL is equipped, among other features, with language elements that arise from studying patterns of subsumption between functions. We show how to use this UML dialect for capturing the structure of molecular functions. Furthermore, we propose and discuss some refactoring options concerning fragments of MFO. FueL enables the systematic, graphical representation of functions and their interrelations, including making information explicit that is currently either implicit in MFO or is mainly captured in textual descriptions. Moreover, the considered subsumption patterns lend themselves to the methodical analysis of refactoring options with respect to MFO. On this basis we argue that the approach can increase the comprehensibility of the structure of MFO for humans and can support communication, for example, during revision and further development.

Working with the HL7 metamodel in a Model Driven Engineering context.

PubMed

Martínez-García, A; García-García, J A; Escalona, M J; Parra-Calderón, C L

2015-10-01

HL7 (Health Level 7) International is an organization that defines health information standards. Most HL7 domain information models have been designed according to a proprietary graphic language whose domain models are based on the HL7 metamodel. Many researchers have considered using HL7 in the MDE (Model-Driven Engineering) context. A limitation has been identified: all MDE tools support UML (Unified Modeling Language), which is a standard model language, but most do not support the HL7 proprietary model language. We want to support software engineers without HL7 experience, thus real-world problems would be modeled by them by defining system requirements in UML that are compliant with HL7 domain models transparently. The objective of the present research is to connect HL7 with software analysis using a generic model-based approach. This paper introduces a first approach to an HL7 MDE solution that considers the MIF (Model Interchange Format) metamodel proposed by HL7 by making use of a plug-in developed in the EA (Enterprise Architect) tool. Copyright © 2015 Elsevier Inc. All rights reserved.

A UML profile for framework modeling.

PubMed

Xu, Xiao-liang; Wang, Le-yu; Zhou, Hong

2004-01-01

The current standard Unified Modeling Language(UML) could not model framework flexibility and extendability adequately due to lack of appropriate constructs to distinguish framework hot-spots from kernel elements. A new UML profile that may customize UML for framework modeling was presented using the extension mechanisms of UML, providing a group of UML extensions to meet the needs of framework modeling. In this profile, the extended class diagrams and sequence diagrams were defined to straightforwardly identify the hot-spots and describe their instantiation restrictions. A transformation model based on design patterns was also put forward, such that the profile based framework design diagrams could be automatically mapped to the corresponding implementation diagrams. It was proved that the presented profile makes framework modeling more straightforwardly and therefore easier to understand and instantiate.

Doclet To Synthesize UML

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2005-01-01

The RoseDoclet computer program extends the capability of Java doclet software to automatically synthesize Unified Modeling Language (UML) content from Java language source code. [Doclets are Java-language programs that use the doclet application programming interface (API) to specify the content and format of the output of Javadoc. Javadoc is a program, originally designed to generate API documentation from Java source code, now also useful as an extensible engine for processing Java source code.] RoseDoclet takes advantage of Javadoc comments and tags already in the source code to produce a UML model of that code. RoseDoclet applies the doclet API to create a doclet passed to Javadoc. The Javadoc engine applies the doclet to the source code, emitting the output format specified by the doclet. RoseDoclet emits a Rose model file and populates it with fully documented packages, classes, methods, variables, and class diagrams identified in the source code. The way in which UML models are generated can be controlled by use of new Javadoc comment tags that RoseDoclet provides. The advantage of using RoseDoclet is that Javadoc documentation becomes leveraged for two purposes: documenting the as-built API and keeping the design documentation up to date.

Fostering Multilinguality in the UMLS: A Computational Approach to Terminology Expansion for Multiple Languages

PubMed Central

Hellrich, Johannes; Hahn, Udo

2014-01-01

We here report on efforts to computationally support the maintenance and extension of multilingual biomedical terminology resources. Our main idea is to treat term acquisition as a classification problem guided by term alignment in parallel multilingual corpora, using termhood information coming from of a named entity recognition system as a novel feature. We report on experiments for Spanish, French, German and Dutch parts of a multilingual UMLS-derived biomedical terminology. These efforts yielded 19k, 18k, 23k and 12k new terms and synonyms, respectively, from which about half relate to concepts without a previously available term label for these non-English languages. Based on expert assessment of a novel German terminology sample, 80% of the newly acquired terms were judged as reasonable additions to the terminology. PMID:25954371

Planned NLM/AHCPR large-scale vocabulary test: using UMLS technology to determine the extent to which controlled vocabularies cover terminology needed for health care and public health.

PubMed Central

Humphreys, B L; Hole, W T; McCray, A T; Fitzmaurice, J M

1996-01-01

The National Library of Medicine (NLM) and the Agency for Health Care Policy and Research (AHCPR) are sponsoring a test to determine the extent to which a combination of existing health-related terminologies covers vocabulary needed in health information systems. The test vocabularies are the 30 that are fully or partially represented in the 1996 edition of the Unified Medical Language System (UMLS) Metathesaurus, plus three planned additions: the portions of SNOMED International not in the 1996 Metathesaurus Read Clinical Classification, and the Logical Observations Identifiers, Names, and Codes (LOINC) system. These vocabularies are available to testers through a special interface to the Internet-based UMLS Knowledge Source Server. The test will determine the ability of the test vocabularies to serve as a source of controlled vocabulary for health data systems and applications. It should provide the basis for realistic resource estimates for developing and maintaining a comprehensive "standard" health vocabulary that is based on existing terminologies. PMID:8816351

Towards comprehensive syntactic and semantic annotations of the clinical narrative

PubMed Central

Albright, Daniel; Lanfranchi, Arrick; Fredriksen, Anwen; Styler, William F; Warner, Colin; Hwang, Jena D; Choi, Jinho D; Dligach, Dmitriy; Nielsen, Rodney D; Martin, James; Ward, Wayne; Palmer, Martha; Savova, Guergana K

2013-01-01

Objective To create annotated clinical narratives with layers of syntactic and semantic labels to facilitate advances in clinical natural language processing (NLP). To develop NLP algorithms and open source components. Methods Manual annotation of a clinical narrative corpus of 127 606 tokens following the Treebank schema for syntactic information, PropBank schema for predicate-argument structures, and the Unified Medical Language System (UMLS) schema for semantic information. NLP components were developed. Results The final corpus consists of 13 091 sentences containing 1772 distinct predicate lemmas. Of the 766 newly created PropBank frames, 74 are verbs. There are 28 539 named entity (NE) annotations spread over 15 UMLS semantic groups, one UMLS semantic type, and the Person semantic category. The most frequent annotations belong to the UMLS semantic groups of Procedures (15.71%), Disorders (14.74%), Concepts and Ideas (15.10%), Anatomy (12.80%), Chemicals and Drugs (7.49%), and the UMLS semantic type of Sign or Symptom (12.46%). Inter-annotator agreement results: Treebank (0.926), PropBank (0.891–0.931), NE (0.697–0.750). The part-of-speech tagger, constituency parser, dependency parser, and semantic role labeler are built from the corpus and released open source. A significant limitation uncovered by this project is the need for the NLP community to develop a widely agreed-upon schema for the annotation of clinical concepts and their relations. Conclusions This project takes a foundational step towards bringing the field of clinical NLP up to par with NLP in the general domain. The corpus creation and NLP components provide a resource for research and application development that would have been previously impossible. PMID:23355458

Describing different brain computer interface systems through a unique model: a UML implementation.

PubMed

Quitadamo, Lucia Rita; Marciani, Maria Grazia; Cardarilli, Gian Carlo; Bianchi, Luigi

2008-01-01

All the protocols currently implemented in brain computer interface (BCI) experiments are characterized by different structural and temporal entities. Moreover, due to the lack of a unique descriptive model for BCI systems, there is not a standard way to define the structure and the timing of a BCI experimental session among different research groups and there is also great discordance on the meaning of the most common terms dealing with BCI, such as trial, run and session. The aim of this paper is to provide a unified modeling language (UML) implementation of BCI systems through a unique dynamic model which is able to describe the main protocols defined in the literature (P300, mu-rhythms, SCP, SSVEP, fMRI) and demonstrates to be reasonable and adjustable according to different requirements. This model includes a set of definitions of the typical entities encountered in a BCI, diagrams which explain the structural correlations among them and a detailed description of the timing of a trial. This last represents an innovation with respect to the models already proposed in the literature. The UML documentation and the possibility of adapting this model to the different BCI systems built to date, make it a basis for the implementation of new systems and a mean for the unification and dissemination of resources. The model with all the diagrams and definitions reported in the paper are the core of the body language framework, a free set of routines and tools for the implementation, optimization and delivery of cross-platform BCI systems.

Improved identification of noun phrases in clinical radiology reports using a high-performance statistical natural language parser augmented with the UMLS specialist lexicon.

PubMed

Huang, Yang; Lowe, Henry J; Klein, Dan; Cucina, Russell J

2005-01-01

The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS(R) Specialist Lexicon to improve noun phrase identification within clinical radiology documents. The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)(R) Clinical Document Architecture (CDA)-compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain.

State-Chart Autocoder

NASA Technical Reports Server (NTRS)

Clark, Kenneth; Watney, Garth; Murray, Alexander; Benowitz, Edward

2007-01-01

A computer program translates Unified Modeling Language (UML) representations of state charts into source code in the C, C++, and Python computing languages. ( State charts signifies graphical descriptions of states and state transitions of a spacecraft or other complex system.) The UML representations constituting the input to this program are generated by using a UML-compliant graphical design program to draw the state charts. The generated source code is consistent with the "quantum programming" approach, which is so named because it involves discrete states and state transitions that have features in common with states and state transitions in quantum mechanics. Quantum programming enables efficient implementation of state charts, suitable for real-time embedded flight software. In addition to source code, the autocoder program generates a graphical-user-interface (GUI) program that, in turn, generates a display of state transitions in response to events triggered by the user. The GUI program is wrapped around, and can be used to exercise the state-chart behavior of, the generated source code. Once the expected state-chart behavior is confirmed, the generated source code can be augmented with a software interface to the rest of the software with which the source code is required to interact.

A methodology for extending domain coverage in SemRep.

PubMed

Rosemblat, Graciela; Shin, Dongwook; Kilicoglu, Halil; Sneiderman, Charles; Rindflesch, Thomas C

2013-12-01

We describe a domain-independent methodology to extend SemRep coverage beyond the biomedical domain. SemRep, a natural language processing application originally designed for biomedical texts, uses the knowledge sources provided by the Unified Medical Language System (UMLS©). Ontological and terminological extensions to the system are needed in order to support other areas of knowledge. We extended SemRep's application by developing a semantic representation of a previously unsupported domain. This was achieved by adapting well-known ontology engineering phases and integrating them with the UMLS knowledge sources on which SemRep crucially depends. While the process to extend SemRep coverage has been successfully applied in earlier projects, this paper presents in detail the step-wise approach we followed and the mechanisms implemented. A case study in the field of medical informatics illustrates how the ontology engineering phases have been adapted for optimal integration with the UMLS. We provide qualitative and quantitative results, which indicate the validity and usefulness of our methodology. Published by Elsevier Inc.

Bioinformatics for transporter pharmacogenomics and systems biology: data integration and modeling with UML.

PubMed

Yan, Qing

2010-01-01

Bioinformatics is the rational study at an abstract level that can influence the way we understand biomedical facts and the way we apply the biomedical knowledge. Bioinformatics is facing challenges in helping with finding the relationships between genetic structures and functions, analyzing genotype-phenotype associations, and understanding gene-environment interactions at the systems level. One of the most important issues in bioinformatics is data integration. The data integration methods introduced here can be used to organize and integrate both public and in-house data. With the volume of data and the high complexity, computational decision support is essential for integrative transporter studies in pharmacogenomics, nutrigenomics, epigenetics, and systems biology. For the development of such a decision support system, object-oriented (OO) models can be constructed using the Unified Modeling Language (UML). A methodology is developed to build biomedical models at different system levels and construct corresponding UML diagrams, including use case diagrams, class diagrams, and sequence diagrams. By OO modeling using UML, the problems of transporter pharmacogenomics and systems biology can be approached from different angles with a more complete view, which may greatly enhance the efforts in effective drug discovery and development. Bioinformatics resources of membrane transporters and general bioinformatics databases and tools that are frequently used in transporter studies are also collected here. An informatics decision support system based on the models presented here is available at http://www.pharmtao.com/transporter . The methodology developed here can also be used for other biomedical fields.

RT-25: Requirements Management for Net-Centric Enterprises. Phase 1

DTIC Science & Technology

2011-04-28

software systems. These include Business Process Modeling Notation ( BPMN ) (White and Miers 2008) and Business Process Execution Language (BPEL) (Sarang...Engineering with SysML/UML: Modeling, Analysis, Design, Morgan Kaufmann/The OMG Press. White, S. A. and D. Miers (2008). BPMN Modeling and Reference

A unified representation of findings in clinical radiology using the UMLS and DICOM.

PubMed

Bertaud, Valérie; Lasbleiz, Jérémy; Mougin, Fleur; Burgun, Anita; Duvauferrier, Régis

2008-09-01

Collecting and analyzing findings constitute the basis of medical activity. Computer assisted medical activity raises the problem of modelling findings. We propose a unified representation of findings integrating the representations of findings in the GAMUTS in Radiology [M.M. Reeder, B. Felson, GAMUTS in radiology Comprehensive lists of roentgen differential diagnosis, fourth ed., 2003], the Unified Medical Language System (UMLS), and the Digital Imaging and Communication in Medicine Structured Report (DICOM-SR). Starting from a corpus of findings in bone and joint radiology [M.M. Reeder, B. Felson, GAMUTS in Radiology comprehensive lists of roentgen differential diagnosis, fourth ed., 2003] (3481 words), an automated mapping to the UMLS was performed with the Metamap Program. The resulting UMLS terms and Semantic Types were analyzed in order to find a generic template in accordance with DICOM-SR structure. UMLS Concepts were missing for 45% of the GAMUTS findings. Three kinds of regularities were observed in the way the Semantic Types were combined: "pathological findings", "physiological findings" and "anatomical findings". A generic and original DICOM-SR template modelling finding was proposed. It was evaluated for representing GAMUTS jaws findings. 21% missing terms had to be picked up from Radlex (5%) or created (16%). This article shows that it is possible to represent findings using the UMLS and the DICOM SR formalism with a semi-automated method. The Metamap program helped to find a model to represent the semantic structure of free texts with standardized terms (UMLS Concepts). Nevertheless, the coverage of the UMLS is not comprehensive. This study shows that the UMLS should include more technical concepts and more concepts regarding findings, signs and symptoms to be suitable for radiology representation. The semi-automated translation of the whole GAMUTS using the UMLS concepts and the DICOM SR relations could help to create or supplement the DCMR Templates and Context Groups pertaining to the description of imaging findings.

Visualization of Learning Scenarios with UML4LD

ERIC Educational Resources Information Center

Laforcade, Pierre

2007-01-01

Present Educational Modelling Languages are used to formally specify abstract learning scenarios in a machine-interpretable format. Current tooling does not provide teachers/designers with some graphical facilities to help them in reusing existent scenarios. They need human-readable representations. This paper discusses the UML4LD experimental…

Identifying UMLS concepts from ECG Impressions using KnowledgeMap

PubMed Central

Denny, Joshua C.; Spickard, Anderson; Miller, Randolph A; Schildcrout, Jonathan; Darbar, Dawood; Rosenbloom, S. Trent; Peterson, Josh F.

2005-01-01

Electrocardiogram (ECG) impressions represent a wealth of medical information for potential decision support and drug-effect discovery. Much of this information is inaccessible to automated methods in the free-text portion of the ECG report. We studied the application of the KnowledgeMap concept identifier (KMCI) to map Unified Medical Language System (UMLS) concepts from ECG impressions. ECGs were processed by KMCI and the results scored for accuracy by multiple raters. Reviewers also recorded unidentified concepts through the scoring interface. Overall, KMCI correctly identified 1059 out of 1171 concepts for a recall of 0.90. Precision, indicating the proportion of ECG concepts correctly identified, was 0.94. KMCI was particularly effective at identifying ECG rhythms (330/333), perfusion changes (65/66), and noncardiac medical concepts (11/11). In conclusion, KMCI is an effective method for mapping ECG impressions to UMLS concepts. PMID:16779029

Dynamical and Mechanistic Reconstructive Approaches of T Lymphocyte Dynamics: Using Visual Modeling Languages to Bridge the Gap between Immunologists, Theoreticians, and Programmers

PubMed Central

Thomas-Vaslin, Véronique; Six, Adrien; Ganascia, Jean-Gabriel; Bersini, Hugues

2013-01-01

Dynamic modeling of lymphocyte behavior has primarily been based on populations based differential equations or on cellular agents moving in space and interacting each other. The final steps of this modeling effort are expressed in a code written in a programing language. On account of the complete lack of standardization of the different steps to proceed, we have to deplore poor communication and sharing between experimentalists, theoreticians and programmers. The adoption of diagrammatic visual computer language should however greatly help the immunologists to better communicate, to more easily identify the models similarities and facilitate the reuse and extension of existing software models. Since immunologists often conceptualize the dynamical evolution of immune systems in terms of “state-transitions” of biological objects, we promote the use of unified modeling language (UML) state-transition diagram. To demonstrate the feasibility of this approach, we present a UML refactoring of two published models on thymocyte differentiation. Originally built with different modeling strategies, a mathematical ordinary differential equation-based model and a cellular automata model, the two models are now in the same visual formalism and can be compared. PMID:24101919

The Primary Care Electronic Library: RSS feeds using SNOMED-CT indexing for dynamic content delivery.

PubMed

Robinson, Judas; de Lusignan, Simon; Kostkova, Patty; Madge, Bruce; Marsh, A; Biniaris, C

2006-01-01

Rich Site Summary (RSS) feeds are a method for disseminating and syndicating the contents of a website using extensible mark-up language (XML). The Primary Care Electronic Library (PCEL) distributes recent additions to the site in the form of an RSS feed. When new resources are added to PCEL, they are manually assigned medical subject headings (MeSH terms), which are then automatically mapped to SNOMED-CT terms using the Unified Medical Language System (UMLS) Metathesaurus. The library is thus searchable using MeSH or SNOMED-CT. Our syndicate partner wished to have remote access to PCEL coronary heart disease (CHD) information resources based on SNOMED-CT search terms. To pilot the supply of relevant information resources in response to clinically coded requests, using RSS syndication for transmission between web servers. Our syndicate partner provided a list of CHD SNOMED-CT terms to its end-users, a list which was coded according to UMLS specifications. When the end-user requested relevant information resources, this request was relayed from our syndicate partner's web server to the PCEL web server. The relevant resources were retrieved from the PCEL MySQL database. This database is accessed using a server side scripting language (PHP), which enables the production of dynamic RSS feeds on the basis of Source Asserted Identifiers (CODEs) contained in UMLS. Retrieving resources using SNOMED-CT terms using syndication can be used to build a functioning application. The process from request to display of syndicated resources took less than one second. The results of the pilot illustrate that it is possible to exchange data between servers using RSS syndication. This method could be utilised dynamically to supply digital library resources to a clinical system with SNOMED-CT data used as the standard of reference.

Unified Modeling Language (UML) for hospital-based cancer registration processes.

PubMed

Shiki, Naomi; Ohno, Yuko; Fujii, Ayumi; Murata, Taizo; Matsumura, Yasushi

2008-01-01

Hospital-based cancer registry involves complex processing steps that span across multiple departments. In addition, management techniques and registration procedures differ depending on each medical facility. Establishing processes for hospital-based cancer registry requires clarifying specific functions and labor needed. In recent years, the business modeling technique, in which management evaluation is done by clearly spelling out processes and functions, has been applied to business process analysis. However, there are few analytical reports describing the applications of these concepts to medical-related work. In this study, we initially sought to model hospital-based cancer registration processes using the Unified Modeling Language (UML), to clarify functions. The object of this study was the cancer registry of Osaka University Hospital. We organized the hospital-based cancer registration processes based on interview and observational surveys, and produced an As-Is model using activity, use-case, and class diagrams. After drafting every UML model, it was fed-back to practitioners to check its validity and improved. We were able to define the workflow for each department using activity diagrams. In addition, by using use-case diagrams we were able to classify each department within the hospital as a system, and thereby specify the core processes and staff that were responsible for each department. The class diagrams were effective in systematically organizing the information to be used for hospital-based cancer registries. Using UML modeling, hospital-based cancer registration processes were broadly classified into three separate processes, namely, registration tasks, quality control, and filing data. An additional 14 functions were also extracted. Many tasks take place within the hospital-based cancer registry office, but the process of providing information spans across multiple departments. Moreover, additional tasks were required in comparison to using a standardized system because the hospital-based cancer registration system was constructed with the pre-existing computer system in Osaka University Hospital. Difficulty of utilization of useful information for cancer registration processes was shown to increase the task workload. By using UML, we were able to clarify functions and extract the typical processes for a hospital-based cancer registry. Modeling can provide a basis of process analysis for establishment of efficient hospital-based cancer registration processes in each institute.

Automatic Debugging Support for UML Designs

NASA Technical Reports Server (NTRS)

Schumann, Johann; Swanson, Keith (Technical Monitor)

2001-01-01

Design of large software systems requires rigorous application of software engineering methods covering all phases of the software process. Debugging during the early design phases is extremely important, because late bug-fixes are expensive. In this paper, we describe an approach which facilitates debugging of UML requirements and designs. The Unified Modeling Language (UML) is a set of notations for object-orient design of a software system. We have developed an algorithm which translates requirement specifications in the form of annotated sequence diagrams into structured statecharts. This algorithm detects conflicts between sequence diagrams and inconsistencies in the domain knowledge. After synthesizing statecharts from sequence diagrams, these statecharts usually are subject to manual modification and refinement. By using the "backward" direction of our synthesis algorithm. we are able to map modifications made to the statechart back into the requirements (sequence diagrams) and check for conflicts there. Fed back to the user conflicts detected by our algorithm are the basis for deductive-based debugging of requirements and domain theory in very early development stages. Our approach allows to generate explanations oil why there is a conflict and which parts of the specifications are affected.

Formal verification of software-based medical devices considering medical guidelines.

PubMed

Daw, Zamira; Cleaveland, Rance; Vetter, Marcus

2014-01-01

Software-based devices have increasingly become an important part of several clinical scenarios. Due to their critical impact on human life, medical devices have very strict safety requirements. It is therefore necessary to apply verification methods to ensure that the safety requirements are met. Verification of software-based devices is commonly limited to the verification of their internal elements without considering the interaction that these elements have with other devices as well as the application environment in which they are used. Medical guidelines define clinical procedures, which contain the necessary information to completely verify medical devices. The objective of this work was to incorporate medical guidelines into the verification process in order to increase the reliability of the software-based medical devices. Medical devices are developed using the model-driven method deterministic models for signal processing of embedded systems (DMOSES). This method uses unified modeling language (UML) models as a basis for the development of medical devices. The UML activity diagram is used to describe medical guidelines as workflows. The functionality of the medical devices is abstracted as a set of actions that is modeled within these workflows. In this paper, the UML models are verified using the UPPAAL model-checker. For this purpose, a formalization approach for the UML models using timed automaton (TA) is presented. A set of requirements is verified by the proposed approach for the navigation-guided biopsy. This shows the capability for identifying errors or optimization points both in the workflow and in the system design of the navigation device. In addition to the above, an open source eclipse plug-in was developed for the automated transformation of UML models into TA models that are automatically verified using UPPAAL. The proposed method enables developers to model medical devices and their clinical environment using clinical workflows as one UML diagram. Additionally, the system design can be formally verified automatically.

Analyzing polysemous concepts from a clinical perspective: Application to auditing concept categorization in the UMLS

PubMed Central

Mougin, Fleur; Bodenreider, Olivier; Burgun, Anita

2015-01-01

Objectives Polysemy is a frequent issue in biomedical terminologies. In the Unified Medical Language System (UMLS), polysemous terms are either represented as several independent concepts, or clustered into a single, multiply-categorized concept. The objective of this study is to analyze polysemous concepts in the UMLS through their categorization and hierarchical relations for auditing purposes. Methods We used the association of a concept with multiple Semantic Groups (SGs) as a surrogate for polysemy. We first extracted multi-SG (MSG) concepts from the UMLS Metathesaurus and characterized them in terms of the combinations of SGs with which they are associated. We then clustered MSG concepts in order to identify major types of polysemy. We also analyzed the inheritance of SGs in MSG concepts. Finally, we manually reviewed the categorization of the MSG concepts for auditing purposes. Results The 1208 MSG concepts in the Metathesaurus are associated with 30 distinct pairs of SGs. We created 75 semantically homogeneous clusters of MSG concepts, and 276 MSG concepts could not be clustered for lack of hierarchical relations. The clusters were characterized by the most frequent pairs of semantic types of their constituent MSG concepts. MSG concepts exhibit limited semantic compatibility with their parent and child concepts. A large majority of MSG concepts (92%) are adequately categorized. Examples of miscategorized concepts are presented. Conclusion This work is a systematic analysis and manual review of all concepts categorized by multiple SGs in the UMLS. The correctly-categorized MSG concepts do reflect polysemy in the UMLS Metathesaurus. The analysis of inheritance of SGs proved useful for auditing concept categorization in the UMLS. PMID:19303057

Relating UMLS semantic types and task-based ontology to computer-interpretable clinical practice guidelines.

PubMed

Kumar, Anand; Ciccarese, Paolo; Quaglini, Silvana; Stefanelli, Mario; Caffi, Ezio; Boiocchi, Lorenzo

2003-01-01

Medical knowledge in clinical practice guideline (GL) texts is the source of task-based computer-interpretable clinical guideline models (CIGMs). We have used Unified Medical Language System (UMLS) semantic types (STs) to understand the percentage of GL text which belongs to a particular ST. We also use UMLS semantic network together with the CIGM-specific ontology to derive a semantic meaning behind the GL text. In order to achieve this objective, we took nine GL texts from the National Guideline Clearinghouse (NGC) and marked up the text dealing with a particular ST. The STs we took into consideration were restricted taking into account the requirements of a task-based CIGM. We used DARPA Agent Markup Language and Ontology Inference Layer (DAML + OIL) to create the UMLS and CIGM specific semantic network. For the latter, as a bench test, we used the 1999 WHO-International Society of Hypertension Guidelines for the Management of Hypertension. We took into consideration the UMLS STs closest to the clinical tasks. The percentage of the GL text dealing with the ST "Health Care Activity" and subtypes "Laboratory Procedure", "Diagnostic Procedure" and "Therapeutic or Preventive Procedure" were measured. The parts of text belonging to other STs or comments were separated. A mapping of terms belonging to other STs was done to the STs under "HCA" for representation in DAML + OIL. As a result, we found that the three STs under "HCA" were the predominant STs present in the GL text. In cases where the terms of related STs existed, they were mapped into one of the three STs. The DAML + OIL representation was able to describe the hierarchy in task-based CIGMs. To conclude, we understood that the three STs could be used to represent the semantic network of the task-bases CIGMs. We identified some mapping operators which could be used for the mapping of other STs into these.

Generating Models of Surgical Procedures using UMLS Concepts and Multiple Sequence Alignment

PubMed Central

Meng, Frank; D’Avolio, Leonard W.; Chen, Andrew A.; Taira, Ricky K.; Kangarloo, Hooshang

2005-01-01

Surgical procedures can be viewed as a process composed of a sequence of steps performed on, by, or with the patient’s anatomy. This sequence is typically the pattern followed by surgeons when generating surgical report narratives for documenting surgical procedures. This paper describes a methodology for semi-automatically deriving a model of conducted surgeries, utilizing a sequence of derived Unified Medical Language System (UMLS) concepts for representing surgical procedures. A multiple sequence alignment was computed from a collection of such sequences and was used for generating the model. These models have the potential of being useful in a variety of informatics applications such as information retrieval and automatic document generation. PMID:16779094

Corpus-based Statistical Screening for Phrase Identification

PubMed Central

Kim, Won; Wilbur, W. John

2000-01-01

Purpose: The authors study the extraction of useful phrases from a natural language database by statistical methods. The aim is to leverage human effort by providing preprocessed phrase lists with a high percentage of useful material. Method: The approach is to develop six different scoring methods that are based on different aspects of phrase occurrence. The emphasis here is not on lexical information or syntactic structure but rather on the statistical properties of word pairs and triples that can be obtained from a large database. Measurements: The Unified Medical Language System (UMLS) incorporates a large list of humanly acceptable phrases in the medical field as a part of its structure. The authors use this list of phrases as a gold standard for validating their methods. A good method is one that ranks the UMLS phrases high among all phrases studied. Measurements are 11-point average precision values and precision-recall curves based on the rankings. Result: The authors find of six different scoring methods that each proves effective in identifying UMLS quality phrases in a large subset of MEDLINE. These methods are applicable both to word pairs and word triples. All six methods are optimally combined to produce composite scoring methods that are more effective than any single method. The quality of the composite methods appears sufficient to support the automatic placement of hyperlinks in text at the site of highly ranked phrases. Conclusion: Statistical scoring methods provide a promising approach to the extraction of useful phrases from a natural language database for the purpose of indexing or providing hyperlinks in text. PMID:10984469

Dependability modeling and assessment in UML-based software development.

PubMed

Bernardi, Simona; Merseguer, José; Petriu, Dorina C

2012-01-01

Assessment of software nonfunctional properties (NFP) is an important problem in software development. In the context of model-driven development, an emerging approach for the analysis of different NFPs consists of the following steps: (a) to extend the software models with annotations describing the NFP of interest; (b) to transform automatically the annotated software model to the formalism chosen for NFP analysis; (c) to analyze the formal model using existing solvers; (d) to assess the software based on the results and give feedback to designers. Such a modeling→analysis→assessment approach can be applied to any software modeling language, be it general purpose or domain specific. In this paper, we focus on UML-based development and on the dependability NFP, which encompasses reliability, availability, safety, integrity, and maintainability. The paper presents the profile used to extend UML with dependability information, the model transformation to generate a DSPN formal model, and the assessment of the system properties based on the DSPN results.

Dependability Modeling and Assessment in UML-Based Software Development

PubMed Central

Bernardi, Simona; Merseguer, José; Petriu, Dorina C.

2012-01-01

Assessment of software nonfunctional properties (NFP) is an important problem in software development. In the context of model-driven development, an emerging approach for the analysis of different NFPs consists of the following steps: (a) to extend the software models with annotations describing the NFP of interest; (b) to transform automatically the annotated software model to the formalism chosen for NFP analysis; (c) to analyze the formal model using existing solvers; (d) to assess the software based on the results and give feedback to designers. Such a modeling→analysis→assessment approach can be applied to any software modeling language, be it general purpose or domain specific. In this paper, we focus on UML-based development and on the dependability NFP, which encompasses reliability, availability, safety, integrity, and maintainability. The paper presents the profile used to extend UML with dependability information, the model transformation to generate a DSPN formal model, and the assessment of the system properties based on the DSPN results. PMID:22988428

Evaluation of PROforma as a language for implementing medical guidelines in a practical context

PubMed Central

Sutton, David R; Taylor, Paul; Earle, Kenneth

2006-01-01

Background PROforma is one of several languages that allow clinical guidelines to be expressed in a computer-interpretable manner. How these languages should be compared, and what requirements they should meet, are questions that are being actively addressed by a community of interested researchers. Methods We have developed a system to allow hypertensive patients to be monitored and assessed without visiting their GPs (except in the most urgent cases). Blood pressure measurements are performed at the patients' pharmacies and a web-based system, created using PROforma, makes recommendations for continued monitoring, and/or changes in medication. The recommendations and measurements are transmitted electronically to a practitioner with authority to issue and change prescriptions. We evaluated the use of PROforma during the knowledge acquisition, analysis, design and implementation of this system. The analysis focuses on the logical adequacy, heuristic power, notational convenience, and explanation support provided by the PROforma language. Results PROforma proved adequate as a language for the implementation of the clinical reasoning required by this project. However a lack of notational convenience led us to use UML activity diagrams, rather than PROforma process descriptions, to create the models that were used during the knowledge acquisition and analysis phases of the project. These UML diagrams were translated into PROforma during the implementation of the project. Conclusion The experience accumulated during this study highlighted the importance of structure preserving design, that is to say that the models used in the design and implementation of a knowledge-based system should be structurally similar to those created during knowledge acquisition and analysis. Ideally the same language should be used for all of these models. This means that great importance has to be attached to the notational convenience of these languages, by which we mean the ease with which they can be read, written, and understood by human beings. The importance of notational convenience arises from the fact that a language used during knowledge acquisition and analysis must be intelligible to the potential users of a system, and to the domain experts who provide the knowledge that will be used in its construction. PMID:16597341

Evaluation of PROforma as a language for implementing medical guidelines in a practical context.

PubMed

Sutton, David R; Taylor, Paul; Earle, Kenneth

2006-04-05

PROforma is one of several languages that allow clinical guidelines to be expressed in a computer-interpretable manner. How these languages should be compared, and what requirements they should meet, are questions that are being actively addressed by a community of interested researchers. We have developed a system to allow hypertensive patients to be monitored and assessed without visiting their GPs (except in the most urgent cases). Blood pressure measurements are performed at the patients' pharmacies and a web-based system, created using PROforma, makes recommendations for continued monitoring, and/or changes in medication. The recommendations and measurements are transmitted electronically to a practitioner with authority to issue and change prescriptions. We evaluated the use of PROforma during the knowledge acquisition, analysis, design and implementation of this system. The analysis focuses on the logical adequacy, heuristic power, notational convenience, and explanation support provided by the PROforma language. PROforma proved adequate as a language for the implementation of the clinical reasoning required by this project. However a lack of notational convenience led us to use UML activity diagrams, rather than PROforma process descriptions, to create the models that were used during the knowledge acquisition and analysis phases of the project. These UML diagrams were translated into PROforma during the implementation of the project. The experience accumulated during this study highlighted the importance of structure preserving design, that is to say that the models used in the design and implementation of a knowledge-based system should be structurally similar to those created during knowledge acquisition and analysis. Ideally the same language should be used for all of these models. This means that great importance has to be attached to the notational convenience of these languages, by which we mean the ease with which they can be read, written, and understood by human beings. The importance of notational convenience arises from the fact that a language used during knowledge acquisition and analysis must be intelligible to the potential users of a system, and to the domain experts who provide the knowledge that will be used in its construction.

A Systematic Software, Firmware, and Hardware Codesign Methodology for Digital Signal Processing

DTIC Science & Technology

2014-03-01

possible mappings ...................................................60 Table 25. Possible optimal leaf -nodes... size weight and power UAV unmanned aerial vehicle UHF ultra-high frequency UML universal modeling language Verilog verify logic VHDL VHSIC...optimal leaf -nodes to some design patterns for embedded system design. Software and hardware partitioning is a very difficult challenge in the field of

Developing a Philippine Cancer Grid. Part 1: Building a Prototype for a Data Retrieval System for Breast Cancer Research Using Medical Ontologies

NASA Astrophysics Data System (ADS)

Coronel, Andrei D.; Saldana, Rafael P.

Cancer is a leading cause of morbidity and mortality in the Philippines. Developed within the context of a Philippine Cancer Grid, the present study used web development technologies such as PHP, MySQL, and Apache server to build a prototype data retrieval system for breast cancer research that incorporates medical ontologies from the Unified Medical Language System (UMLS).

Auditing the multiply-related concepts within the UMLS

PubMed Central

Mougin, Fleur; Grabar, Natalia

2014-01-01

Objective This work focuses on multiply-related Unified Medical Language System (UMLS) concepts, that is, concepts associated through multiple relations. The relations involved in such situations are audited to determine whether they are provided by source vocabularies or result from the integration of these vocabularies within the UMLS. Methods We study the compatibility of the multiple relations which associate the concepts under investigation and try to explain the reason why they co-occur. Towards this end, we analyze the relations both at the concept and term levels. In addition, we randomly select 288 concepts associated through contradictory relations and manually analyze them. Results At the UMLS scale, only 0.7% of combinations of relations are contradictory, while homogeneous combinations are observed in one-third of situations. At the scale of source vocabularies, one-third do not contain more than one relation between the concepts under investigation. Among the remaining source vocabularies, seven of them mainly present multiple non-homogeneous relations between terms. Analysis at the term level also shows that only in a quarter of cases are the source vocabularies responsible for the presence of multiply-related concepts in the UMLS. These results are available at: http://www.isped.u-bordeaux2.fr/ArticleJAMIA/results_multiply_related_concepts.aspx. Discussion Manual analysis was useful to explain the conceptualization difference in relations between terms across source vocabularies. The exploitation of source relations was helpful for understanding why some source vocabularies describe multiple relations between a given pair of terms. PMID:24464853

An early illness recognition framework using a temporal Smith Waterman algorithm and NLP.

PubMed

Hajihashemi, Zahra; Popescu, Mihail

2013-01-01

In this paper we propose a framework for detecting health patterns based on non-wearable sensor sequence similarity and natural language processing (NLP). In TigerPlace, an aging in place facility from Columbia, MO, we deployed 47 sensor networks together with a nursing electronic health record (EHR) system to provide early illness recognition. The proposed framework utilizes sensor sequence similarity and NLP on EHR nursing comments to automatically notify the physician when health problems are detected. The reported methodology is inspired by genomic sequence annotation using similarity algorithms such as Smith Waterman (SW). Similarly, for each sensor sequence, we associate health concepts extracted from the nursing notes using Metamap, a NLP tool provided by Unified Medical Language System (UMLS). Since sensor sequences, unlike genomics ones, have an associated time dimension we propose a temporal variant of SW (TSW) to account for time. The main challenges presented by our framework are finding the most suitable time sequence similarity and aggregation of the retrieved UMLS concepts. On a pilot dataset from three Tiger Place residents, with a total of 1685 sensor days and 626 nursing records, we obtained an average precision of 0.64 and a recall of 0.37.

The caCORE Software Development Kit: streamlining construction of interoperable biomedical information services.

PubMed

Phillips, Joshua; Chilukuri, Ram; Fragoso, Gilberto; Warzel, Denise; Covitz, Peter A

2006-01-06

Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for caBIG. The caCORE SDK substantially lowers the barrier to implementing systems that are syntactically and semantically interoperable by providing workflow and automation tools that standardize and expedite modeling, development, and deployment. It has gained acceptance among developers in the caBIG program, and is expected to provide a common mechanism for creating data service nodes on the data grid that is under development.

Graphical tool for navigation within the semantic network of the UMLS metathesaurus on a locally installed database.

PubMed

Frankewitsch, T; Prokosch, H U

2000-01-01

Knowledge in the environment of information technologies is bound to structured vocabularies. Medical data dictionaries are necessary for uniquely describing findings like diagnoses, procedures or functions. Therefore we decided to locally install a version of the Unified Medical Language System (UMLS) of the U.S. National Library of Medicine as a repository for defining entries of a medical multimedia database. Because of the requirement to extend the vocabulary in concepts and relations between existing concepts a graphical tool for appending new items to the database has been developed: Although the database is an instance of a semantic network the focus on single entries offers the opportunity of reducing the net to a tree within this detail. Based on the graph theorem, there are definitions of nodes of concepts and nodes of knowledge. The UMLS additionally offers the specification of sub-relations, which can be represented, too. Using this view it is possible to manage these 1:n-Relations in a simple tree view. On this background an explorer like graphical user interface has been realised to add new concepts and define new relationships between those and existing entries for adapting the UMLS for specific purposes such as describing medical multimedia objects.

Improved Identification of Noun Phrases in Clinical Radiology Reports Using a High-Performance Statistical Natural Language Parser Augmented with the UMLS Specialist Lexicon

PubMed Central

Huang, Yang; Lowe, Henry J.; Klein, Dan; Cucina, Russell J.

2005-01-01

Objective: The aim of this study was to develop and evaluate a method of extracting noun phrases with full phrase structures from a set of clinical radiology reports using natural language processing (NLP) and to investigate the effects of using the UMLS® Specialist Lexicon to improve noun phrase identification within clinical radiology documents. Design: The noun phrase identification (NPI) module is composed of a sentence boundary detector, a statistical natural language parser trained on a nonmedical domain, and a noun phrase (NP) tagger. The NPI module processed a set of 100 XML-represented clinical radiology reports in Health Level 7 (HL7)® Clinical Document Architecture (CDA)–compatible format. Computed output was compared with manual markups made by four physicians and one author for maximal (longest) NP and those made by one author for base (simple) NP, respectively. An extended lexicon of biomedical terms was created from the UMLS Specialist Lexicon and used to improve NPI performance. Results: The test set was 50 randomly selected reports. The sentence boundary detector achieved 99.0% precision and 98.6% recall. The overall maximal NPI precision and recall were 78.9% and 81.5% before using the UMLS Specialist Lexicon and 82.1% and 84.6% after. The overall base NPI precision and recall were 88.2% and 86.8% before using the UMLS Specialist Lexicon and 93.1% and 92.6% after, reducing false-positives by 31.1% and false-negatives by 34.3%. Conclusion: The sentence boundary detector performs excellently. After the adaptation using the UMLS Specialist Lexicon, the statistical parser's NPI performance on radiology reports increased to levels comparable to the parser's native performance in its newswire training domain and to that reported by other researchers in the general nonmedical domain. PMID:15684131

Augmented halal food traceability system: analysis and design using UML

NASA Astrophysics Data System (ADS)

Usman, Y. V.; Fauzi, A. M.; Irawadi, T. T.; Djatna, T.

2018-04-01

Augmented halal food traceability is expanding the range of halal traceability in food supply chain where currently only available for tracing from the source of raw material to the industrial warehouse or inbound logistic. The halal traceability system must be developed in the integrated form that includes inbound and outbound logistics. The objective of this study was to develop a reliable initial model of integrated traceability system of halal food supply chain. The method was based on unified modeling language (UML) such as use case, sequence, and business process diagram. A goal programming model was formulated considering two objective functions which include (1) minimization of risk of halal traceability failures happened potentially during outbound logistics activities and (2) maximization of quality of halal product information. The result indicates the supply of material is the most important point to be considered in minimizing the risk of failure of halal food traceability system whereas no risk observed in manufacturing and distribution.

Dynamic partial reconfiguration of logic controllers implemented in FPGAs

NASA Astrophysics Data System (ADS)

Bazydło, Grzegorz; Wiśniewski, Remigiusz

2016-09-01

Technological progress in recent years benefits in digital circuits containing millions of logic gates with the capability for reprogramming and reconfiguring. On the one hand it provides the unprecedented computational power, but on the other hand the modelled systems are becoming increasingly complex, hierarchical and concurrent. Therefore, abstract modelling supported by the Computer Aided Design tools becomes a very important task. Even the higher consumption of the basic electronic components seems to be acceptable because chip manufacturing costs tend to fall over the time. The paper presents a modelling approach for logic controllers with the use of Unified Modelling Language (UML). Thanks to the Model Driven Development approach, starting with a UML state machine model, through the construction of an intermediate Hierarchical Concurrent Finite State Machine model, a collection of Verilog files is created. The system description generated in hardware description language can be synthesized and implemented in reconfigurable devices, such as FPGAs. Modular specification of the prototyped controller permits for further dynamic partial reconfiguration of the prototyped system. The idea bases on the exchanging of the functionality of the already implemented controller without stopping of the FPGA device. It means, that a part (for example a single module) of the logic controller is replaced by other version (called context), while the rest of the system is still running. The method is illustrated by a practical example by an exemplary Home Area Network system.

Prototyping an institutional IAIMS/UMLS information environment for an academic medical center.

PubMed

Miller, P L; Paton, J A; Clyman, J I; Powsner, S M

1992-07-01

The paper describes a prototype information environment designed to link network-based information resources in an integrated fashion and thus enhance the information capabilities of an academic medical center. The prototype was implemented on a single Macintosh computer to permit exploration of the overall "information architecture" and to demonstrate the various desired capabilities prior to full-scale network-based implementation. At the heart of the prototype are two components: a diverse set of information resources available over an institutional computer network and an information sources map designed to assist users in finding and accessing information resources relevant to their needs. The paper describes these and other components of the prototype and presents a scenario illustrating its use. The prototype illustrates the link between the goals of two National Library of Medicine initiatives, the Integrated Academic Information Management System (IAIMS) and the Unified Medical Language System (UMLS).

Toward a Bio-Medical Thesaurus: Building the Foundation of the UMLS

PubMed Central

Tuttle, Mark S.; Blois, Marsden S.; Erlbaum, Mark S.; Nelson, Stuart J.; Sherertz, David D.

1988-01-01

The Unified Medical Language System (UMLS) is being designed to provide a uniform user interface to heterogeneous machine-readable bio-medical information resources, such as bibliographic databases, genetic databases, expert systems and patient records.1 Such an interface will have to recognize different ways of saying the same thing, and provide links to ways of saying related things. One way to represent the necessary associations is via a domain thesaurus. As no such thesaurus exists, and because, once built, it will be both sizable and in need of continuous maintenance, its design should include a methodology for building and maintaining it. We propose a methodology, utilizing lexically expanded schema inversion, and a design, called T. Lex, which together form one approach to the problem of defining and building a bio-medical thesaurus. We argue that the semantic locality implicit in such a thesaurus will support model-based reasoning in bio-medicine.2

Colaborated Architechture Framework for Composition UML 2.0 in Zachman Framework

NASA Astrophysics Data System (ADS)

Hermawan; Hastarista, Fika

2016-01-01

Zachman Framework (ZF) is the framework of enterprise architechture that most widely adopted in the Enterprise Information System (EIS) development. In this study, has been developed Colaborated Architechture Framework (CAF) to collaborate ZF with Unified Modeling Language (UML) 2.0 modeling. The CAF provides the composition of ZF matrix that each cell is consist of the Model Driven architechture (MDA) from the various UML models and many Software Requirement Specification (SRS) documents. Implementation of this modeling is used to develops Enterprise Resource Planning (ERP). Because ERP have a coverage of applications in large numbers and complexly relations, it is necessary to use Agile Model Driven Design (AMDD) approach as an advanced method to transforms MDA into components of application modules with efficiently and accurately. Finally, through the using of the CAF, give good achievement in fullfilment the needs from all stakeholders that are involved in the overall process stage of Rational Unified Process (RUP), and also obtaining a high satisfaction to fullfiled the functionality features of the ERP software in PT. Iglas (Persero) Gresik.

Use cases and DEMO: aligning functional features of ICT-infrastructure to business processes.

PubMed

Maij, E; Toussaint, P J; Kalshoven, M; Poerschke, M; Zwetsloot-Schonk, J H M

2002-11-12

The proper alignment of functional features of the ICT-infrastructure to business processes is a major challenge in health care organisations. This alignment takes into account that the organisational structure not only shapes the ICT-infrastructure, but that the inverse also holds. To solve the alignment problem, relevant features of the ICT-infrastructure should be derived from the organisational structure and the influence of this envisaged ICT to the work practices should be pointed out. The objective of our study was to develop a method to solve this alignment problem. In a previous study we demonstrated the appropriateness of the business process modelling methodology Dynamic Essential Modelling of Organizations (DEMO). A proven and widely used modelling language for expressing functional features is Unified Modelling Language (UML). In the context of a specific case study at the University Medical Centre Utrecht in the Netherlands we investigated if the combined use of DEMO and UML could solve the alignment problem. The study demonstrated that the DEMO models were suited as a starting point in deriving system functionality by using the use case concept of UML. Further, the case study demonstrated that in using this approach for the alignment problem, insight is gained into the mutual influence of ICT-infrastructure and organisation structure: (a) specification of independent, re-usable components-as a set of related functionalities-is realised, and (b) a helpful representation of the current and future work practice is provided for in relation to the envisaged ICT support.

"Understanding" medical school curriculum content using KnowledgeMap.

PubMed

Denny, Joshua C; Smithers, Jeffrey D; Miller, Randolph A; Spickard, Anderson

2003-01-01

To describe the development and evaluation of computational tools to identify concepts within medical curricular documents, using information derived from the National Library of Medicine's Unified Medical Language System (UMLS). The long-term goal of the KnowledgeMap (KM) project is to provide faculty and students with an improved ability to develop, review, and integrate components of the medical school curriculum. The KM concept identifier uses lexical resources partially derived from the UMLS (SPECIALIST lexicon and Metathesaurus), heuristic language processing techniques, and an empirical scoring algorithm. KM differentiates among potentially matching Metathesaurus concepts within a source document. The authors manually identified important "gold standard" biomedical concepts within selected medical school full-content lecture documents and used these documents to compare KM concept recognition with that of a known state-of-the-art "standard"-the National Library of Medicine's MetaMap program. The number of "gold standard" concepts in each lecture document identified by either KM or MetaMap, and the cause of each failure or relative success in a random subset of documents. For 4,281 "gold standard" concepts, MetaMap matched 78% and KM 82%. Precision for "gold standard" concepts was 85% for MetaMap and 89% for KM. The heuristics of KM accurately matched acronyms, concepts underspecified in the document, and ambiguous matches. The most frequent cause of matching failures was absence of target concepts from the UMLS Metathesaurus. The prototypic KM system provided an encouraging rate of concept extraction for representative medical curricular texts. Future versions of KM should be evaluated for their ability to allow administrators, lecturers, and students to navigate through the medical curriculum to locate redundancies, find interrelated information, and identify omissions. In addition, the ability of KM to meet specific, personal information needs should be assessed.

Integrating unified medical language system and association mining techniques into relevance feedback for biomedical literature search.

PubMed

Ji, Yanqing; Ying, Hao; Tran, John; Dews, Peter; Massanari, R Michael

2016-07-19

Finding highly relevant articles from biomedical databases is challenging not only because it is often difficult to accurately express a user's underlying intention through keywords but also because a keyword-based query normally returns a long list of hits with many citations being unwanted by the user. This paper proposes a novel biomedical literature search system, called BiomedSearch, which supports complex queries and relevance feedback. The system employed association mining techniques to build a k-profile representing a user's relevance feedback. More specifically, we developed a weighted interest measure and an association mining algorithm to find the strength of association between a query and each concept in the article(s) selected by the user as feedback. The top concepts were utilized to form a k-profile used for the next-round search. BiomedSearch relies on Unified Medical Language System (UMLS) knowledge sources to map text files to standard biomedical concepts. It was designed to support queries with any levels of complexity. A prototype of BiomedSearch software was made and it was preliminarily evaluated using the Genomics data from TREC (Text Retrieval Conference) 2006 Genomics Track. Initial experiment results indicated that BiomedSearch increased the mean average precision (MAP) for a set of queries. With UMLS and association mining techniques, BiomedSearch can effectively utilize users' relevance feedback to improve the performance of biomedical literature search.

Word sense disambiguation in the clinical domain: a comparison of knowledge-rich and knowledge-poor unsupervised methods

PubMed Central

Chasin, Rachel; Rumshisky, Anna; Uzuner, Ozlem; Szolovits, Peter

2014-01-01

Objective To evaluate state-of-the-art unsupervised methods on the word sense disambiguation (WSD) task in the clinical domain. In particular, to compare graph-based approaches relying on a clinical knowledge base with bottom-up topic-modeling-based approaches. We investigate several enhancements to the topic-modeling techniques that use domain-specific knowledge sources. Materials and methods The graph-based methods use variations of PageRank and distance-based similarity metrics, operating over the Unified Medical Language System (UMLS). Topic-modeling methods use unlabeled data from the Multiparameter Intelligent Monitoring in Intensive Care (MIMIC II) database to derive models for each ambiguous word. We investigate the impact of using different linguistic features for topic models, including UMLS-based and syntactic features. We use a sense-tagged clinical dataset from the Mayo Clinic for evaluation. Results The topic-modeling methods achieve 66.9% accuracy on a subset of the Mayo Clinic's data, while the graph-based methods only reach the 40–50% range, with a most-frequent-sense baseline of 56.5%. Features derived from the UMLS semantic type and concept hierarchies do not produce a gain over bag-of-words features in the topic models, but identifying phrases from UMLS and using syntax does help. Discussion Although topic models outperform graph-based methods, semantic features derived from the UMLS prove too noisy to improve performance beyond bag-of-words. Conclusions Topic modeling for WSD provides superior results in the clinical domain; however, integration of knowledge remains to be effectively exploited. PMID:24441986

Quality evaluation of value sets from cancer study common data elements using the UMLS semantic groups

PubMed Central

Solbrig, Harold R; Chute, Christopher G

2012-01-01

Objective The objective of this study is to develop an approach to evaluate the quality of terminological annotations on the value set (ie, enumerated value domain) components of the common data elements (CDEs) in the context of clinical research using both unified medical language system (UMLS) semantic types and groups. Materials and methods The CDEs of the National Cancer Institute (NCI) Cancer Data Standards Repository, the NCI Thesaurus (NCIt) concepts and the UMLS semantic network were integrated using a semantic web-based framework for a SPARQL-enabled evaluation. First, the set of CDE-permissible values with corresponding meanings in external controlled terminologies were isolated. The corresponding value meanings were then evaluated against their NCI- or UMLS-generated semantic network mapping to determine whether all of the meanings fell within the same semantic group. Results Of the enumerated CDEs in the Cancer Data Standards Repository, 3093 (26.2%) had elements drawn from more than one UMLS semantic group. A random sample (n=100) of this set of elements indicated that 17% of them were likely to have been misclassified. Discussion The use of existing semantic web tools can support a high-throughput mechanism for evaluating the quality of large CDE collections. This study demonstrates that the involvement of multiple semantic groups in an enumerated value domain of a CDE is an effective anchor to trigger an auditing point for quality evaluation activities. Conclusion This approach produces a useful quality assurance mechanism for a clinical study CDE repository. PMID:22511016

Using UMLS to construct a generalized hierarchical concept-based dictionary of brain functions for information extraction from the fMRI literature.

PubMed

Hsiao, Mei-Yu; Chen, Chien-Chung; Chen, Jyh-Horng

2009-10-01

With a rapid progress in the field, a great many fMRI studies are published every year, to the extent that it is now becoming difficult for researchers to keep up with the literature, since reading papers is extremely time-consuming and labor-intensive. Thus, automatic information extraction has become an important issue. In this study, we used the Unified Medical Language System (UMLS) to construct a hierarchical concept-based dictionary of brain functions. To the best of our knowledge, this is the first generalized dictionary of this kind. We also developed an information extraction system for recognizing, mapping and classifying terms relevant to human brain study. The precision and recall of our system was on a par with that of human experts in term recognition, term mapping and term classification. Our approach presented in this paper presents an alternative to the more laborious, manual entry approach to information extraction.

Standard Generalized Markup Language for self-defining structured reports.

PubMed

Kahn, C E

1999-01-01

Structured reporting is the process of using standardized data elements and predetermined data-entry formats to record observations. The Standard Generalized Markup Language (SGML; International Standards Organization (ISO) 8879:1986)--an open, internationally accepted standard for document interchange was used to encode medical observations acquired in an Internet-based structured reporting system. The resulting report is self-documenting: it includes a definition of its allowable data fields and values encoded as a report-specific SGML document type definition (DTD). The data-entry forms, DTD, and report document instances are based on report specifications written in a simple, SGML-based language designed for that purpose. Reporting concepts can be linked with those of external vocabularies such as the Unified Medical Language System (UMLS) Metathesaurus. The use of open standards such as SGML is an important step in the creation of open, universally comprehensible structured reports.

A HyperCard Implementation of Meta-1: The First Version of the UMLS Metathesaurus*

PubMed Central

Sherertz, David; Tuttle, Mark; Cole, William; Erlbaum, Mark; Olson, Nels; Nelson, Stuart

1989-01-01

The Unified Medical Language System (UMLS) is being designed to provide uniform access to computer-based resources in biomedicine. For the foreseeable future, the foundation of the UMLS will be a metathesaurus of concepts, synthesized from existing biomedical nomenclatures. Meta-1, the first version of the Metathesaurus, will contain all of MeSH, a selection of terms from primary care, clinical medicine, and other domains, and all terms from SNOMED, ICD-9-CM, and CPT-4 which “match” them -- about 30,000 terms. In addition, Meta-1 will contain information about the occurrence and co-occurrence of its terms in selected resources, such as MEDLINE. As Meta-1 will contain about 100MB of terms and relationships, it is unlikely that it will be “printed.” Instead, some UMLS applications will support Metathesaurus browsing. One way of browsing Meta-1 will be via the Apple Macintosh® application called HyperCard®. A demonstration of a HyperCard interface, called Meta-Card™ will first acquaint viewers with the contents of the pre-human-review version of Meta-1, and second, illustrate how an object-oriented interface can be programmed to support various visual metaphors, e.g. “click-to-get-more-information,” and “click-to-follow-a-semantic-link,” and the notion of a Metathesaurus esthetic.

VLTI auxiliary telescopes: a full object-oriented approach

NASA Astrophysics Data System (ADS)

Chiozzi, Gianluca; Duhoux, Philippe; Karban, Robert

2000-06-01

The Very Large Telescope (VLT) Telescope Control Software (TCS) is a portable system. It is now in use or will be used in a whole family of ESO telescopes VLT Unit Telescopes, VLTI Auxiliary Telescopes, NTT, La Silla 3.6, VLT Survey Telescope and Astronomical Site Monitors in Paranal and La Silla). Although it has been developed making extensive usage of Object Oriented (OO) methodologies, the overall development process chosen at the beginning of the project used traditional methods. In order to warranty a longer lifetime to the system (improving documentation and maintainability) and to prepare for future projects, we have introduced a full OO process. We have taken as a basis the United Software Development Process with the Unified Modeling Language (UML) and we have adapted the process to our specific needs. This paper describes how the process has been applied to the VLTI Auxiliary Telescopes Control Software (ATCS). The ATCS is based on the portable VLT TCS, but some subsystems are new or have specific characteristics. The complete process has been applied to the new subsystems, while reused code has been integrated in the UML models. We have used the ATCS on one side to tune the process and train the team members and on the other side to provide a UML and WWW based documentation for the portable VLT TCS.

Pedagogical Issues in Object Orientation.

ERIC Educational Resources Information Center

Nerur, Sridhar; Ramanujan, Sam; Kesh, Someswar

2002-01-01

Discusses the need for people with object-oriented (OO) skills, explains benefits of OO in software development, and addresses some of the difficulties in teaching OO. Topics include the evolution of programming languages; differences between OO and traditional approaches; differences from data modeling; and Unified Modeling Language (UML) and…

XMI2USE: A Tool for Transforming XMI to USE Specifications

NASA Astrophysics Data System (ADS)

Sun, Wuliang; Song, Eunjee; Grabow, Paul C.; Simmonds, Devon M.

The UML-based Specification Environment (USE) tool supports syntactic analysis, type checking, consistency checking, and dynamic validation of invariants and pre-/post conditions specified in the Object Constraint Language (OCL). Due to its animation and analysis power, it is useful when checking critical non-functional properties such as security policies. However, the USE tool requires one to specify (i.e., "write") a model using its own textual language and does not allow one to import any model specification files created by other UML modeling tools. Hence, to make the best use of existing UML tools, we often create a model with OCL constraints using a modeling tool such as the IBM Rational Software Architect (RSA) and then use the USE tool for model validation. This approach, however, requires a manual transformation between the specifications of two different tool formats, which is error-prone and diminishes the benefit of automated model-level validations. In this paper, we describe our own implementation of a specification transformation engine that is based on the Model Driven Architecture (MDA) framework and currently supports automatic tool-level transformations from RSA to USE.

Integration of the MIP Command and Control Information Exchange Data Model into National Systems

DTIC Science & Technology

2005-06-01

Solutions for the Java programming language include Hibernate ( Hibernate , 2005), Java Data Objects (JDO, 2005), J2EE Container Managed Persistence (CMP) and... Java , C++, or UML classes in a first step. The semantical gap between the relational and the object-oriented world, also called O-R impedance, is a...cannot be achieved at the interfaces – it needs to be established in the core of national systems! References Hibernate (2005). www.hibernate.org. JDO

The caCORE Software Development Kit: Streamlining construction of interoperable biomedical information services

PubMed Central

Phillips, Joshua; Chilukuri, Ram; Fragoso, Gilberto; Warzel, Denise; Covitz, Peter A

2006-01-01

Background Robust, programmatically accessible biomedical information services that syntactically and semantically interoperate with other resources are challenging to construct. Such systems require the adoption of common information models, data representations and terminology standards as well as documented application programming interfaces (APIs). The National Cancer Institute (NCI) developed the cancer common ontologic representation environment (caCORE) to provide the infrastructure necessary to achieve interoperability across the systems it develops or sponsors. The caCORE Software Development Kit (SDK) was designed to provide developers both within and outside the NCI with the tools needed to construct such interoperable software systems. Results The caCORE SDK requires a Unified Modeling Language (UML) tool to begin the development workflow with the construction of a domain information model in the form of a UML Class Diagram. Models are annotated with concepts and definitions from a description logic terminology source using the Semantic Connector component. The annotated model is registered in the Cancer Data Standards Repository (caDSR) using the UML Loader component. System software is automatically generated using the Codegen component, which produces middleware that runs on an application server. The caCORE SDK was initially tested and validated using a seven-class UML model, and has been used to generate the caCORE production system, which includes models with dozens of classes. The deployed system supports access through object-oriented APIs with consistent syntax for retrieval of any type of data object across all classes in the original UML model. The caCORE SDK is currently being used by several development teams, including by participants in the cancer biomedical informatics grid (caBIG) program, to create compatible data services. caBIG compatibility standards are based upon caCORE resources, and thus the caCORE SDK has emerged as a key enabling technology for caBIG. Conclusion The caCORE SDK substantially lowers the barrier to implementing systems that are syntactically and semantically interoperable by providing workflow and automation tools that standardize and expedite modeling, development, and deployment. It has gained acceptance among developers in the caBIG program, and is expected to provide a common mechanism for creating data service nodes on the data grid that is under development. PMID:16398930

Consumers' Use of UMLS Concepts on Social Media: Diabetes-Related Textual Data Analysis in Blog and Social Q&A Sites.

PubMed

Park, Min Sook; He, Zhe; Chen, Zhiwei; Oh, Sanghee; Bian, Jiang

2016-11-24

The widely known terminology gap between health professionals and health consumers hinders effective information seeking for consumers. The aim of this study was to better understand consumers' usage of medical concepts by evaluating the coverage of concepts and semantic types of the Unified Medical Language System (UMLS) on diabetes-related postings in 2 types of social media: blogs and social question and answer (Q&A). We collected 2 types of social media data: (1) a total of 3711 blogs tagged with "diabetes" on Tumblr posted between February and October 2015; and (2) a total of 58,422 questions and associated answers posted between 2009 and 2014 in the diabetes category of Yahoo! Answers. We analyzed the datasets using a widely adopted biomedical text processing framework Apache cTAKES and its extension YTEX. First, we applied the named entity recognition (NER) method implemented in YTEX to identify UMLS concepts in the datasets. We then analyzed the coverage and the popularity of concepts in the UMLS source vocabularies across the 2 datasets (ie, blogs and social Q&A). Further, we conducted a concept-level comparative coverage analysis between SNOMED Clinical Terms (SNOMED CT) and Open-Access Collaborative Consumer Health Vocabulary (OAC CHV)-the top 2 UMLS source vocabularies that have the most coverage on our datasets. We also analyzed the UMLS semantic types that were frequently observed in our datasets. We identified 2415 UMLS concepts from blog postings, 6452 UMLS concepts from social Q&A questions, and 10,378 UMLS concepts from the answers. The medical concepts identified in the blogs can be covered by 56 source vocabularies in the UMLS, while those in questions and answers can be covered by 58 source vocabularies. SNOMED CT was the dominant vocabulary in terms of coverage across all the datasets, ranging from 84.9% to 95.9%. It was followed by OAC CHV (between 73.5% and 80.0%) and Metathesaurus Names (MTH) (between 55.7% and 73.5%). All of the social media datasets shared frequent semantic types such as "Amino Acid, Peptide, or Protein," "Body Part, Organ, or Organ Component," and "Disease or Syndrome." Although the 3 social media datasets vary greatly in size, they exhibited similar conceptual coverage among UMLS source vocabularies and the identified concepts showed similar semantic type distributions. As such, concepts that are both frequently used by consumers and also found in professional vocabularies such as SNOMED CT can be suggested to OAC CHV to improve its coverage. ©Min Sook Park, Zhe He, Zhiwei Chen, Sanghee Oh, Jiang Bian. Originally published in JMIR Medical Informatics (http://medinform.jmir.org), 24.11.2016.

Consumers’ Use of UMLS Concepts on Social Media: Diabetes-Related Textual Data Analysis in Blog and Social Q&A Sites

PubMed Central

Chen, Zhiwei; Oh, Sanghee; Bian, Jiang

2016-01-01

Background The widely known terminology gap between health professionals and health consumers hinders effective information seeking for consumers. Objective The aim of this study was to better understand consumers’ usage of medical concepts by evaluating the coverage of concepts and semantic types of the Unified Medical Language System (UMLS) on diabetes-related postings in 2 types of social media: blogs and social question and answer (Q&A). Methods We collected 2 types of social media data: (1) a total of 3711 blogs tagged with “diabetes” on Tumblr posted between February and October 2015; and (2) a total of 58,422 questions and associated answers posted between 2009 and 2014 in the diabetes category of Yahoo! Answers. We analyzed the datasets using a widely adopted biomedical text processing framework Apache cTAKES and its extension YTEX. First, we applied the named entity recognition (NER) method implemented in YTEX to identify UMLS concepts in the datasets. We then analyzed the coverage and the popularity of concepts in the UMLS source vocabularies across the 2 datasets (ie, blogs and social Q&A). Further, we conducted a concept-level comparative coverage analysis between SNOMED Clinical Terms (SNOMED CT) and Open-Access Collaborative Consumer Health Vocabulary (OAC CHV)—the top 2 UMLS source vocabularies that have the most coverage on our datasets. We also analyzed the UMLS semantic types that were frequently observed in our datasets. Results We identified 2415 UMLS concepts from blog postings, 6452 UMLS concepts from social Q&A questions, and 10,378 UMLS concepts from the answers. The medical concepts identified in the blogs can be covered by 56 source vocabularies in the UMLS, while those in questions and answers can be covered by 58 source vocabularies. SNOMED CT was the dominant vocabulary in terms of coverage across all the datasets, ranging from 84.9% to 95.9%. It was followed by OAC CHV (between 73.5% and 80.0%) and Metathesaurus Names (MTH) (between 55.7% and 73.5%). All of the social media datasets shared frequent semantic types such as “Amino Acid, Peptide, or Protein,” “Body Part, Organ, or Organ Component,” and “Disease or Syndrome.” Conclusions Although the 3 social media datasets vary greatly in size, they exhibited similar conceptual coverage among UMLS source vocabularies and the identified concepts showed similar semantic type distributions. As such, concepts that are both frequently used by consumers and also found in professional vocabularies such as SNOMED CT can be suggested to OAC CHV to improve its coverage. PMID:27884812

Qumquad: a UML-based approach for remodeling of legacy systems in health care.

PubMed

Garde, Sebastian; Knaup, Petra; Herold, Ralf

2003-07-01

Health care information systems still comprise legacy systems to a certain extent. For reengineering legacy systems a thorough remodeling is inalienable. Current modeling techniques like the Unified Modeling Language (UML) do not offer a systematic and comprehensive process-oriented method for remodeling activities. We developed a systematic method for remodeling legacy systems in health care called Qumquad. Qumquad consists of three major steps: (i) modeling the actual state of the application system, (ii) systematic identification of weak points in this model and (iii) development of a target concept for the reimplementation considering the identified weak points. We applied Qumquad for remodeling a documentation and therapy planning system for pediatric oncology (DOSPO). As a result of our remodeling activities we regained an abstract model of the system, an analysis of the current weak points of DOSPO and possible (partly alternative) solutions to overcome the weak points. Qumquad proved to be very helpful in the reengineering process of DOSPO since we now have at our disposal a comprehensive model for the reimplementation of DOSPO that current users of the system agree on. Qumquad can easily be applied to other reengineering projects in health care.

COHeRE: Cross-Ontology Hierarchical Relation Examination for Ontology Quality Assurance.

PubMed

Cui, Licong

Biomedical ontologies play a vital role in healthcare information management, data integration, and decision support. Ontology quality assurance (OQA) is an indispensable part of the ontology engineering cycle. Most existing OQA methods are based on the knowledge provided within the targeted ontology. This paper proposes a novel cross-ontology analysis method, Cross-Ontology Hierarchical Relation Examination (COHeRE), to detect inconsistencies and possible errors in hierarchical relations across multiple ontologies. COHeRE leverages the Unified Medical Language System (UMLS) knowledge source and the MapReduce cloud computing technique for systematic, large-scale ontology quality assurance work. COHeRE consists of three main steps with the UMLS concepts and relations as the input. First, the relations claimed in source vocabularies are filtered and aggregated for each pair of concepts. Second, inconsistent relations are detected if a concept pair is related by different types of relations in different source vocabularies. Finally, the uncovered inconsistent relations are voted according to their number of occurrences across different source vocabularies. The voting result together with the inconsistent relations serve as the output of COHeRE for possible ontological change. The highest votes provide initial suggestion on how such inconsistencies might be fixed. In UMLS, 138,987 concept pairs were found to have inconsistent relationships across multiple source vocabularies. 40 inconsistent concept pairs involving hierarchical relationships were randomly selected and manually reviewed by a human expert. 95.8% of the inconsistent relations involved in these concept pairs indeed exist in their source vocabularies rather than being introduced by mistake in the UMLS integration process. 73.7% of the concept pairs with suggested relationship were agreed by the human expert. The effectiveness of COHeRE indicates that UMLS provides a promising environment to enhance qualities of biomedical ontologies by performing cross-ontology examination.

Auditing the multiply-related concepts within the UMLS.

PubMed

Mougin, Fleur; Grabar, Natalia

2014-10-01

This work focuses on multiply-related Unified Medical Language System (UMLS) concepts, that is, concepts associated through multiple relations. The relations involved in such situations are audited to determine whether they are provided by source vocabularies or result from the integration of these vocabularies within the UMLS. We study the compatibility of the multiple relations which associate the concepts under investigation and try to explain the reason why they co-occur. Towards this end, we analyze the relations both at the concept and term levels. In addition, we randomly select 288 concepts associated through contradictory relations and manually analyze them. At the UMLS scale, only 0.7% of combinations of relations are contradictory, while homogeneous combinations are observed in one-third of situations. At the scale of source vocabularies, one-third do not contain more than one relation between the concepts under investigation. Among the remaining source vocabularies, seven of them mainly present multiple non-homogeneous relations between terms. Analysis at the term level also shows that only in a quarter of cases are the source vocabularies responsible for the presence of multiply-related concepts in the UMLS. These results are available at: http://www.isped.u-bordeaux2.fr/ArticleJAMIA/results_multiply_related_concepts.aspx. Manual analysis was useful to explain the conceptualization difference in relations between terms across source vocabularies. The exploitation of source relations was helpful for understanding why some source vocabularies describe multiple relations between a given pair of terms. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Concepts and Synonymy in the UMLS Metathesaurus

PubMed Central

Merrill, Gary H.

2009-01-01

This paper advances a detailed exploration of the complex relationships among terms, concepts, and syn­onymy in the UMLS (Unified Medical Language System) Metathesaurus, and proposes the study and under­standing of the Metathesaurus from a model-theoretic perspective. Initial sections provide the background and motivation for such an approach, and a careful informal treatment of these notions is offered as a con­text and basis for the formal analysis. What emerges from this is a set of puzzles and confusions in the Metathesaurus and its literature pertaining to synonymy and its relation to terms and concepts. A model theory for a segment of the Metathesaurus is then constructed, and its adequacy relative to the informal treatment is demonstrated. Finally, it is shown how this approach clarifies and addresses the puzzles educed from the informal discussion, and how the model-theoretic perspective may be employed to eval­uate some fundamental criticisms of the Metathesaurus. For users of the UMLS, two significant results of this analysis are a rigorous clarification of the different senses of synonymy that appear in treatments of the Metathesaurus and an illustration of the dangers in computing inferences involving ambiguous terms. PMID:19838995

Aspect-Oriented Subprogram Synthesizes UML Sequence Diagrams

NASA Technical Reports Server (NTRS)

Barry, Matthew R.; Osborne, Richard N.

2006-01-01

The Rational Sequence computer program described elsewhere includes a subprogram that utilizes the capability for aspect-oriented programming when that capability is present. This subprogram is denoted the Rational Sequence (AspectJ) component because it uses AspectJ, which is an extension of the Java programming language that introduces aspect-oriented programming techniques into the language

Towards a portal and search engine to facilitate academic and research collaboration in engineering and education

NASA Astrophysics Data System (ADS)

Bonilla Villarreal, Isaura Nathaly

While international academic and research collaborations are of great importance at this time, it is not easy to find researchers in the engineering field that publish in languages other than English. Because of this disconnect, there exists a need for a portal to find Who's Who in Engineering Education in the Americas. The objective of this thesis is to built an object-oriented architecture for this proposed portal. The Unified Modeling Language (UML) model developed in this thesis incorporates the basic structure of a social network for academic purposes. Reverse engineering of three social networks portals yielded important aspects of their structures that have been incorporated in the proposed UML model. Furthermore, the present work includes a pattern for academic social networks..

Rule-based support system for multiple UMLS semantic type assignments

PubMed Central

Geller, James; He, Zhe; Perl, Yehoshua; Morrey, C. Paul; Xu, Julia

2012-01-01

Background When new concepts are inserted into the UMLS, they are assigned one or several semantic types from the UMLS Semantic Network by the UMLS editors. However, not every combination of semantic types is permissible. It was observed that many concepts with rare combinations of semantic types have erroneous semantic type assignments or prohibited combinations of semantic types. The correction of such errors is resource-intensive. Objective We design a computational system to inform UMLS editors as to whether a specific combination of two, three, four, or five semantic types is permissible or prohibited or questionable. Methods We identify a set of inclusion and exclusion instructions in the UMLS Semantic Network documentation and derive corresponding rule-categories as well as rule-categories from the UMLS concept content. We then design an algorithm adviseEditor based on these rule-categories. The algorithm specifies rules for an editor how to proceed when considering a tuple (pair, triple, quadruple, quintuple) of semantic types to be assigned to a concept. Results Eight rule-categories were identified. A Web-based system was developed to implement the adviseEditor algorithm, which returns for an input combination of semantic types whether it is permitted, prohibited or (in a few cases) requires more research. The numbers of semantic type pairs assigned to each rule-category are reported. Interesting examples for each rule-category are illustrated. Cases of semantic type assignments that contradict rules are listed, including recently introduced ones. Conclusion The adviseEditor system implements explicit and implicit knowledge available in the UMLS in a system that informs UMLS editors about the permissibility of a desired combination of semantic types. Using adviseEditor might help accelerate the work of the UMLS editors and prevent erroneous semantic type assignments. PMID:23041716

Towards linking patients and clinical information: detecting UMLS concepts in e-mail.

PubMed

Brennan, Patricia Flatley; Aronson, Alan R

2003-01-01

The purpose of this project is to explore the feasibility of detecting terms within the electronic messages of patients that could be used to effectively search electronic knowledge resources and bring health information resources into the hands of patients. Our team is exploring the application of the natural language processing (NLP) tools built within the Lister Hill Center at the National Library of Medicine (NLM) to the challenge of detecting relevant concepts from the Unified Medical Language System (UMLS) within the free text of lay people's electronic messages (e-mail). We obtained a sample of electronic messages sent by patients participating in a randomized field evaluation of an internet-based home care support service to the project nurse, and we subjected elements of these messages to a series of analyses using several vocabularies from the UMLS Metathesaurus and the selected NLP tools. The nursing vocabularies provide an excellent starting point for this exercise because their domain encompasses patient's responses to health challenges. In successive runs we augmented six nursing vocabularies (NANDA Nursing Diagnosis, Nursing Interventions Classification, Nursing Outcomes Classification, Home Health Classification, Omaha System, and the Patient Care Data Set) with selected sets of clinical terminologies (International Classification of Primary Care; International Classification of Primary Care- American English; Micromedex DRUGDEX; National Drug Data File; Thesaurus of Psychological Terms; WHO Adverse Drug Reaction Terminology) and then additionally with either Medical Subject Heading (MeSH) or SNOMED International terms. The best performance was obtained when the nursing vocabularies were complemented with selected clinical terminologies. These findings have implications not only for facilitating lay people's access to electronic knowledge resources but may also be of assistance in developing new tools to aid in linking free text (e.g., clinical notes) to lexically complex knowledge resources such as those emerging from the Human Genome Project.

An investigation of difficulties experienced by students developing unified modelling language (UML) class and sequence diagrams

NASA Astrophysics Data System (ADS)

Sien, Ven Yu

2011-12-01

Object-oriented analysis and design (OOAD) is not an easy subject to learn. There are many challenges confronting students when studying OOAD. Students have particular difficulty abstracting real-world problems within the context of OOAD. They are unable to effectively build object-oriented (OO) models from the problem domain because they essentially do not know "what" to model. This article investigates the difficulties and misconceptions undergraduate students have with analysing systems using unified modelling language analysis class and sequence diagrams. These models were chosen because they represent important static and dynamic aspects of the software system under development. The results of this study will help students produce effective OO models, and facilitate software engineering lecturers design learning materials and approaches for introductory OOAD courses.

UML as a cell and biochemistry modeling language.

PubMed

Webb, Ken; White, Tony

2005-06-01

The systems biology community is building increasingly complex models and simulations of cells and other biological entities, and are beginning to look at alternatives to traditional representations such as those provided by ordinary differential equations (ODE). The lessons learned over the years by the software development community in designing and building increasingly complex telecommunication and other commercial real-time reactive systems, can be advantageously applied to the problems of modeling in the biology domain. Making use of the object-oriented (OO) paradigm, the unified modeling language (UML) and Real-Time Object-Oriented Modeling (ROOM) visual formalisms, and the Rational Rose RealTime (RRT) visual modeling tool, we describe a multi-step process we have used to construct top-down models of cells and cell aggregates. The simple example model described in this paper includes membranes with lipid bilayers, multiple compartments including a variable number of mitochondria, substrate molecules, enzymes with reaction rules, and metabolic pathways. We demonstrate the relevance of abstraction, reuse, objects, classes, component and inheritance hierarchies, multiplicity, visual modeling, and other current software development best practices. We show how it is possible to start with a direct diagrammatic representation of a biological structure such as a cell, using terminology familiar to biologists, and by following a process of gradually adding more and more detail, arrive at a system with structure and behavior of arbitrary complexity that can run and be observed on a computer. We discuss our CellAK (Cell Assembly Kit) approach in terms of features found in SBML, CellML, E-CELL, Gepasi, Jarnac, StochSim, Virtual Cell, and membrane computing systems.

Auditing Associative Relations across Two Knowledge Sources

PubMed Central

Vizenor, Lowell T.; Bodenreider, Olivier; McCray, Alexa T.

2009-01-01

Objectives This paper proposes a novel semantic method for auditing associative relations in biomedical terminologies. We tested our methodology on two Unified Medical Language System (UMLS) knowledge sources. Methods We use the UMLS semantic groups as high-level representations of the domain and range of relationships in the Metathesaurus and in the Semantic Network. A mapping created between Metathesaurus relationships and Semantic Network relationships forms the basis for comparing the signatures of a given Metathesaurus relationship to the signatures of the semantic relationship to which it is mapped. The consistency of Metathesaurus relations is studied for each relationship. Results Of the 177 associative relationships in the Metathesaurus, 84 (48%) exhibit a high degree of consistency with the corresponding Semantic Network relationships. Overall, 63% of the 1.8M associative relations in the Metathesaurus are consistent with relations in the Semantic Network. Conclusion The semantics of associative relationships in biomedical terminologies should be defined explicitly by their developers. The Semantic Network would benefit from being extended with new relationships and with new relations for some existing relationships. The UMLS editing environment could take advantage of the correspondence established between relationships in the Metathesaurus and the Semantic Network. Finally, the auditing method also yielded useful information for refining the mapping of associative relationships between the two sources. PMID:19475724

Dynamic Data-Driven Prognostics and Condition Monitoring of On-board Electronics

DTIC Science & Technology

2012-08-27

of functionality and accessibility; it is an open language unlike Java or Visual meaning that it is also free. It is also one of the most popular...and C# are able to run without the use of a virtual machine like Java . 4.2.1.5 Implementation For building of an OSA-CBM system, the primer...documentation [7] recommends the following steps: 1. Choose a middleware technology (DCOM, CORBA, Web Services, Java RMI, etc.). 2. Transform OSA-CBM UML

Sharing behavioral data through a grid infrastructure using data standards

PubMed Central

Min, Hua; Ohira, Riki; Collins, Michael A; Bondy, Jessica; Avis, Nancy E; Tchuvatkina, Olga; Courtney, Paul K; Moser, Richard P; Shaikh, Abdul R; Hesse, Bradford W; Cooper, Mary; Reeves, Dianne; Lanese, Bob; Helba, Cindy; Miller, Suzanne M; Ross, Eric A

2014-01-01

Objective In an effort to standardize behavioral measures and their data representation, the present study develops a methodology for incorporating measures found in the National Cancer Institute's (NCI) grid-enabled measures (GEM) portal, a repository for behavioral and social measures, into the cancer data standards registry and repository (caDSR). Methods The methodology consists of four parts for curating GEM measures into the caDSR: (1) develop unified modeling language (UML) models for behavioral measures; (2) create common data elements (CDE) for UML components; (3) bind CDE with concepts from the NCI thesaurus; and (4) register CDE in the caDSR. Results UML models have been developed for four GEM measures, which have been registered in the caDSR as CDE. New behavioral concepts related to these measures have been created and incorporated into the NCI thesaurus. Best practices for representing measures using UML models have been utilized in the practice (eg, caDSR). One dataset based on a GEM-curated measure is available for use by other systems and users connected to the grid. Conclusions Behavioral and population science data can be standardized by using and extending current standards. A new branch of CDE for behavioral science was developed for the caDSR. It expands the caDSR domain coverage beyond the clinical and biological areas. In addition, missing terms and concepts specific to the behavioral measures addressed in this paper were added to the NCI thesaurus. A methodology was developed and refined for curation of behavioral and population science data. PMID:24076749

A Framework to Manage Information Models

NASA Astrophysics Data System (ADS)

Hughes, J. S.; King, T.; Crichton, D.; Walker, R.; Roberts, A.; Thieman, J.

2008-05-01

The Information Model is the foundation on which an Information System is built. It defines the entities to be processed, their attributes, and the relationships that add meaning. The development and subsequent management of the Information Model is the single most significant factor for the development of a successful information system. A framework of tools has been developed that supports the management of an information model with the rigor typically afforded to software development. This framework provides for evolutionary and collaborative development independent of system implementation choices. Once captured, the modeling information can be exported to common languages for the generation of documentation, application databases, and software code that supports both traditional and semantic web applications. This framework is being successfully used for several science information modeling projects including those for the Planetary Data System (PDS), the International Planetary Data Alliance (IPDA), the National Cancer Institute's Early Detection Research Network (EDRN), and several Consultative Committee for Space Data Systems (CCSDS) projects. The objective of the Space Physics Archive Search and Exchange (SPASE) program is to promote collaboration and coordination of archiving activity for the Space Plasma Physics community and ensure the compatibility of the architectures used for a global distributed system and the individual data centers. Over the past several years, the SPASE data model working group has made great progress in developing the SPASE Data Model and supporting artifacts including a data dictionary, XML Schema, and two ontologies. The authors have captured the SPASE Information Model in this framework. This allows the generation of documentation that presents the SPASE Information Model in object-oriented notation including UML class diagrams and class hierarchies. The modeling information can also be exported to semantic web languages such as OWL and RDF and written to XML Metadata Interchange (XMI) files for import into UML tools.

Building a genome database using an object-oriented approach.

PubMed

Barbasiewicz, Anna; Liu, Lin; Lang, B Franz; Burger, Gertraud

2002-01-01

GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

An Infrastructure for UML-Based Code Generation Tools

NASA Astrophysics Data System (ADS)

Wehrmeister, Marco A.; Freitas, Edison P.; Pereira, Carlos E.

The use of Model-Driven Engineering (MDE) techniques in the domain of distributed embedded real-time systems are gain importance in order to cope with the increasing design complexity of such systems. This paper discusses an infrastructure created to build GenERTiCA, a flexible tool that supports a MDE approach, which uses aspect-oriented concepts to handle non-functional requirements from embedded and real-time systems domain. GenERTiCA generates source code from UML models, and also performs weaving of aspects, which have been specified within the UML model. Additionally, this paper discusses the Distributed Embedded Real-Time Compact Specification (DERCS), a PIM created to support UML-based code generation tools. Some heuristics to transform UML models into DERCS, which have been implemented in GenERTiCA, are also discussed.

The use of geospatial web services for exchanging utilities data

NASA Astrophysics Data System (ADS)

Kuczyńska, Joanna

2013-04-01

Geographic information technologies and related geo-information systems currently play an important role in the management of public administration in Poland. One of these tasks is to maintain and update Geodetic Evidence of Public Utilities (GESUT), part of the National Geodetic and Cartographic Resource, which contains an important for many institutions information of technical infrastructure. It requires an active exchange of data between the Geodesy and Cartography Documentation Centers and institutions, which administrate transmission lines. The administrator of public utilities, is legally obliged to provide information about utilities to GESUT. The aim of the research work was to develop a universal data exchange methodology, which can be implemented on a variety of hardware and software platforms. This methodology use Unified Modeling Language (UML), eXtensible Markup Language (XML), and Geography Markup Language (GML). The proposed methodology is based on the two different strategies: Model Driven Architecture (MDA) and Service Oriented Architecture (SOA). Used solutions are consistent with the INSPIRE Directive and ISO 19100 series standards for geographic information. On the basis of analysis of the input data structures, conceptual models were built for both databases. Models were written in the universal modeling language: UML. Combined model that defines a common data structure was also built. This model was transformed into developed for the exchange of geographic information GML standard. The structure of the document describing the data that may be exchanged is defined in the .xsd file. Network services were selected and implemented in the system designed for data exchange based on open source tools. Methodology was implemented and tested. Data in the agreed data structure and metadata were set up on the server. Data access was provided by geospatial network services: data searching possibilities by Catalog Service for the Web (CSW), data collection by Web Feature Service (WFS). WFS provides also operation for modification data, for example to update them by utility administrator. The proposed solution significantly increases the efficiency of data exchange and facilitates maintenance the National Geodetic and Cartographic Resource.

Applying Real-Time UML: Real-World Experiences

NASA Astrophysics Data System (ADS)

Cooling, Niall; Pachschwoell, Stefan

2004-06-01

This paper presents Austrian Aerospace's experiences of applying UML for the design of an embedded real-time avionics system based on Feabhas' "Pragma Process". It describes the complete lifecycle from adoption of UML, through training, CASE-tool selection, system analysis, and software design and development of the project itself. It concludes by reflecting on the experiences obtained and some lessons learnt.

Sharing behavioral data through a grid infrastructure using data standards.

PubMed

Min, Hua; Ohira, Riki; Collins, Michael A; Bondy, Jessica; Avis, Nancy E; Tchuvatkina, Olga; Courtney, Paul K; Moser, Richard P; Shaikh, Abdul R; Hesse, Bradford W; Cooper, Mary; Reeves, Dianne; Lanese, Bob; Helba, Cindy; Miller, Suzanne M; Ross, Eric A

2014-01-01

In an effort to standardize behavioral measures and their data representation, the present study develops a methodology for incorporating measures found in the National Cancer Institute's (NCI) grid-enabled measures (GEM) portal, a repository for behavioral and social measures, into the cancer data standards registry and repository (caDSR). The methodology consists of four parts for curating GEM measures into the caDSR: (1) develop unified modeling language (UML) models for behavioral measures; (2) create common data elements (CDE) for UML components; (3) bind CDE with concepts from the NCI thesaurus; and (4) register CDE in the caDSR. UML models have been developed for four GEM measures, which have been registered in the caDSR as CDE. New behavioral concepts related to these measures have been created and incorporated into the NCI thesaurus. Best practices for representing measures using UML models have been utilized in the practice (eg, caDSR). One dataset based on a GEM-curated measure is available for use by other systems and users connected to the grid. Behavioral and population science data can be standardized by using and extending current standards. A new branch of CDE for behavioral science was developed for the caDSR. It expands the caDSR domain coverage beyond the clinical and biological areas. In addition, missing terms and concepts specific to the behavioral measures addressed in this paper were added to the NCI thesaurus. A methodology was developed and refined for curation of behavioral and population science data. Published by the BMJ Publishing Group Limited. For permission to use (where not already granted under a licence) please go to http://group.bmj.com/group/rights-licensing/permissions.

Development of the Plate Tectonics and Seismology markup languages with XML

NASA Astrophysics Data System (ADS)

Babaie, H.; Babaei, A.

2003-04-01

The Extensible Markup Language (XML) and its specifications such as the XSD Schema, allow geologists to design discipline-specific vocabularies such as Seismology Markup Language (SeismML) or Plate Tectonics Markup Language (TectML). These languages make it possible to store and interchange structured geological information over the Web. Development of a geological markup language requires mapping geological concepts, such as "Earthquake" or "Plate" into a UML object model, applying a modeling and design environment. We have selected four inter-related geological concepts: earthquake, fault, plate, and orogeny, and developed four XML Schema Definitions (XSD), that define the relationships, cardinalities, hierarchies, and semantics of these concepts. In such a geological concept model, the UML object "Earthquake" is related to one or more "Wave" objects, each arriving to a seismic station at a specific "DateTime", and relating to a specific "Epicenter" object that lies at a unique "Location". The "Earthquake" object occurs along a "Segment" of a "Fault" object, which is related to a specific "Plate" object. The "Fault" has its own associations with such things as "Bend", "Step", and "Segment", and could be of any kind (e.g., "Thrust", "Transform'). The "Plate" is related to many other objects such as "MOR", "Subduction", and "Forearc", and is associated with an "Orogeny" object that relates to "Deformation" and "Strain" and several other objects. These UML objects were mapped into XML Metadata Interchange (XMI) formats, which were then converted into four XSD Schemas. The schemas were used to create and validate the XML instance documents, and to create a relational database hosting the plate tectonics and seismological data in the Microsoft Access format. The SeismML and TectML allow seismologists and structural geologists, among others, to submit and retrieve structured geological data on the Internet. A seismologist, for example, can submit peer-reviewed and reliable data about a specific earthquake to a Java Server Page on our web site hosting the XML application. Other geologists can readily retrieve the submitted data, saved in files or special tables of the designed database, through a search engine designed with J2EE (JSP, servlet, Java Bean) and XML specifications such as XPath, XPointer, and XSLT. When extended to include all the important concepts of seismology and plate tectonics, the two markup languages will make global interchange of geological data a reality.

Phase II evaluation of clinical coding schemes: completeness, taxonomy, mapping, definitions, and clarity. CPRI Work Group on Codes and Structures.

PubMed

Campbell, J R; Carpenter, P; Sneiderman, C; Cohn, S; Chute, C G; Warren, J

1997-01-01

To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for "parent" and "child" codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p < .00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56, UMLS 3.17; READ 2.14, *p < .005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p < .00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p < .004) associated with a loss of clarity. No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. Is suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record.

Phase II Evaluation of Clinical Coding Schemes

PubMed Central

Campbell, James R.; Carpenter, Paul; Sneiderman, Charles; Cohn, Simon; Chute, Christopher G.; Warren, Judith

1997-01-01

Abstract Objective: To compare three potential sources of controlled clinical terminology (READ codes version 3.1, SNOMED International, and Unified Medical Language System (UMLS) version 1.6) relative to attributes of completeness, clinical taxonomy, administrative mapping, term definitions and clarity (duplicate coding rate). Methods: The authors assembled 1929 source concept records from a variety of clinical information taken from four medical centers across the United States. The source data included medical as well as ample nursing terminology. The source records were coded in each scheme by an investigator and checked by the coding scheme owner. The codings were then scored by an independent panel of clinicians for acceptability. Codes were checked for definitions provided with the scheme. Codes for a random sample of source records were analyzed by an investigator for “parent” and “child” codes within the scheme. Parent and child pairs were scored by an independent panel of medical informatics specialists for clinical acceptability. Administrative and billing code mapping from the published scheme were reviewed for all coded records and analyzed by independent reviewers for accuracy. The investigator for each scheme exhaustively searched a sample of coded records for duplications. Results: SNOMED was judged to be significantly more complete in coding the source material than the other schemes (SNOMED* 70%; READ 57%; UMLS 50%; *p <.00001). SNOMED also had a richer clinical taxonomy judged by the number of acceptable first-degree relatives per coded concept (SNOMED* 4.56; UMLS 3.17; READ 2.14, *p <.005). Only the UMLS provided any definitions; these were found for 49% of records which had a coding assignment. READ and UMLS had better administrative mappings (composite score: READ* 40.6%; UMLS* 36.1%; SNOMED 20.7%, *p <. 00001), and SNOMED had substantially more duplications of coding assignments (duplication rate: READ 0%; UMLS 4.2%; SNOMED* 13.9%, *p <. 004) associated with a loss of clarity. Conclusion: No major terminology source can lay claim to being the ideal resource for a computer-based patient record. However, based upon this analysis of releases for April 1995, SNOMED International is considerably more complete, has a compositional nature and a richer taxonomy. It suffers from less clarity, resulting from a lack of syntax and evolutionary changes in its coding scheme. READ has greater clarity and better mapping to administrative schemes (ICD-10 and OPCS-4), is rapidly changing and is less complete. UMLS is a rich lexical resource, with mappings to many source vocabularies. It provides definitions for many of its terms. However, due to the varying granularities and purposes of its source schemes, it has limitations for representation of clinical concepts within a computer-based patient record. PMID:9147343

Load shifting with the use of home energy management system implemented in FPGA

NASA Astrophysics Data System (ADS)

Bazydło, Grzegorz; Wermiński, Szymon

2017-08-01

The increases for power demand in the Electrical Power System (EPS) causes a significant increase of power in daily load curve and transmission line overload. The large variability in energy consumption in EPS combined with unpredictable weather events can lead to a situation in which to save the stability of the EPS, the power limits must be introduced or even industrial customers in a given area have to be disconnected, which causes financial losses. Nowadays, a Transmission System Operator is looking for additional solutions to reduce peak power, because existing approaches (mainly building new intervention power unit or tariff programs) are not satisfactory due to the high cost of services in combination with insufficient power reduction effect. The paper presents an approach to load shifting with the use of home Energy Management System (EMS) installed at small end-users. The home energy management algorithm, executed by EMS controller, is modeled using Unified Modeling Language (UML). Then, the UML model is translated into Verilog description, and is finally implemented in the Field Programmable Gate Arrays. The advantages of the proposed approach are the relatively low cost of reduction service, small loss of end-users' comfort, and the convenient maintenance of EMS. A practical example illustrating the proposed approach and calculation of potential gains from its implementation are also presented.

Requirements Management for Net-Centric Enterprises. Phase 1

DTIC Science & Technology

2011-04-28

These include Business Process Modeling Notation ( BPMN ) (White and Miers 2008) and Business Process Execution Language (BPEL) (Sarang, Juric et al...UML: Modeling, Analysis, Design, Morgan Kaufmann/The OMG Press. White, S. A. and D. Miers (2008). BPMN Modeling and Reference Guide, Future

A Collaborative Support Approach on UML Sequence Diagrams for Aspect-Oriented Software

NASA Astrophysics Data System (ADS)

de Almeida Naufal, Rafael; Silveira, Fábio F.; Guerra, Eduardo M.

AOP and its broader application on software projects brings the importance to provide the separation between aspects and OO components at design time, to leverage the understanding of AO systems, promote aspects' reuse and obtain the benefits of AO modularization. Since the UML is a standard for modeling OO systems, it can be applied to model the decoupling between aspects and OO components. The application of UML to this area is the subject of constant study and is the focus of this paper. In this paper it is presented an extension based on the default UML meta-model, named MIMECORA-DS, to show object-object, object-aspect and aspect-aspect interactions applying the UML's sequence diagram. This research also presents the application of MIMECORA-DS in a case example, to assess its applicability.

UML and Model Checking

NASA Technical Reports Server (NTRS)

Schneider, F.

1999-01-01

UML use cases conceptually identify function points or major requirements that a software system must satisfy. Sequence diagrams expand each use case to show in temporal sequence a more detailed notion of intended system behavior.

An Enriched Unified Medical Language System Semantic Network with a Multiple Subsumption Hierarchy

PubMed Central

Zhang, Li; Perl, Yehoshua; Halper, Michael; Geller, James; Cimino, James J.

2004-01-01

Objective: The Unified Medical Language System's (UMLS's) Semantic Network's (SN's) two-tree structure is restrictive because it does not allow a semantic type to be a specialization of several other semantic types. In this article, the SN is expanded into a multiple subsumption structure with a directed acyclic graph (DAG) IS-A hierarchy, allowing a semantic type to have multiple parents. New viable IS-A links are added as warranted. Design: Two methodologies are presented to identify and add new viable IS-A links. The first methodology is based on imposing the characteristic of connectivity on a previously presented partition of the SN. Four transformations are provided to find viable IS-A links in the process of converting the partition's disconnected groups into connected ones. The second methodology identifies new IS-A links through a string matching process involving names and definitions of various semantic types in the SN. A domain expert is needed to review all the results to determine the validity of the new IS-A links. Results: Nineteen new IS-A links are added to the SN, and four new semantic types are also created to support the multiple subsumption framework. The resulting network, called the Enriched Semantic Network (ESN), exhibits a DAG-structured hierarchy. A partition of the ESN containing 19 connected groups is also derived. Conclusion: The ESN is an expanded abstraction of the UMLS compared with the original SN. Its multiple subsumption hierarchy can accommodate semantic types with multiple parents. Its representation thus provides direct access to a broader range of subsumption knowledge. PMID:14764611

Modeling stroke rehabilitation processes using the Unified Modeling Language (UML).

PubMed

Ferrante, Simona; Bonacina, Stefano; Pinciroli, Francesco

2013-10-01

In organising and providing rehabilitation procedures for stroke patients, the usual need for many refinements makes it inappropriate to attempt rigid standardisation, but greater detail is required concerning workflow. The aim of this study was to build a model of the post-stroke rehabilitation process. The model, implemented in the Unified Modeling Language, was grounded on international guidelines and refined following the clinical pathway adopted at local level by a specialized rehabilitation centre. The model describes the organisation of the rehabilitation delivery and it facilitates the monitoring of recovery during the process. Indeed, a system software was developed and tested to support clinicians in the digital administration of clinical scales. The model flexibility assures easy updating after process evolution. Copyright © 2013 Elsevier Ltd. All rights reserved.

An object-oriented approach for harmonization of multimedia markup languages

NASA Astrophysics Data System (ADS)

Chen, Yih-Feng; Kuo, May-Chen; Sun, Xiaoming; Kuo, C.-C. Jay

2003-12-01

An object-oriented methodology is proposed to harmonize several different markup languages in this research. First, we adopt the Unified Modelling Language (UML) as the data model to formalize the concept and the process of the harmonization process between the eXtensible Markup Language (XML) applications. Then, we design the Harmonization eXtensible Markup Language (HXML) based on the data model and formalize the transformation between the Document Type Definitions (DTDs) of the original XML applications and HXML. The transformation between instances is also discussed. We use the harmonization of SMIL and X3D as an example to demonstrate the proposed methodology. This methodology can be generalized to various application domains.

Translation from UML to Markov Model: A Performance Modeling Framework

NASA Astrophysics Data System (ADS)

Khan, Razib Hayat; Heegaard, Poul E.

Performance engineering focuses on the quantitative investigation of the behavior of a system during the early phase of the system development life cycle. Bearing this on mind, we delineate a performance modeling framework of the application for communication system that proposes a translation process from high level UML notation to Continuous Time Markov Chain model (CTMC) and solves the model for relevant performance metrics. The framework utilizes UML collaborations, activity diagrams and deployment diagrams to be used for generating performance model for a communication system. The system dynamics will be captured by UML collaboration and activity diagram as reusable specification building blocks, while deployment diagram highlights the components of the system. The collaboration and activity show how reusable building blocks in the form of collaboration can compose together the service components through input and output pin by highlighting the behavior of the components and later a mapping between collaboration and system component identified by deployment diagram will be delineated. Moreover the UML models are annotated to associate performance related quality of service (QoS) information which is necessary for solving the performance model for relevant performance metrics through our proposed framework. The applicability of our proposed performance modeling framework in performance evaluation is delineated in the context of modeling a communication system.

The Cooperate Assistive Teamwork Environment for Software Description Languages.

PubMed

Groenda, Henning; Seifermann, Stephan; Müller, Karin; Jaworek, Gerhard

2015-01-01

Versatile description languages such as the Unified Modeling Language (UML) are commonly used in software engineering across different application domains in theory and practice. They often use graphical notations and leverage visual memory for expressing complex relations. Those notations are hard to access for people with visual impairment and impede their smooth inclusion in an engineering team. Existing approaches provide textual notations but require manual synchronization between the notations. This paper presents requirements for an accessible and language-aware team work environment as well as our plan for the assistive implementation of Cooperate. An industrial software engineering team consisting of people with and without visual impairment will evaluate the implementation.

Transforming Functional Requirements from UML into BPEL to Efficiently Develop SOA-Based Systems

NASA Astrophysics Data System (ADS)

Vemulapalli, Anisha; Subramanian, Nary

The intended behavior of any system such as services, tasks or functions can be captured by functional requirements of the system. As our dependence on online services has grown steadily, the web applications are being developed employing the SOA. BPEL4WS provides a means for expressing functional requirements of an SOA-based system by providing constructs to capture business goals and objectives for the system. In this paper we propose an approach for transforming user-centered requirements captured using UML into a corresponding BPEL specification, where the business processes are captured by means of use-cases from which UML sequence diagrams and activity diagrams are extracted. Subsequently these UML models are mapped to BPEL specifications that capture the essence of the initial business requirements to develop the SOA-based system by employing CASE tools. A student housing system is used as a case study to illustrate this approach and the system is validated using NetBeans.

UML activity diagram swimlanes in logic controller design

NASA Astrophysics Data System (ADS)

Grobelny, Michał; Grobelna, Iwona

2015-12-01

Logic controller behavior can be specified using various techniques, including UML activity diagrams and control Petri nets. Each technique has its advantages and disadvantages. Application of both specification types in one project allows to take benefits from both of them. Additional elements of UML models make it possible to divide a specification into some parts, considered from other point of view (logic controller, user or system). The paper introduces an idea to use UML activity diagrams with swimlanes to increase the understandability of design models.

A UML approach to process modelling of clinical practice guidelines for enactment.

PubMed

Knape, T; Hederman, L; Wade, V P; Gargan, M; Harris, C; Rahman, Y

2003-01-01

Although clinical practice guidelines (CPGs) have been suggested as a means of encapsulating best practice in evidence-based medical treatment, their usage in clinical environments has been disappointing. Criticisms of guideline representations have been that they are predominantly narrative and are difficult to incorporate into clinical information systems. This paper analyses the use of UML process modelling techniques for guideline representation and proposes the automated generation of executable guidelines using XMI. This hybrid UML-XMI approach provides flexible authoring of guideline decision and control structures whilst integrating appropriate data flow. It also uses an open XMI standard interface to allow the use of authoring tools and process control systems from multiple vendors. The paper first surveys CPG modelling formalisms followed by a brief introduction to process modelling in UMI. Furthermore, the modelling of CPGs in UML is presented leading to a case study of encoding a diabetes mellitus CPG using UML.

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation.

PubMed

Jimeno-Yepes, Antonio J; McInnes, Bridget T; Aronson, Alan R

2011-06-02

Evaluation of Word Sense Disambiguation (WSD) methods in the biomedical domain is difficult because the available resources are either too small or too focused on specific types of entities (e.g. diseases or genes). We present a method that can be used to automatically develop a WSD test collection using the Unified Medical Language System (UMLS) Metathesaurus and the manual MeSH indexing of MEDLINE. We demonstrate the use of this method by developing such a data set, called MSH WSD. In our method, the Metathesaurus is first screened to identify ambiguous terms whose possible senses consist of two or more MeSH headings. We then use each ambiguous term and its corresponding MeSH heading to extract MEDLINE citations where the term and only one of the MeSH headings co-occur. The term found in the MEDLINE citation is automatically assigned the UMLS CUI linked to the MeSH heading. Each instance has been assigned a UMLS Concept Unique Identifier (CUI). We compare the characteristics of the MSH WSD data set to the previously existing NLM WSD data set. The resulting MSH WSD data set consists of 106 ambiguous abbreviations, 88 ambiguous terms and 9 which are a combination of both, for a total of 203 ambiguous entities. For each ambiguous term/abbreviation, the data set contains a maximum of 100 instances per sense obtained from MEDLINE.We evaluated the reliability of the MSH WSD data set using existing knowledge-based methods and compared their performance to that of the results previously obtained by these algorithms on the pre-existing data set, NLM WSD. We show that the knowledge-based methods achieve different results but keep their relative performance except for the Journal Descriptor Indexing (JDI) method, whose performance is below the other methods. The MSH WSD data set allows the evaluation of WSD algorithms in the biomedical domain. Compared to previously existing data sets, MSH WSD contains a larger number of biomedical terms/abbreviations and covers the largest set of UMLS Semantic Types. Furthermore, the MSH WSD data set has been generated automatically reusing already existing annotations and, therefore, can be regenerated from subsequent UMLS versions.

Object-oriented integrated approach for the design of scalable ECG systems.

PubMed

Boskovic, Dusanka; Besic, Ingmar; Avdagic, Zikrija

2009-01-01

The paper presents the implementation of Object-Oriented (OO) integrated approaches to the design of scalable Electro-Cardio-Graph (ECG) Systems. The purpose of this methodology is to preserve real-world structure and relations with the aim to minimize the information loss during the process of modeling, especially for Real-Time (RT) systems. We report on a case study of the design that uses the integration of OO and RT methods and the Unified Modeling Language (UML) standard notation. OO methods identify objects in the real-world domain and use them as fundamental building blocks for the software system. The gained experience based on the strongly defined semantics of the object model is discussed and related problems are analyzed.

A Wittgenstein Approach to the Learning of OO-Modeling

ERIC Educational Resources Information Center

Holmboe, Christian

2004-01-01

The paper uses Ludwig Wittgenstein's theories about the relationship between thought, language, and objects of the world to explore the assumption that OO-thinking resembles natural thinking. The paper imports from research in linguistic philosophy to computer science education research. I show how UML class diagrams (i.e., an artificial…

Modelling and Implementation of Catalogue Cards Using FreeMarker

ERIC Educational Resources Information Center

Radjenovic, Jelen; Milosavljevic, Branko; Surla, Dusan

2009-01-01

Purpose: The purpose of this paper is to report on a study involving the specification (using Unified Modelling Language (UML) 2.0) of information requirements and implementation of the software components for generating catalogue cards. The implementation in a Java environment is developed using the FreeMarker software.…

A New Tool to Facilitate Learning Reading for Early Childhood

ERIC Educational Resources Information Center

Puspitasari, Cita; Subiyanto

2017-01-01

This paper proposes a new android application for early childhood learning reading. The description includes a design, development, and an evaluation experiment of an educational game for learning reading on android. Before developing the game, Unified Modeling Language (UML) diagrams, interfaces, animation, narrative or audio were designed.…

The ALFA (Activity Log Files Aggregation) toolkit: a method for precise observation of the consultation.

PubMed

de Lusignan, Simon; Kumarapeli, Pushpa; Chan, Tom; Pflug, Bernhard; van Vlymen, Jeremy; Jones, Beryl; Freeman, George K

2008-09-08

There is a lack of tools to evaluate and compare Electronic patient record (EPR) systems to inform a rational choice or development agenda. To develop a tool kit to measure the impact of different EPR system features on the consultation. We first developed a specification to overcome the limitations of existing methods. We divided this into work packages: (1) developing a method to display multichannel video of the consultation; (2) code and measure activities, including computer use and verbal interactions; (3) automate the capture of nonverbal interactions; (4) aggregate multiple observations into a single navigable output; and (5) produce an output interpretable by software developers. We piloted this method by filming live consultations (n = 22) by 4 general practitioners (GPs) using different EPR systems. We compared the time taken and variations during coded data entry, prescribing, and blood pressure (BP) recording. We used nonparametric tests to make statistical comparisons. We contrasted methods of BP recording using Unified Modeling Language (UML) sequence diagrams. We found that 4 channels of video were optimal. We identified an existing application for manual coding of video output. We developed in-house tools for capturing use of keyboard and mouse and to time stamp speech. The transcript is then typed within this time stamp. Although we managed to capture body language using pattern recognition software, we were unable to use this data quantitatively. We loaded these observational outputs into our aggregation tool, which allows simultaneous navigation and viewing of multiple files. This also creates a single exportable file in XML format, which we used to develop UML sequence diagrams. In our pilot, the GP using the EMIS LV (Egton Medical Information Systems Limited, Leeds, UK) system took the longest time to code data (mean 11.5 s, 95% CI 8.7-14.2). Nonparametric comparison of EMIS LV with the other systems showed a significant difference, with EMIS PCS (Egton Medical Information Systems Limited, Leeds, UK) (P = .007), iSoft Synergy (iSOFT, Banbury, UK) (P = .014), and INPS Vision (INPS, London, UK) (P = .006) facilitating faster coding. In contrast, prescribing was fastest with EMIS LV (mean 23.7 s, 95% CI 20.5-26.8), but nonparametric comparison showed no statistically significant difference. UML sequence diagrams showed that the simplest BP recording interface was not the easiest to use, as users spent longer navigating or looking up previous blood pressures separately. Complex interfaces with free-text boxes left clinicians unsure of what to add. The ALFA method allows the precise observation of the clinical consultation. It enables rigorous comparison of core elements of EPR systems. Pilot data suggests its capacity to demonstrate differences between systems. Its outputs could provide the evidence base for making more objective choices between systems.

[Modeling the requirements on routine data of general practitioners from the health-care researcher's point of view with the help of unified modeling langauge (UML)].

PubMed

Kersting, M; Hauswaldt, J; Lingner, H

2012-08-01

Health-care research is, besides primary acquired study data, based on data from widely differing secondary sources. In order to link, compare and analyze data sources uniform models and methods are needed. This could be facilitated by a more structured description of requirements, models and methods of health-care research than those currently used. Suitable methods of presentation were sought in an approach to this target and the unified modeling language (UML) identified as a possible alternative. Using different tools 3 UML diagrams were created to represent some individual aspects of a scientific use file (SUF): A use case diagram as well as an activity and a class diagram. In the use case diagram we attempted to represent the general use cases of an SUF based on general practitioners routine data. Secondly a class diagram was constructed to visualize the contents and structure of a SUF. Thirdly an activity diagram was developed to graphically represent the concept of a general practitioner's episode of care. The creation of the UML diagrams was possible without any technical difficulties. Regarding the content the 3 diagrams must still be considered as prototypes. The use case diagram shows possible uses and users of an SUF, e. g. a research worker, industry but also the general practitioner who supplies the data. The class diagram reveals a general data structure that can serve information processes in practice and research. Besides aggregation, possibilities for specialization and generalization are essential elements of the class diagram that can be used meaningfully. The activity diagram for the schematic representation of a general practitioner's episode of care reveals the existence of multiple endpoints of an episode and the possibility to form relationships by means of episodes (diagnosis>therapy). The constructed diagrams are preliminary results and should be refined in future steps. Use case diagrams enable a rapid overview of the meaning and purpose of a system, in this case an SUF. Class diagrams can help at a professional level to describe relationships between entities (classes/objects) more clearly than with the existing methods of representation. Activity diagrams are successors to classic flow charts. They are complemented appropriately by status diagrams. UML is suitable to uniformly and graphically describe a system (here an SUF) from various points of view. In future, validated UML models will help us to present scientific concepts and results in a more structured form than before and to promote the technological use of these concepts in practice. © Georg Thieme Verlag KG Stuttgart · New York.

State-transition diagrams for biologists.

PubMed

Bersini, Hugues; Klatzmann, David; Six, Adrien; Thomas-Vaslin, Véronique

2012-01-01

It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines.

State-Transition Diagrams for Biologists

PubMed Central

Bersini, Hugues; Klatzmann, David; Six, Adrien; Thomas-Vaslin, Véronique

2012-01-01

It is clearly in the tradition of biologists to conceptualize the dynamical evolution of biological systems in terms of state-transitions of biological objects. This paper is mainly concerned with (but obviously not limited too) the immunological branch of biology and shows how the adoption of UML (Unified Modeling Language) state-transition diagrams can ease the modeling, the understanding, the coding, the manipulation or the documentation of population-based immune software model generally defined as a set of ordinary differential equations (ODE), describing the evolution in time of populations of various biological objects. Moreover, that same UML adoption naturally entails a far from negligible representational economy since one graphical item of the diagram might have to be repeated in various places of the mathematical model. First, the main graphical elements of the UML state-transition diagram and how they can be mapped onto a corresponding ODE mathematical model are presented. Then, two already published immune models of thymocyte behavior and time evolution in the thymus, the first one originally conceived as an ODE population-based model whereas the second one as an agent-based one, are refactored and expressed in a state-transition form so as to make them much easier to understand and their respective code easier to access, to modify and run. As an illustrative proof, for any immunologist, it should be possible to understand faithfully enough what the two software models are supposed to reproduce and how they execute with no need to plunge into the Java or Fortran lines. PMID:22844438

Model-Based GUI Testing Using Uppaal at Novo Nordisk

NASA Astrophysics Data System (ADS)

Hjort, Ulrik H.; Illum, Jacob; Larsen, Kim G.; Petersen, Michael A.; Skou, Arne

This paper details a collaboration between Aalborg University and Novo Nordiskin developing an automatic model-based test generation tool for system testing of the graphical user interface of a medical device on an embedded platform. The tool takes as input an UML Statemachine model and generates a test suite satisfying some testing criterion, such as edge or state coverage, and converts the individual test case into a scripting language that can be automatically executed against the target. The tool has significantly reduced the time required for test construction and generation, and reduced the number of test scripts while increasing the coverage.

An Information System Development Method Connecting Business Process Modeling and its Experimental Evaluation

NASA Astrophysics Data System (ADS)

Okawa, Tsutomu; Kaminishi, Tsukasa; Kojima, Yoshiyuki; Hirabayashi, Syuichi; Koizumi, Hisao

Business process modeling (BPM) is gaining attention as a measure of analysis and improvement of the business process. BPM analyses the current business process as an AS-IS model and solves problems to improve the current business and moreover it aims to create a business process, which produces values, as a TO-BE model. However, researches of techniques that connect the business process improvement acquired by BPM to the implementation of the information system seamlessly are rarely reported. If the business model obtained by BPM is converted into UML, and the implementation can be carried out by the technique of UML, we can expect the improvement in efficiency of information system implementation. In this paper, we describe a method of the system development, which converts the process model obtained by BPM into UML and the method is evaluated by modeling a prototype of a parts procurement system. In the evaluation, comparison with the case where the system is implemented by the conventional UML technique without going via BPM is performed.

A Dependable Massive Storage Service for Medical Imaging.

PubMed

Núñez-Gaona, Marco Antonio; Marcelín-Jiménez, Ricardo; Gutiérrez-Martínez, Josefina; Aguirre-Meneses, Heriberto; Gonzalez-Compean, José Luis

2018-05-18

We present the construction of Babel, a distributed storage system that meets stringent requirements on dependability, availability, and scalability. Together with Babel, we developed an application that uses our system to store medical images. Accordingly, we show the feasibility of our proposal to provide an alternative solution for massive scientific storage and describe the software architecture style that manages the DICOM images life cycle, utilizing Babel like a virtual local storage component for a picture archiving and communication system (PACS-Babel Interface). Furthermore, we describe the communication interface in the Unified Modeling Language (UML) and show how it can be extended to manage the hard work associated with data migration processes on PACS in case of updates or disaster recovery.

Enhancement Approachof Object Constraint Language Generation

NASA Astrophysics Data System (ADS)

Salemi, Samin; Selamat, Ali

2018-01-01

OCL is the most prevalent language to document system constraints that are annotated in UML. Writing OCL specifications is not an easy task due to the complexity of the OCL syntax. Therefore, an approach to help and assist developers to write OCL specifications is needed. There are two approaches to do so: First, creating an OCL specifications by a tool called COPACABANA. Second, an MDA-based approach to help developers in writing OCL specification by another tool called NL2OCLviaSBVR that generates OCL specification automatically. This study presents another MDA-based approach called En2OCL, and its objective is twofold. 1- to improve the precison of the existing works. 2- to present a benchmark of these approaches. The benchmark shows that the accuracy of COPACABANA, NL2OCLviaSBVR, and En2OCL are 69.23, 84.64, and 88.40 respectively.

A Pilot Study of Contextual UMLS Indexing to Improve the Precision of Concept-based Representation in XML-structured Clinical Radiology Reports

PubMed Central

Huang, Yang; Lowe, Henry J.; Hersh, William R.

2003-01-01

Objective: Despite the advantages of structured data entry, much of the patient record is still stored as unstructured or semistructured narrative text. The issue of representing clinical document content remains problematic. The authors' prior work using an automated UMLS document indexing system has been encouraging but has been affected by the generally low indexing precision of such systems. In an effort to improve precision, the authors have developed a context-sensitive document indexing model to calculate the optimal subset of UMLS source vocabularies used to index each document section. This pilot study was performed to evaluate the utility of this indexing approach on a set of clinical radiology reports. Design: A set of clinical radiology reports that had been indexed manually using UMLS concept descriptors was indexed automatically by the SAPHIRE indexing engine. Using the data generated by this process the authors developed a system that simulated indexing, at the document section level, of the same document set using many permutations of a subset of the UMLS constituent vocabularies. Measurements: The precision and recall scores generated by simulated indexing for each permutation of two or three UMLS constituent vocabularies were determined. Results: While there was considerable variation in precision and recall values across the different subtypes of radiology reports, the overall effect of this indexing strategy using the best combination of two or three UMLS constituent vocabularies was an improvement in precision without significant impact of recall. Conclusion: In this pilot study a contextual indexing strategy improved overall precision in a set of clinical radiology reports. PMID:12925544

A pilot study of contextual UMLS indexing to improve the precision of concept-based representation in XML-structured clinical radiology reports.

PubMed

Huang, Yang; Lowe, Henry J; Hersh, William R

2003-01-01

Despite the advantages of structured data entry, much of the patient record is still stored as unstructured or semistructured narrative text. The issue of representing clinical document content remains problematic. The authors' prior work using an automated UMLS document indexing system has been encouraging but has been affected by the generally low indexing precision of such systems. In an effort to improve precision, the authors have developed a context-sensitive document indexing model to calculate the optimal subset of UMLS source vocabularies used to index each document section. This pilot study was performed to evaluate the utility of this indexing approach on a set of clinical radiology reports. A set of clinical radiology reports that had been indexed manually using UMLS concept descriptors was indexed automatically by the SAPHIRE indexing engine. Using the data generated by this process the authors developed a system that simulated indexing, at the document section level, of the same document set using many permutations of a subset of the UMLS constituent vocabularies. The precision and recall scores generated by simulated indexing for each permutation of two or three UMLS constituent vocabularies were determined. While there was considerable variation in precision and recall values across the different subtypes of radiology reports, the overall effect of this indexing strategy using the best combination of two or three UMLS constituent vocabularies was an improvement in precision without significant impact of recall. In this pilot study a contextual indexing strategy improved overall precision in a set of clinical radiology reports.

Implementation of Markerless Augmented Reality Technology Based on Android to Introduction Lontara in Marine Society

NASA Astrophysics Data System (ADS)

Jumarlis, Mila; Mirfan, Mirfan

2018-05-01

Local language learning had been leaving by people especially young people had affected technology advances so that involved lack of interest to learn culture especially local language. So required interactive and interest learning media for introduction Lontara. This research aims to design and implement augmented reality on introduction Lontara on mobile device especially android. Application of introduction Lontara based on Android was designed by Vuforia and Unity. Data collection method were observation, interview, and literature review. That data was analysed for being information. The system was designed by Unified Modeling Language (UML). The method used is a marker. The test result found that application of Augmented Reality on introduction Lontara based on Android could improve public interest for introducing local language particularly young people in learning about Lontara because of using technology. Application of introduction of Lontara based on Android used augmented reality occurred sound and how to write Lontara with animation. This application could be running without an internet connection, so that its used more efficient and could maximize from user.

An introduction to the Semantic Web for health sciences librarians.

PubMed

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-04-01

The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. The paper is structured into two main parts. "Semantic Web Technology" provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. "Semantic Web Applications and Research Projects in the Biomedical Field" is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects.

The MP (Materialization Pattern) Model for Representing Math Educational Standards

NASA Astrophysics Data System (ADS)

Choi, Namyoun; Song, Il-Yeol; An, Yuan

Representing natural languages with UML has been an important research issue for various reasons. Little work has been done for modeling imperative mood sentences which are the sentence structure of math educational standard statements. In this paper, we propose the MP (Materialization Pattern) model that captures the semantics of English sentences used in math educational standards. The MP model is based on the Reed-Kellogg sentence diagrams and creates MP schemas with the UML notation. The MP model explicitly represents the semantics of the sentences by extracting math concepts and the cognitive process of math concepts from math educational standard statements, and simplifies modeling. This MP model is also developed to be used for aligning math educational standard statements via schema matching.

[Research on tumor information grid framework].

PubMed

Zhang, Haowei; Qin, Zhu; Liu, Ying; Tan, Jianghao; Cao, Haitao; Chen, Youping; Zhang, Ke; Ding, Yuqing

2013-10-01

In order to realize tumor disease information sharing and unified management, we utilized grid technology to make the data and software resources which distributed in various medical institutions for effective integration so that we could make the heterogeneous resources consistent and interoperable in both semantics and syntax aspects. This article describes the tumor grid framework, the type of the service being packaged in Web Service Description Language (WSDL) and extensible markup language schemas definition (XSD), the client use the serialized document to operate the distributed resources. The service objects could be built by Unified Modeling Language (UML) as middle ware to create application programming interface. All of the grid resources are registered in the index and released in the form of Web Services based on Web Services Resource Framework (WSRF). Using the system we can build a multi-center, large sample and networking tumor disease resource sharing framework to improve the level of development in medical scientific research institutions and the patient's quality of life.

Using a Combination of UML, C2RM, XML, and Metadata Registries to Support Long-Term Development/Engineering

DTIC Science & Technology

2003-01-01

Authenticat’n (XCBF) Authorizat’n (XACML) (SAML) Privacy (P3P) Digital Rights Management (XrML) Content Mngmnt (DASL) (WebDAV) Content Syndicat’n...Registry/ Repository BPSS eCommerce XML/EDI Universal Business Language (UBL) Internet & Computing Human Resources (HR-XML) Semantic KEY XML SPECIFICATIONS

Using ontology-based semantic similarity to facilitate the article screening process for systematic reviews.

PubMed

Ji, Xiaonan; Ritter, Alan; Yen, Po-Yin

2017-05-01

Systematic Reviews (SRs) are utilized to summarize evidence from high quality studies and are considered the preferred source of evidence-based practice (EBP). However, conducting SRs can be time and labor intensive due to the high cost of article screening. In previous studies, we demonstrated utilizing established (lexical) article relationships to facilitate the identification of relevant articles in an efficient and effective manner. Here we propose to enhance article relationships with background semantic knowledge derived from Unified Medical Language System (UMLS) concepts and ontologies. We developed a pipelined semantic concepts representation process to represent articles from an SR into an optimized and enriched semantic space of UMLS concepts. Throughout the process, we leveraged concepts and concept relations encoded in biomedical ontologies (SNOMED-CT and MeSH) within the UMLS framework to prompt concept features of each article. Article relationships (similarities) were established and represented as a semantic article network, which was readily applied to assist with the article screening process. We incorporated the concept of active learning to simulate an interactive article recommendation process, and evaluated the performance on 15 completed SRs. We used work saved over sampling at 95% recall (WSS95) as the performance measure. We compared the WSS95 performance of our ontology-based semantic approach to existing lexical feature approaches and corpus-based semantic approaches, and found that we had better WSS95 in most SRs. We also had the highest average WSS95 of 43.81% and the highest total WSS95 of 657.18%. We demonstrated using ontology-based semantics to facilitate the identification of relevant articles for SRs. Effective concepts and concept relations derived from UMLS ontologies can be utilized to establish article semantic relationships. Our approach provided a promising performance and can easily apply to any SR topics in the biomedical domain with generalizability. Copyright © 2017 Elsevier Inc. All rights reserved.

Resources for comparing the speed and performance of medical autocoders.

PubMed

Berman, Jules J

2004-06-15

Concept indexing is a popular method for characterizing medical text, and is one of the most important early steps in many data mining efforts. Concept indexing differs from simple word or phrase indexing because concepts are typically represented by a nomenclature code that binds a medical concept to all equivalent representations. A concept search on the term renal cell carcinoma would be expected to find occurrences of hypernephroma, and renal carcinoma (concept equivalents). The purpose of this study is to provide freely available resources to compare speed and performance among different autocoders. These tools consist of: 1) a public domain autocoder written in Perl (a free and open source programming language that installs on any operating system); 2) a nomenclature database derived from the unencumbered subset of the publicly available Unified Medical Language System; 3) a large corpus of autocoded output derived from a publicly available medical text. A simple lexical autocoder was written that parses plain-text into a listing of all 1,2,3, and 4-word strings contained in text, assigning a nomenclature code for text strings that match terms in the nomenclature. The nomenclature used is the unencumbered subset of the 2003 Unified Medical Language System (UMLS). The unencumbered subset of UMLS was reduced to exclude homonymous one-word terms and proper names, resulting in a term/code data dictionary containing about a half million medical terms. The Online Mendelian Inheritance in Man (OMIM), a 92+ Megabyte publicly available medical opus, was used as sample medical text for the autocoder. The autocoding Perl script is remarkably short, consisting of just 38 command lines. The 92+ Megabyte OMIM file was completely autocoded in 869 seconds on a 2.4 GHz processor (less than 10 seconds per Megabyte of text). The autocoded output file (9,540,442 bytes) contains 367,963 coded terms from OMIM and is distributed with this manuscript. A public domain Perl script is provided that can parse through plain-text files of any length, matching concepts against an external nomenclature. The script and associated files can be used freely to compare the speed and performance of autocoding software.

Medical subdomain classification of clinical notes using a machine learning-based natural language processing approach.

PubMed

Weng, Wei-Hung; Wagholikar, Kavishwar B; McCray, Alexa T; Szolovits, Peter; Chueh, Henry C

2017-12-01

The medical subdomain of a clinical note, such as cardiology or neurology, is useful content-derived metadata for developing machine learning downstream applications. To classify the medical subdomain of a note accurately, we have constructed a machine learning-based natural language processing (NLP) pipeline and developed medical subdomain classifiers based on the content of the note. We constructed the pipeline using the clinical NLP system, clinical Text Analysis and Knowledge Extraction System (cTAKES), the Unified Medical Language System (UMLS) Metathesaurus, Semantic Network, and learning algorithms to extract features from two datasets - clinical notes from Integrating Data for Analysis, Anonymization, and Sharing (iDASH) data repository (n = 431) and Massachusetts General Hospital (MGH) (n = 91,237), and built medical subdomain classifiers with different combinations of data representation methods and supervised learning algorithms. We evaluated the performance of classifiers and their portability across the two datasets. The convolutional recurrent neural network with neural word embeddings trained-medical subdomain classifier yielded the best performance measurement on iDASH and MGH datasets with area under receiver operating characteristic curve (AUC) of 0.975 and 0.991, and F1 scores of 0.845 and 0.870, respectively. Considering better clinical interpretability, linear support vector machine-trained medical subdomain classifier using hybrid bag-of-words and clinically relevant UMLS concepts as the feature representation, with term frequency-inverse document frequency (tf-idf)-weighting, outperformed other shallow learning classifiers on iDASH and MGH datasets with AUC of 0.957 and 0.964, and F1 scores of 0.932 and 0.934 respectively. We trained classifiers on one dataset, applied to the other dataset and yielded the threshold of F1 score of 0.7 in classifiers for half of the medical subdomains we studied. Our study shows that a supervised learning-based NLP approach is useful to develop medical subdomain classifiers. The deep learning algorithm with distributed word representation yields better performance yet shallow learning algorithms with the word and concept representation achieves comparable performance with better clinical interpretability. Portable classifiers may also be used across datasets from different institutions.

Mapping patient flow in a regional Australian emergency department: a model driven approach.

PubMed

Martin, Mary; Champion, Robert; Kinsman, Leigh; Masman, Kevin

2011-04-01

Unified Modelling Language (UML) models of the patient journey in a regional Australian emergency department (ED) were used to develop an accurate, complete representation of ED processes and drive the collection of comprehensive quantitative and qualitative service delivery and patient treatment data as an evidence base for hospital service planning. The focus was to identify bottle-necks that contribute to over-crowding. Data was collected entirely independently of the routine hospital data collection system. The greatest source of delay in patient flow was the waiting time from a bed request to exit from the ED for hospital admission. It represented 61% of the time that these patients occupied ED cubicles. The physical layout of the triage area was identified as counterproductive to efficient triaging, and the results of investigations were often observed to be available for some time before clinical staff became aware. The use of independent primary data to construct UML models of the patient journey was effective in identifying sources of delay in patient flow, and aspects of ED activity that could be improved. The findings contributed to recent department re-design and informed an initiative to develop a business intelligence system for predicting impending occurrence of access block. Copyright © 2010 Elsevier Ltd. All rights reserved.

Tracing the Rationale Behind UML Model Change Through Argumentation

NASA Astrophysics Data System (ADS)

Jureta, Ivan J.; Faulkner, Stéphane

Neglecting traceability—i.e., the ability to describe and follow the life of a requirement—is known to entail misunderstanding and miscommunication, leading to the engineering of poor quality systems. Following the simple principles that (a) changes to UML model instances ought be justified to the stakeholders, (b) justification should proceed in a structured manner to ensure rigor in discussions, critique, and revisions of model instances, and (c) the concept of argument instantiated in a justification process ought to be well defined and understood, the present paper introduces the UML Traceability through Argumentation Method (UML-TAM) to enable the traceability of design rationale in UML while allowing the appropriateness of model changes to be checked by analysis of the structure of the arguments provided to justify such changes.

A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources.

PubMed

Moon, Sungrim; Pakhomov, Serguei; Liu, Nathan; Ryan, James O; Melton, Genevieve B

2014-01-01

To create a sense inventory of abbreviations and acronyms from clinical texts. The most frequently occurring abbreviations and acronyms from 352,267 dictated clinical notes were used to create a clinical sense inventory. Senses of each abbreviation and acronym were manually annotated from 500 random instances and lexically matched with long forms within the Unified Medical Language System (UMLS V.2011AB), Another Database of Abbreviations in Medline (ADAM), and Stedman's Dictionary, Medical Abbreviations, Acronyms & Symbols, 4th edition (Stedman's). Redundant long forms were merged after they were lexically normalized using Lexical Variant Generation (LVG). The clinical sense inventory was found to have skewed sense distributions, practice-specific senses, and incorrect uses. Of 440 abbreviations and acronyms analyzed in this study, 949 long forms were identified in clinical notes. This set was mapped to 17,359, 5233, and 4879 long forms in UMLS, ADAM, and Stedman's, respectively. After merging long forms, only 2.3% matched across all medical resources. The UMLS, ADAM, and Stedman's covered 5.7%, 8.4%, and 11% of the merged clinical long forms, respectively. The sense inventory of clinical abbreviations and acronyms and anonymized datasets generated from this study are available for public use at http://www.bmhi.umn.edu/ihi/research/nlpie/resources/index.htm ('Sense Inventories', website). Clinical sense inventories of abbreviations and acronyms created using clinical notes and medical dictionary resources demonstrate challenges with term coverage and resource integration. Further work is needed to help with standardizing abbreviations and acronyms in clinical care and biomedicine to facilitate automated processes such as text-mining and information extraction.

An Investigation of Difficulties Experienced by Students Developing Unified Modelling Language (UML) Class and Sequence Diagrams

ERIC Educational Resources Information Center

Sien, Ven Yu

2011-01-01

Object-oriented analysis and design (OOAD) is not an easy subject to learn. There are many challenges confronting students when studying OOAD. Students have particular difficulty abstracting real-world problems within the context of OOAD. They are unable to effectively build object-oriented (OO) models from the problem domain because they…

Exploiting MeSH indexing in MEDLINE to generate a data set for word sense disambiguation

PubMed Central

2011-01-01

Background Evaluation of Word Sense Disambiguation (WSD) methods in the biomedical domain is difficult because the available resources are either too small or too focused on specific types of entities (e.g. diseases or genes). We present a method that can be used to automatically develop a WSD test collection using the Unified Medical Language System (UMLS) Metathesaurus and the manual MeSH indexing of MEDLINE. We demonstrate the use of this method by developing such a data set, called MSH WSD. Methods In our method, the Metathesaurus is first screened to identify ambiguous terms whose possible senses consist of two or more MeSH headings. We then use each ambiguous term and its corresponding MeSH heading to extract MEDLINE citations where the term and only one of the MeSH headings co-occur. The term found in the MEDLINE citation is automatically assigned the UMLS CUI linked to the MeSH heading. Each instance has been assigned a UMLS Concept Unique Identifier (CUI). We compare the characteristics of the MSH WSD data set to the previously existing NLM WSD data set. Results The resulting MSH WSD data set consists of 106 ambiguous abbreviations, 88 ambiguous terms and 9 which are a combination of both, for a total of 203 ambiguous entities. For each ambiguous term/abbreviation, the data set contains a maximum of 100 instances per sense obtained from MEDLINE. We evaluated the reliability of the MSH WSD data set using existing knowledge-based methods and compared their performance to that of the results previously obtained by these algorithms on the pre-existing data set, NLM WSD. We show that the knowledge-based methods achieve different results but keep their relative performance except for the Journal Descriptor Indexing (JDI) method, whose performance is below the other methods. Conclusions The MSH WSD data set allows the evaluation of WSD algorithms in the biomedical domain. Compared to previously existing data sets, MSH WSD contains a larger number of biomedical terms/abbreviations and covers the largest set of UMLS Semantic Types. Furthermore, the MSH WSD data set has been generated automatically reusing already existing annotations and, therefore, can be regenerated from subsequent UMLS versions. PMID:21635749

A comprehensive strategy for designing a Web-based medical curriculum.

PubMed Central

Zucker, J.; Chase, H.; Molholt, P.; Bean, C.; Kahn, R. M.

1996-01-01

In preparing for a full featured online curriculum, it is necessary to develop scaleable strategies for software design that will support the pedagogical goals of the curriculum and which will address the issues of acquisition and updating of materials, of robust content-based linking, and of integration of the online materials into other methods of learning. A complete online curriculum, as distinct from an individual computerized module, must provide dynamic updating of both content and structure and an easy pathway from the professor's notes to the finished online product. At the College of Physicians and Surgeons, we are developing such strategies including a scripted text conversion process that uses the Hypertext Markup Language (HTML) as structural markup rather than as display markup, automated linking by the use of relational databases and the Unified Medical Language System (UMLS), integration of text, images, and multimedia along with interface designs which promote multiple contexts and collaborative study. PMID:8947624

The ALFA (Activity Log Files Aggregation) Toolkit: A Method for Precise Observation of the Consultation

PubMed Central

2008-01-01

Background There is a lack of tools to evaluate and compare Electronic patient record (EPR) systems to inform a rational choice or development agenda. Objective To develop a tool kit to measure the impact of different EPR system features on the consultation. Methods We first developed a specification to overcome the limitations of existing methods. We divided this into work packages: (1) developing a method to display multichannel video of the consultation; (2) code and measure activities, including computer use and verbal interactions; (3) automate the capture of nonverbal interactions; (4) aggregate multiple observations into a single navigable output; and (5) produce an output interpretable by software developers. We piloted this method by filming live consultations (n = 22) by 4 general practitioners (GPs) using different EPR systems. We compared the time taken and variations during coded data entry, prescribing, and blood pressure (BP) recording. We used nonparametric tests to make statistical comparisons. We contrasted methods of BP recording using Unified Modeling Language (UML) sequence diagrams. Results We found that 4 channels of video were optimal. We identified an existing application for manual coding of video output. We developed in-house tools for capturing use of keyboard and mouse and to time stamp speech. The transcript is then typed within this time stamp. Although we managed to capture body language using pattern recognition software, we were unable to use this data quantitatively. We loaded these observational outputs into our aggregation tool, which allows simultaneous navigation and viewing of multiple files. This also creates a single exportable file in XML format, which we used to develop UML sequence diagrams. In our pilot, the GP using the EMIS LV (Egton Medical Information Systems Limited, Leeds, UK) system took the longest time to code data (mean 11.5 s, 95% CI 8.7-14.2). Nonparametric comparison of EMIS LV with the other systems showed a significant difference, with EMIS PCS (Egton Medical Information Systems Limited, Leeds, UK) (P = .007), iSoft Synergy (iSOFT, Banbury, UK) (P = .014), and INPS Vision (INPS, London, UK) (P = .006) facilitating faster coding. In contrast, prescribing was fastest with EMIS LV (mean 23.7 s, 95% CI 20.5-26.8), but nonparametric comparison showed no statistically significant difference. UML sequence diagrams showed that the simplest BP recording interface was not the easiest to use, as users spent longer navigating or looking up previous blood pressures separately. Complex interfaces with free-text boxes left clinicians unsure of what to add. Conclusions The ALFA method allows the precise observation of the clinical consultation. It enables rigorous comparison of core elements of EPR systems. Pilot data suggests its capacity to demonstrate differences between systems. Its outputs could provide the evidence base for making more objective choices between systems. PMID:18812313

Medical Concept Normalization in Social Media Posts with Recurrent Neural Networks.

PubMed

Tutubalina, Elena; Miftahutdinov, Zulfat; Nikolenko, Sergey; Malykh, Valentin

2018-06-12

Text mining of scientific libraries and social media has already proven itself as a reliable tool for drug repurposing and hypothesis generation. The task of mapping a disease mention to a concept in a controlled vocabulary, typically to the standard thesaurus in the Unified Medical Language System (UMLS), is known as medical concept normalization. This task is challenging due to the differences in the use of medical terminology between health care professionals and social media texts coming from the lay public. To bridge this gap, we use sequence learning with recurrent neural networks and semantic representation of one- or multi-word expressions: we develop end-to-end architectures directly tailored to the task, including bidirectional Long Short-Term Memory, Gated Recurrent Units with an attention mechanism, and additional semantic similarity features based on UMLS. Our evaluation against a standard benchmark shows that recurrent neural networks improve results over an effective baseline for classification based on convolutional neural networks. A qualitative examination of mentions discovered in a dataset of user reviews collected from popular online health information platforms as well as a quantitative evaluation both show improvements in the semantic representation of health-related expressions in social media. Copyright © 2018. Published by Elsevier Inc.

Object-oriented Approach to High-level Network Monitoring and Management

NASA Technical Reports Server (NTRS)

Mukkamala, Ravi

2000-01-01

An absolute prerequisite for the management of large investigating methods to build high-level monitoring computer networks is the ability to measure their systems that are built on top of existing monitoring performance. Unless we monitor a system, we cannot tools. Due to the heterogeneous nature of the hope to manage and control its performance. In this underlying systems at NASA Langley Research Center, paper, we describe a network monitoring system that we use an object-oriented approach for the design, we are currently designing and implementing. Keeping, first, we use UML (Unified Modeling Language) to in mind the complexity of the task and the required model users' requirements. Second, we identify the flexibility for future changes, we use an object-oriented existing capabilities of the underlying monitoring design methodology. The system is built using the system. Third, we try to map the former with the latter. APIs offered by the HP OpenView system.

Evaluation of a UMLS Auditing Process of Semantic Type Assignments

PubMed Central

Gu, Huanying; Hripcsak, George; Chen, Yan; Morrey, C. Paul; Elhanan, Gai; Cimino, James J.; Geller, James; Perl, Yehoshua

2007-01-01

The UMLS is a terminological system that integrates many source terminologies. Each concept in the UMLS is assigned one or more semantic types from the Semantic Network, an upper level ontology for biomedicine. Due to the complexity of the UMLS, errors exist in the semantic type assignments. Finding assignment errors may unearth modeling errors. Even with sophisticated tools, discovering assignment errors requires manual review. In this paper we describe the evaluation of an auditing project of UMLS semantic type assignments. We studied the performance of the auditors who reviewed potential errors. We found that four auditors, interacting according to a multi-step protocol, identified a high rate of errors (one or more errors in 81% of concepts studied) and that results were sufficiently reliable (0.67 to 0.70) for the two most common types of errors. However, reliability was low for each individual auditor, suggesting that review of potential errors is resource-intensive. PMID:18693845

Semi-Supervised Learning to Identify UMLS Semantic Relations.

PubMed

Luo, Yuan; Uzuner, Ozlem

2014-01-01

The UMLS Semantic Network is constructed by experts and requires periodic expert review to update. We propose and implement a semi-supervised approach for automatically identifying UMLS semantic relations from narrative text in PubMed. Our method analyzes biomedical narrative text to collect semantic entity pairs, and extracts multiple semantic, syntactic and orthographic features for the collected pairs. We experiment with seeded k-means clustering with various distance metrics. We create and annotate a ground truth corpus according to the top two levels of the UMLS semantic relation hierarchy. We evaluate our system on this corpus and characterize the learning curves of different clustering configuration. Using KL divergence consistently performs the best on the held-out test data. With full seeding, we obtain macro-averaged F-measures above 70% for clustering the top level UMLS relations (2-way), and above 50% for clustering the second level relations (7-way).

An introduction to the Semantic Web for health sciences librarians*

PubMed Central

Robu, Ioana; Robu, Valentin; Thirion, Benoit

2006-01-01

Objectives: The paper (1) introduces health sciences librarians to the main concepts and principles of the Semantic Web (SW) and (2) briefly reviews a number of projects on the handling of biomedical information that uses SW technology. Methodology: The paper is structured into two main parts. “Semantic Web Technology” provides a high-level description, with examples, of the main standards and concepts: extensible markup language (XML), Resource Description Framework (RDF), RDF Schema (RDFS), ontologies, and their utility in information retrieval, concluding with mention of more advanced SW languages and their characteristics. “Semantic Web Applications and Research Projects in the Biomedical Field” is a brief review of the Unified Medical Language System (UMLS), Generalised Architecture for Languages, Encyclopedias and Nomenclatures in Medicine (GALEN), HealthCyberMap, LinkBase, and the thesaurus of the National Cancer Institute (NCI). The paper also mentions other benefits and by-products of the SW, citing projects related to them. Discussion and Conclusions: Some of the problems facing the SW vision are presented, especially the ways in which the librarians' expertise in organizing knowledge and in structuring information may contribute to SW projects. PMID:16636713

MODeLeR: A Virtual Constructivist Learning Environment and Methodology for Object-Oriented Design

ERIC Educational Resources Information Center

Coffey, John W.; Koonce, Robert

2008-01-01

This article contains a description of the organization and method of use of an active learning environment named MODeLeR, (Multimedia Object Design Learning Resource), a tool designed to facilitate the learning of concepts pertaining to object modeling with the Unified Modeling Language (UML). MODeLeR was created to provide an authentic,…

The Future of Architecture Collaborative Information Sharing: DoDAF Version 2.03 Updates

DTIC Science & Technology

2012-04-30

Salamander x Select Solution Factory Select Business Solutions BPMN , UML x SimonTool Simon Labs x SimProcess CACI BPMN x System Architecture Management...for DoDAF Mega UML x Metastorm ProVision Metastorm BPMN x Naval Simulation System - 4 Aces METRON x NetViz CA x OPNET OPNET x Tool Name Vendor Primary

eRAM: encyclopedia of rare disease annotations for precision medicine.

PubMed

Jia, Jinmeng; An, Zhongxin; Ming, Yue; Guo, Yongli; Li, Wei; Liang, Yunxiang; Guo, Dongming; Li, Xin; Tai, Jun; Chen, Geng; Jin, Yaqiong; Liu, Zhimei; Ni, Xin; Shi, Tieliu

2018-01-04

Rare diseases affect over a hundred million people worldwide, most of these patients are not accurately diagnosed and effectively treated. The limited knowledge of rare diseases forms the biggest obstacle for improving their treatment. Detailed clinical phenotyping is considered as a keystone of deciphering genes and realizing the precision medicine for rare diseases. Here, we preset a standardized system for various types of rare diseases, called encyclopedia of Rare disease Annotations for Precision Medicine (eRAM). eRAM was built by text-mining nearly 10 million scientific publications and electronic medical records, and integrating various data in existing recognized databases (such as Unified Medical Language System (UMLS), Human Phenotype Ontology, Orphanet, OMIM, GWAS). eRAM systematically incorporates currently available data on clinical manifestations and molecular mechanisms of rare diseases and uncovers many novel associations among diseases. eRAM provides enriched annotations for 15 942 rare diseases, yielding 6147 human disease related phenotype terms, 31 661 mammalians phenotype terms, 10,202 symptoms from UMLS, 18 815 genes and 92 580 genotypes. eRAM can not only provide information about rare disease mechanism but also facilitate clinicians to make accurate diagnostic and therapeutic decisions towards rare diseases. eRAM can be freely accessed at http://www.unimd.org/eram/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Development of a State Machine Sequencer for the Keck Interferometer: Evolution, Development and Lessons Learned using a CASE Tool Approach

NASA Technical Reports Server (NTRS)

Rede, Leonard J.; Booth, Andrew; Hsieh, Jonathon; Summer, Kellee

2004-01-01

This paper presents a discussion of the evolution of a sequencer from a simple EPICS (Experimental Physics and Industrial Control System) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a CASE (Computer Aided Software Engineering) tool approach. The main purpose of the sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Hare1 finite state machine, software program designed to orchestrate several lower-level hardware and software hard real time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORB A, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

Development of a state machine sequencer for the Keck Interferometer: evolution, development, and lessons learned using a CASE tool approach

NASA Astrophysics Data System (ADS)

Reder, Leonard J.; Booth, Andrew; Hsieh, Jonathan; Summers, Kellee R.

2004-09-01

This paper presents a discussion of the evolution of a sequencer from a simple Experimental Physics and Industrial Control System (EPICS) based sequencer into a complex implementation designed utilizing UML (Unified Modeling Language) methodologies and a Computer Aided Software Engineering (CASE) tool approach. The main purpose of the Interferometer Sequencer (called the IF Sequencer) is to provide overall control of the Keck Interferometer to enable science operations to be carried out by a single operator (and/or observer). The interferometer links the two 10m telescopes of the W. M. Keck Observatory at Mauna Kea, Hawaii. The IF Sequencer is a high-level, multi-threaded, Harel finite state machine software program designed to orchestrate several lower-level hardware and software hard real-time subsystems that must perform their work in a specific and sequential order. The sequencing need not be done in hard real-time. Each state machine thread commands either a high-speed real-time multiple mode embedded controller via CORBA, or slower controllers via EPICS Channel Access interfaces. The overall operation of the system is simplified by the automation. The UML is discussed and our use of it to implement the sequencer is presented. The decision to use the Rhapsody product as our CASE tool is explained and reflected upon. Most importantly, a section on lessons learned is presented and the difficulty of integrating CASE tool automatically generated C++ code into a large control system consisting of multiple infrastructures is presented.

Design of an UML conceptual model and implementation of a GIS with metadata information for a seismic hazard assessment cooperative project.

NASA Astrophysics Data System (ADS)

Torres, Y.; Escalante, M. P.

2009-04-01

This work illustrates the advantages of using a Geographic Information System in a cooperative project with researchers of different countries, such as the RESIS II project (financed by the Norwegian Government and managed by CEPREDENAC) for seismic hazard assessment of Central America. As input data present different formats, cover distinct geographical areas and are subjected to different interpretations, data inconsistencies may appear and their management get complicated. To achieve data homogenization and to integrate them in a GIS, it is required previously to develop a conceptual model. This is accomplished in two phases: requirements analysis and conceptualization. The Unified Modeling Language (UML) is used to compose the conceptual model of the GIS. UML complies with ISO 19100 norms and allows the designer defining model architecture and interoperability. The GIS provides a frame for the combination of large geographic-based data volumes, with an uniform geographic reference and avoiding duplications. All this information contains its own metadata following ISO 19115 normative. In this work, the integration in the same environment of active faults and subduction slabs geometries, combined with the epicentres location, has facilitated the definition of seismogenetic regions. This is a great support for national specialists of different countries to make easier their teamwork. The GIS capacity for making queries (by location and by attributes) and geostatistical analyses is used to interpolate discrete data resulting from seismic hazard calculations and to create continuous maps as well as to check and validate partial results of the study. GIS-based products, such as complete, homogenised databases and thematic cartography of the region, are distributed to all researchers, facilitating cross-national communication, the project execution and results dissemination.

A sense inventory for clinical abbreviations and acronyms created using clinical notes and medical dictionary resources

PubMed Central

Moon, Sungrim; Pakhomov, Serguei; Liu, Nathan; Ryan, James O; Melton, Genevieve B

2014-01-01

Objective To create a sense inventory of abbreviations and acronyms from clinical texts. Methods The most frequently occurring abbreviations and acronyms from 352 267 dictated clinical notes were used to create a clinical sense inventory. Senses of each abbreviation and acronym were manually annotated from 500 random instances and lexically matched with long forms within the Unified Medical Language System (UMLS V.2011AB), Another Database of Abbreviations in Medline (ADAM), and Stedman's Dictionary, Medical Abbreviations, Acronyms & Symbols, 4th edition (Stedman's). Redundant long forms were merged after they were lexically normalized using Lexical Variant Generation (LVG). Results The clinical sense inventory was found to have skewed sense distributions, practice-specific senses, and incorrect uses. Of 440 abbreviations and acronyms analyzed in this study, 949 long forms were identified in clinical notes. This set was mapped to 17 359, 5233, and 4879 long forms in UMLS, ADAM, and Stedman's, respectively. After merging long forms, only 2.3% matched across all medical resources. The UMLS, ADAM, and Stedman's covered 5.7%, 8.4%, and 11% of the merged clinical long forms, respectively. The sense inventory of clinical abbreviations and acronyms and anonymized datasets generated from this study are available for public use at http://www.bmhi.umn.edu/ihi/research/nlpie/resources/index.htm (‘Sense Inventories’, website). Conclusions Clinical sense inventories of abbreviations and acronyms created using clinical notes and medical dictionary resources demonstrate challenges with term coverage and resource integration. Further work is needed to help with standardizing abbreviations and acronyms in clinical care and biomedicine to facilitate automated processes such as text-mining and information extraction. PMID:23813539

Ontology Matching with Semantic Verification.

PubMed

Jean-Mary, Yves R; Shironoshita, E Patrick; Kabuka, Mansur R

2009-09-01

ASMOV (Automated Semantic Matching of Ontologies with Verification) is a novel algorithm that uses lexical and structural characteristics of two ontologies to iteratively calculate a similarity measure between them, derives an alignment, and then verifies it to ensure that it does not contain semantic inconsistencies. In this paper, we describe the ASMOV algorithm, and then present experimental results that measure its accuracy using the OAEI 2008 tests, and that evaluate its use with two different thesauri: WordNet, and the Unified Medical Language System (UMLS). These results show the increased accuracy obtained by combining lexical, structural and extensional matchers with semantic verification, and demonstrate the advantage of using a domain-specific thesaurus for the alignment of specialized ontologies.

A case study for a digital seabed database: Bohai Sea engineering geology database

NASA Astrophysics Data System (ADS)

Tianyun, Su; Shikui, Zhai; Baohua, Liu; Ruicai, Liang; Yanpeng, Zheng; Yong, Wang

2006-07-01

This paper discusses the designing plan of ORACLE-based Bohai Sea engineering geology database structure from requisition analysis, conceptual structure analysis, logical structure analysis, physical structure analysis and security designing. In the study, we used the object-oriented Unified Modeling Language (UML) to model the conceptual structure of the database and used the powerful function of data management which the object-oriented and relational database ORACLE provides to organize and manage the storage space and improve its security performance. By this means, the database can provide rapid and highly effective performance in data storage, maintenance and query to satisfy the application requisition of the Bohai Sea Oilfield Paradigm Area Information System.

Enhanced semantic interoperability by profiling health informatics standards.

PubMed

López, Diego M; Blobel, Bernd

2009-01-01

Several standards applied to the healthcare domain support semantic interoperability. These standards are far from being completely adopted in health information system development, however. The objective of this paper is to provide a method and suggest the necessary tooling for reusing standard health information models, by that way supporting the development of semantically interoperable systems and components. The approach is based on the definition of UML Profiles. UML profiling is a formal modeling mechanism to specialize reference meta-models in such a way that it is possible to adapt those meta-models to specific platforms or domains. A health information model can be considered as such a meta-model. The first step of the introduced method identifies the standard health information models and tasks in the software development process in which healthcare information models can be reused. Then, the selected information model is formalized as a UML Profile. That Profile is finally applied to system models, annotating them with the semantics of the information model. The approach is supported on Eclipse-based UML modeling tools. The method is integrated into a comprehensive framework for health information systems development, and the feasibility of the approach is demonstrated in the analysis, design, and implementation of a public health surveillance system, reusing HL7 RIM and DIMs specifications. The paper describes a method and the necessary tooling for reusing standard healthcare information models. UML offers several advantages such as tooling support, graphical notation, exchangeability, extensibility, semi-automatic code generation, etc. The approach presented is also applicable for harmonizing different standard specifications.

System Modeling of a large FPGA project: the SKA Tile Processing Module

NASA Astrophysics Data System (ADS)

Belli, C.; Comoretto, G.

Large projects like the SKA have an intrinsic complexity due to their scale. In this context, the application of a management design system becomes fundamental. For this purpose the SysML language, a UML customization for engineering applications, has been applied. As far as our work is concerned, we focused on the SKA Low Telescope - Tile Processing Module, designing diagrams at different detail levels. We designed a conceptual model of the TPM, primarily focusing on the main interfaces and the major data flows between product items. Functionalities are derived from use cases and allocated to hardware modules in order to guarantee the project's internal consistency and features. This model has been used both as internal documentation and as job specification, to commit part of the design to external entities.

Vertical distribution and composition of phytoplankton under the influence of an upper mixed layer.

PubMed

Ryabov, Alexei B; Rudolf, Lars; Blasius, Bernd

2010-03-07

The vertical distribution of phytoplankton is of fundamental importance for the dynamics and structure of aquatic communities. Here, using an advection-reaction-diffusion model, we investigate the distribution and competition of phytoplankton species in a water column, in which inverse resource gradients of light and a nutrient can limit growth of the biomass. This problem poses a challenge for ecologists, as the location of a production layer is not fixed, but rather depends on many internal parameters and environmental factors. In particular, we study the influence of an upper mixed layer (UML) in this system and show that it leads to a variety of dynamic effects: (i) Our model predicts alternative density profiles with a maximum of biomass either within or below the UML, thereby the system may be bistable or the relaxation from an unstable state may require a long-lasting transition. (ii) Reduced mixing in the deep layer can induce oscillations of the biomass; we show that a UML can sustain these oscillations even if the diffusivity is less than the critical mixing for a sinking phytoplankton population. (iii) A UML can strongly modify the outcome of competition between different phytoplankton species, yielding bistability both in the spatial distribution and in the species composition. (iv) A light limited species can obtain a competitive advantage if the diffusivity in the deep layers is reduced below a critical value. This yields a subtle competitive exclusion effect, where the oscillatory states in the deep layers are displaced by steady solutions in the UML. Finally, we present a novel graphical approach for deducing the competition outcome and for the analysis of the role of a UML in aquatic systems. 2009 Elsevier Ltd. All rights reserved.

Time process study with UML.

PubMed

Shiki, N; Ohno, Y; Fujii, A; Murata, T; Matsumura, Y

2009-01-01

We propose a new business-process analysis approach, Time Process Study (TPS), which comprises process analysis and time and motion studies (TMS). TPS offsets weaknesses of TMS; the cost of field studies and the difficulties in applying them to tasks whose time span differs from those of usual tasks. In TPS, the job procedures are first displayed using a unified modeling language (UML). Next, time and manpower for each procedure are studied through interviews and TMS, and the information is appended to the UML diagram. We applied TPS in the case of a hospital-based cancer registry (HCR) of a university hospital to clarify the work procedure and the time required, and investigated TPS's availability. Meetings for the study were held once a month from July to September in 2008, and one inquirer committed a total of eight hours to the hospital survey. TPS revealed that HCR consisted of three tasks and 14 functions. The registration required 123 hours/month/person, the quality control required 6.5 hours/ 6 months/person and filing data into the population-based cancer registry required 0.5 hours/6 months/person. Of the total tasks involved in registration, 116.5 hours/month/person were undertaken by a registration worker, which shows the necessity of employing one full-time staff. With TPS, it is straightforward to share the concept among the study-team because the job procedure is first displayed using UML. Therefore, it requires a few workload to conduct TMS and interview. The obtained results were adopted for the review of staff assignment of HCR by Japanese government.

Students' different understandings of class diagrams

NASA Astrophysics Data System (ADS)

Boustedt, Jonas

2012-03-01

The software industry needs well-trained software designers and one important aspect of software design is the ability to model software designs visually and understand what visual models represent. However, previous research indicates that software design is a difficult task to many students. This article reports empirical findings from a phenomenographic investigation on how students understand class diagrams, Unified Modeling Language (UML) symbols, and relations to object-oriented (OO) concepts. The informants were 20 Computer Science students from four different universities in Sweden. The results show qualitatively different ways to understand and describe UML class diagrams and the "diamond symbols" representing aggregation and composition. The purpose of class diagrams was understood in a varied way, from describing it as a documentation to a more advanced view related to communication. The descriptions of class diagrams varied from seeing them as a specification of classes to a more advanced view, where they were described to show hierarchic structures of classes and relations. The diamond symbols were seen as "relations" and a more advanced way was seeing the white and the black diamonds as different symbols for aggregation and composition. As a consequence of the results, it is recommended that UML should be adopted in courses. It is briefly indicated how the phenomenographic results in combination with variation theory can be used by teachers to enhance students' possibilities to reach advanced understanding of phenomena related to UML class diagrams. Moreover, it is recommended that teachers should put more effort in assessing skills in proper usage of the basic symbols and models and students should be provided with opportunities to practise collaborative design, e.g. using whiteboards.

Object-oriented software design in semiautomatic building extraction

NASA Astrophysics Data System (ADS)

Guelch, Eberhard; Mueller, Hardo

1997-08-01

Developing a system for semiautomatic building acquisition is a complex process, that requires constant integration and updating of software modules and user interfaces. To facilitate these processes we apply an object-oriented design not only for the data but also for the software involved. We use the unified modeling language (UML) to describe the object-oriented modeling of the system in different levels of detail. We can distinguish between use cases from the users point of view, that represent a sequence of actions, yielding in an observable result and the use cases for the programmers, who can use the system as a class library to integrate the acquisition modules in their own software. The structure of the system is based on the model-view-controller (MVC) design pattern. An example from the integration of automated texture extraction for the visualization of results demonstrate the feasibility of this approach.

Mobile Food Ordering Application using Android OS Platform

NASA Astrophysics Data System (ADS)

Yosep Ricky, Michael

2014-03-01

The purpose of this research is making an ordering food application based on Android with New Order, Order History, Restaurant Profile, Order Status, Tracking Order, and Setting Profile features. The research method used in this research is water model of System Development Life Cycle (SDLC) method with following phases: requirement definition, analyzing and determining the features needed in developing application and making the detail definition of each features, system and software design, designing the flow of developing application by using storyboard design, user experience design, Unified Modeling Language (UML) design, and database structure design, implementation an unit testing, making database and translating the result of designs to programming language code then doing unit testing, integration and System testing, integrating unit program to one unit system then doing system testing, operation and maintenance, operating the result of system testing and if any changes and reparations needed then the previous phases could be back. The result of this research is an ordering food application based on Android for customer and courier user, and a website for restaurant and admin user. The conclusion of this research is to help customer in making order easily, to give detail information needed by customer, to help restaurant in receiving order, and to help courier while doing delivery.

The caBIG® Life Science Business Architecture Model.

PubMed

Boyd, Lauren Becnel; Hunicke-Smith, Scott P; Stafford, Grace A; Freund, Elaine T; Ehlman, Michele; Chandran, Uma; Dennis, Robert; Fernandez, Anna T; Goldstein, Stephen; Steffen, David; Tycko, Benjamin; Klemm, Juli D

2011-05-15

Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG®) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research. LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model's current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ).

Exploring supervised and unsupervised methods to detect topics in biomedical text

PubMed Central

Lee, Minsuk; Wang, Weiqing; Yu, Hong

2006-01-01

Background Topic detection is a task that automatically identifies topics (e.g., "biochemistry" and "protein structure") in scientific articles based on information content. Topic detection will benefit many other natural language processing tasks including information retrieval, text summarization and question answering; and is a necessary step towards the building of an information system that provides an efficient way for biologists to seek information from an ocean of literature. Results We have explored the methods of Topic Spotting, a task of text categorization that applies the supervised machine-learning technique naïve Bayes to assign automatically a document into one or more predefined topics; and Topic Clustering, which apply unsupervised hierarchical clustering algorithms to aggregate documents into clusters such that each cluster represents a topic. We have applied our methods to detect topics of more than fifteen thousand of articles that represent over sixteen thousand entries in the Online Mendelian Inheritance in Man (OMIM) database. We have explored bag of words as the features. Additionally, we have explored semantic features; namely, the Medical Subject Headings (MeSH) that are assigned to the MEDLINE records, and the Unified Medical Language System (UMLS) semantic types that correspond to the MeSH terms, in addition to bag of words, to facilitate the tasks of topic detection. Our results indicate that incorporating the MeSH terms and the UMLS semantic types as additional features enhances the performance of topic detection and the naïve Bayes has the highest accuracy, 66.4%, for predicting the topic of an OMIM article as one of the total twenty-five topics. Conclusion Our results indicate that the supervised topic spotting methods outperformed the unsupervised topic clustering; on the other hand, the unsupervised topic clustering methods have the advantages of being robust and applicable in real world settings. PMID:16539745

Automating lexical cross-mapping of ICNP to SNOMED CT.

PubMed

Kim, Tae Youn

2016-01-01

The purpose of this study was to examine the feasibility of automating lexical cross-mapping of a logic-based nursing terminology (ICNP) to SNOMED CT using the Unified Medical Language System (UMLS) maintained by the U.S. National Library of Medicine. A two-stage approach included patterns identification, and application and evaluation of an automated term matching procedure. The performance of the automated procedure was evaluated using a test set against a gold standard (i.e. concept equivalency table) created independently by terminology experts. There were lexical similarities between ICNP diagnostic concepts and SNOMED CT. The automated term matching procedure was reliable as presented in recall of 65%, precision of 79%, accuracy of 82%, F-measure of 0.71 and the area under the receiver operating characteristics (ROC) curve of 0.78 (95% CI 0.73-0.83). When the automated procedure was not able to retrieve lexically matched concepts, it was also unlikely for terminology experts to identify a matched SNOMED CT concept. Although further research is warranted to enhance the automated matching procedure, the combination of cross-maps from UMLS and the automated procedure is useful to generate candidate mappings and thus, assist ongoing maintenance of mappings which is a significant burden to terminology developers.

Study of a High-Yield Cellulase System Created by Heavy-Ion Irradiation-Induced Mutagenesis of Aspergillus niger and Mixed Fermentation with Trichoderma reesei

PubMed Central

Chen, Ji-Hong; Li, Wen-Jian; Liu, Jing; Hu, Wei; Xiao, Guo-Qing; Dong, Miao-Yin; Wang, Yu-Chen

2015-01-01

The aim of this study was to evaluate and validate the efficiency of 12C6+ irradiation of Aspergillus niger (A. niger) or mutagenesis via mixed Trichoderma viride (T. viride) culturing as well as a liquid cultivation method for cellulase production via mixed Trichoderma reesei (T. reesei) and A. niger culture fermentation. The first mutagenesis approach was employed to optimize yield from a cellulase-producing strain via heavy-ion mutagenesis and high-throughput screening, and the second was to effectively achieve enzymatic hydrolysis of cellulase from a mixed culture of mutant T. viride and A. niger. We found that 12C6+-ion irradiation induced changes in cellulase biosynthesis in A. niger but had no effect on the time course of the synthesis. It is notable that the exoglucanases (CBH) activities of A. niger strains H11-1 and H differed (6.71 U/mL vs. 6.01 U/mL) and were significantly higher than that of A. niger mutant H3-1. Compared with strain H, the filter paper assay (FPA), endoglucanase (EG) and β-glucosidase (BGL) activities of mutant strain H11-1 were increased by 250.26%, 30.26% and 34.91%, respectively. A mixed culture system was successfully optimized, and the best ratio of T. reesei to A. niger was 5:1 for 96 h with simultaneous inoculation. The BGL activity of the mixed culture increased after 72 h. At 96 h, the FPA and BGL activities of the mixed culture were 689.00 and 797.15 U/mL, respectively, significantly higher than those of monocultures, which were 408.70 and 646.98 U/mL for T. reesei and 447.29 and 658.89 U/mL for A. niger, respectively. The EG activity of the mixed culture was 2342.81 U/mL, a value that was significantly higher than that of monocultures at 2206.57 U/mL for T. reesei and 1727.62 U/mL for A. niger. In summary, cellulose production and hydrolysis yields were significantly enhanced by the proposed combination scheme. PMID:26656155

PatientsLikeMe: Consumer Health Vocabulary as a Folksonomy

PubMed Central

Smith, Catherine Arnott; Wicks, Paul J.

2008-01-01

PatientsLikeMe is an online social networking community for patients. Subcommunities center on three distinct diagnoses: Amyotrophic Lateral Sclerosis, Multiple Sclerosis and Parkinson’s Disease. Community members can describe their symptoms to others in natural language terms, resulting in folksonomic tags available for clinical analysis and for browsing by other users to find “patients like me”. Forty-three percent of PatientsLikeMe symptom terms are present as exact (24%) or synonymous (19%) terms in the Unified Medical Language System Metathesaurus (National Library of Medicine; 2007AC). Slightly more than half of the symptom terms either do not match the UMLS, or are unclassifiable. A clinical vocabulary, SNOMED CT, accounts for 93% of the matching terms. Analysis of the failed matches reveals challenges for online patient communication, not only with healthcare professionals, but with other patients. In a Web 2.0 environment with lowered barriers between consumers and professionals, a deficiency in knowledge representation affects not only the professionals, but the consumers as well. PMID:18999004

Using enterprise architecture to analyse how organisational structure impact motivation and learning

NASA Astrophysics Data System (ADS)

Närman, Pia; Johnson, Pontus; Gingnell, Liv

2016-06-01

When technology, environment, or strategies change, organisations need to adjust their structures accordingly. These structural changes do not always enhance the organisational performance as intended partly because organisational developers do not understand the consequences of structural changes in performance. This article presents a model-based analysis framework for quantitative analysis of the effect of organisational structure on organisation performance in terms of employee motivation and learning. The model is based on Mintzberg's work on organisational structure. The quantitative analysis is formalised using the Object Constraint Language (OCL) and the Unified Modelling Language (UML) and implemented in an enterprise architecture tool.

A computational linguistics motivated mapping of ICPC-2 PLUS to SNOMED CT.

PubMed

Wang, Yefeng; Patrick, Jon; Miller, Graeme; O'Hallaran, Julie

2008-10-27

A great challenge in sharing data across information systems in general practice is the lack of interoperability between different terminologies or coding schema used in the information systems. Mapping of medical vocabularies to a standardised terminology is needed to solve data interoperability problems. We present a system to automatically map an interface terminology ICPC-2 PLUS to SNOMED CT. Three steps of mapping are proposed in this system. The UMLS metathesaurus mapping utilises explicit relationships between ICPC-2 PLUS and SNOMED CT terms in the UMLS library to perform the first stage of the mapping. Computational linguistic mapping uses natural language processing techniques and lexical similarities for the second stage of mapping between terminologies. Finally, the post-coordination mapping allows one ICPC-2 PLUS term to be mapped into an aggregation of two or more SNOMED CT terms. A total 5,971 of all 7,410 ICPC-2 terms (80.58%) were mapped to SNOMED CT using the three stages but with different levels of accuracy. UMLS mapping achieved the mapping of 53.0% ICPC2 PLUS terms to SNOMED CT with the precision rate of 96.46% and overall recall rate of 44.89%. Lexical mapping increased the result to 60.31% and post-coordination mapping gave an increase of 20.27% in mapped terms. A manual review of a part of the mapping shows that the precision of lexical mappings is around 90%. The accuracy of post-coordination has not been evaluated yet. Unmapped terms and mismatched terms are due to the differences in the structures between ICPC-2 PLUS and SNOMED CT. Terms contained in ICPC-2 PLUS but not in SNOMED CT caused a large proportion of the failures in the mappings. Mapping terminologies to a standard vocabulary is a way to facilitate consistent medical data exchange and achieve system interoperability and data standardisation. Broad scale mapping cannot be achieved by any single method and methods based on computational linguistics can be very useful for the task. Automating as much as is possible of this process turns the searching and mapping task into a validation task, which can effectively reduce the cost and increase the efficiency and accuracy of this task over manual methods.

Portal of medical data models: information infrastructure for medical research and healthcare.

PubMed

Dugas, Martin; Neuhaus, Philipp; Meidt, Alexandra; Doods, Justin; Storck, Michael; Bruland, Philipp; Varghese, Julian

2016-01-01

Information systems are a key success factor for medical research and healthcare. Currently, most of these systems apply heterogeneous and proprietary data models, which impede data exchange and integrated data analysis for scientific purposes. Due to the complexity of medical terminology, the overall number of medical data models is very high. At present, the vast majority of these models are not available to the scientific community. The objective of the Portal of Medical Data Models (MDM, https://medical-data-models.org) is to foster sharing of medical data models. MDM is a registered European information infrastructure. It provides a multilingual platform for exchange and discussion of data models in medicine, both for medical research and healthcare. The system is developed in collaboration with the University Library of Münster to ensure sustainability. A web front-end enables users to search, view, download and discuss data models. Eleven different export formats are available (ODM, PDF, CDA, CSV, MACRO-XML, REDCap, SQL, SPSS, ADL, R, XLSX). MDM contents were analysed with descriptive statistics. MDM contains 4387 current versions of data models (in total 10,963 versions). 2475 of these models belong to oncology trials. The most common keyword (n = 3826) is 'Clinical Trial'; most frequent diseases are breast cancer, leukemia, lung and colorectal neoplasms. Most common languages of data elements are English (n = 328,557) and German (n = 68,738). Semantic annotations (UMLS codes) are available for 108,412 data items, 2453 item groups and 35,361 code list items. Overall 335,087 UMLS codes are assigned with 21,847 unique codes. Few UMLS codes are used several thousand times, but there is a long tail of rarely used codes in the frequency distribution. Expected benefits of the MDM portal are improved and accelerated design of medical data models by sharing best practice, more standardised data models with semantic annotation and better information exchange between information systems, in particular Electronic Data Capture (EDC) and Electronic Health Records (EHR) systems. Contents of the MDM portal need to be further expanded to reach broad coverage of all relevant medical domains. Database URL: https://medical-data-models.org. © The Author(s) 2016. Published by Oxford University Press.

UML Profiles for Design Decisions and Non-Functional Requirements

DOE Office of Scientific and Technical Information (OSTI.GOV)

Zhu, Liming; Gorton, Ian

2007-06-30

A software architecture is composed of a collection of design decisions. Each design decision helps or hinders certain Non-Functional Requirements (NFR). Current software architecture views focus on expressing components and connectors in the system. Design decisions and their relationships with non-functional requirements are often captured in separate design documentation, not explicitly expressed in any views. This disassociation makes architecture comprehension and architecture evolution harder. In this paper, we propose a UML profile for modeling design decisions and an associated UML profile for modeling non-functional requirements in a generic way. The two UML profiles treat design decisions and nonfunctional requirements asmore » first-class elements. Modeled design decisions always refer to existing architectural elements and thus maintain traceability between the two. We provide a mechanism for checking consistency over this traceability. An exemplar is given as« less

Control System Architectures, Technologies and Concepts for Near Term and Future Human Exploration of Space

NASA Technical Reports Server (NTRS)

Boulanger, Richard; Overland, David

2004-01-01

Technologies that facilitate the design and control of complex, hybrid, and resource-constrained systems are examined. This paper focuses on design methodologies, and system architectures, not on specific control methods that may be applied to life support subsystems. Honeywell and Boeing have estimated that 60-80Y0 of the effort in developing complex control systems is software development, and only 20-40% is control system development. It has also been shown that large software projects have failure rates of as high as 50-65%. Concepts discussed include the Unified Modeling Language (UML) and design patterns with the goal of creating a self-improving, self-documenting system design process. Successful architectures for control must not only facilitate hardware to software integration, but must also reconcile continuously changing software with much less frequently changing hardware. These architectures rely on software modules or components to facilitate change. Architecting such systems for change leverages the interfaces between these modules or components.

A Model-Driven Development Method for Management Information Systems

NASA Astrophysics Data System (ADS)

Mizuno, Tomoki; Matsumoto, Keinosuke; Mori, Naoki

Traditionally, a Management Information System (MIS) has been developed without using formal methods. By the informal methods, the MIS is developed on its lifecycle without having any models. It causes many problems such as lack of the reliability of system design specifications. In order to overcome these problems, a model theory approach was proposed. The approach is based on an idea that a system can be modeled by automata and set theory. However, it is very difficult to generate automata of the system to be developed right from the start. On the other hand, there is a model-driven development method that can flexibly correspond to changes of business logics or implementing technologies. In the model-driven development, a system is modeled using a modeling language such as UML. This paper proposes a new development method for management information systems applying the model-driven development method to a component of the model theory approach. The experiment has shown that a reduced amount of efforts is more than 30% of all the efforts.

LEGOS: Object-based software components for mission-critical systems. Final report, June 1, 1995--December 31, 1997

DOE Office of Scientific and Technical Information (OSTI.GOV)

NONE

1998-08-01

An estimated 85% of the installed base of software is a custom application with a production quantity of one. In practice, almost 100% of military software systems are custom software. Paradoxically, the marginal costs of producing additional units are near zero. So why hasn`t the software market, a market with high design costs and low productions costs evolved like other similar custom widget industries, such as automobiles and hardware chips? The military software industry seems immune to market pressures that have motivated a multilevel supply chain structure in other widget industries: design cost recovery, improve quality through specialization, and enablemore » rapid assembly from purchased components. The primary goal of the ComponentWare Consortium (CWC) technology plan was to overcome barriers to building and deploying mission-critical information systems by using verified, reusable software components (Component Ware). The adoption of the ComponentWare infrastructure is predicated upon a critical mass of the leading platform vendors` inevitable adoption of adopting emerging, object-based, distributed computing frameworks--initially CORBA and COM/OLE. The long-range goal of this work is to build and deploy military systems from verified reusable architectures. The promise of component-based applications is to enable developers to snap together new applications by mixing and matching prefabricated software components. A key result of this effort is the concept of reusable software architectures. A second important contribution is the notion that a software architecture is something that can be captured in a formal language and reused across multiple applications. The formalization and reuse of software architectures provide major cost and schedule improvements. The Unified Modeling Language (UML) is fast becoming the industry standard for object-oriented analysis and design notation for object-based systems. However, the lack of a standard real-time distributed object operating system, lack of a standard Computer-Aided Software Environment (CASE) tool notation and lack of a standard CASE tool repository has limited the realization of component software. The approach to fulfilling this need is the software component factory innovation. The factory approach takes advantage of emerging standards such as UML, CORBA, Java and the Internet. The key technical innovation of the software component factory is the ability to assemble and test new system configurations as well as assemble new tools on demand from existing tools and architecture design repositories.« less

The role of compositionality in standardized problem list generation.

PubMed

Elkin, P L; Tuttle, M; Keck, K; Campbell, K; Atkin, G; Chute, C G

1998-01-01

Compositionality is the ability of a Vocabulary System to record non-atomic strings. In this manuscript we define the types of composition, which can occur. We will then propose methods for both server based and client-based composition. We will differentiate the terms Pre-Coordination, Post-Coordination, and User-Directed Coordination. A simple grammar for the recording of terms with concept level identification will be presented, with examples from the Unified Medical Language System's (UMLS) Metathesaurus. We present an implementation of a Window's NT based client application and a remote Internet Based Vocabulary Server, which makes use of this method of compositionality. Finally we will suggest a research agenda which we believe is necessary to move forward toward a more complete understanding of compositionality. This work has the promise of paving the way toward a robust and complete Problem List Entry Tool.

Modelling Participatory Geographic Information System for Customary Land Conflict Resolution

NASA Astrophysics Data System (ADS)

Gyamera, E. A.; Arko-Adjei, A.; Duncan, E. E.; Kuma, J. S. Y.

2017-11-01

Since land contributes to about 73 % of most countries Gross Domestic Product (GDP), attention on land rights have tremendously increased globally. Conflicts over land have therefore become part of the major problems associated with land administration. However, the conventional mechanisms for land conflict resolution do not provide satisfactory result to disputants due to various factors. This study sought to develop a Framework of using Participatory Geographic Information System (PGIS) for customary land conflict resolution. The framework was modelled using Unified Modelling Language (UML). The PGIS framework, called butterfly model, consists of three units namely, Social Unit (SU), Technical Unit (TU) and Decision Making Unit (DMU). The name butterfly model for land conflict resolution was adopted for the framework based on its features and properties. The framework has therefore been recommended to be adopted for land conflict resolution in customary areas.

Model-Drive Architecture for Agent-Based Systems

NASA Technical Reports Server (NTRS)

Gradanin, Denis; Singh, H. Lally; Bohner, Shawn A.; Hinchey, Michael G.

2004-01-01

The Model Driven Architecture (MDA) approach uses a platform-independent model to define system functionality, or requirements, using some specification language. The requirements are then translated to a platform-specific model for implementation. An agent architecture based on the human cognitive model of planning, the Cognitive Agent Architecture (Cougaar) is selected for the implementation platform. The resulting Cougaar MDA prescribes certain kinds of models to be used, how those models may be prepared and the relationships of the different kinds of models. Using the existing Cougaar architecture, the level of application composition is elevated from individual components to domain level model specifications in order to generate software artifacts. The software artifacts generation is based on a metamodel. Each component maps to a UML structured component which is then converted into multiple artifacts: Cougaar/Java code, documentation, and test cases.

Computer-assisted update of a consumer health vocabulary through mining of social network data.

PubMed

Doing-Harris, Kristina M; Zeng-Treitler, Qing

2011-05-17

Consumer health vocabularies (CHVs) have been developed to aid consumer health informatics applications. This purpose is best served if the vocabulary evolves with consumers' language. Our objective was to create a computer assisted update (CAU) system that works with live corpora to identify new candidate terms for inclusion in the open access and collaborative (OAC) CHV. The CAU system consisted of three main parts: a Web crawler and an HTML parser, a candidate term filter that utilizes natural language processing tools including term recognition methods, and a human review interface. In evaluation, the CAU system was applied to the health-related social network website PatientsLikeMe.com. The system's utility was assessed by comparing the candidate term list it generated to a list of valid terms hand extracted from the text of the crawled webpages. The CAU system identified 88,994 unique terms 1- to 7-grams ("n-grams" are n consecutive words within a sentence) in 300 crawled PatientsLikeMe.com webpages. The manual review of the crawled webpages identified 651 valid terms not yet included in the OAC CHV or the Unified Medical Language System (UMLS) Metathesaurus, a collection of vocabularies amalgamated to form an ontology of medical terms, (ie, 1 valid term per 136.7 candidate n-grams). The term filter selected 774 candidate terms, of which 237 were valid terms, that is, 1 valid term among every 3 or 4 candidates reviewed. The CAU system is effective for generating a list of candidate terms for human review during CHV development.

A UML-based meta-framework for system design in public health informatics.

PubMed

Orlova, Anna O; Lehmann, Harold

2002-01-01

The National Agenda for Public Health Informatics calls for standards in data and knowledge representation within public health, which requires a multi-level framework that links all aspects of public health. The literature of public health informatics and public health informatics application were reviewed. A UML-based systems analysis was performed. Face validity of results was evaluated in analyzing the public health domain of lead poisoning. The core class of the UML-based system of public health is the Public Health Domain, which is associated with multiple Problems, for which Actors provide Perspectives. Actors take Actions that define, generate, utilize and/or evaluate Data Sources. The life cycle of the domain is a sequence of activities attributed to its problems that spirals through multiple iterations and realizations within a domain. The proposed Public Health Informatics Meta-Framework broadens efforts in applying informatics principles to the field of public health

The Latin American laws of correct nutrition: Review, unified interpretation, model and tools.

PubMed

Chávez-Bosquez, Oscar; Pozos-Parra, Pilar

2016-03-01

The "Laws of Correct Nutrition": the Law of Quantity, the Law of Quality, the Law of Harmony and the Law of Adequacy, provide the basis of a proper diet, i.e. one that provides the body with the energy required and nutrients it needs for daily activities and maintenance of vital functions. For several decades, these Laws have been the basis of nourishing menus designed in Latin America; however, they are stated in a colloquial language, which leads to differences in interpretation and ambiguities for non-experts and even experts in the field. We present a review of the different interpretations of the Laws and describe a consensus. We represent concepts related to nourishing menu design employing the Unified Modeling Language (UML). We formalize the Laws using the Object Constraint Language (OCL). We design a nourishing menu for a particular user through enforcement of the Laws. We designed a domain model with the essential elements to plan a nourishing menu and we expressed the necessary constraints to make the model׳s behavior conform to the four Laws. We made a formal verification and validation of the model via USE (UML-based Specification Environment) and we developed a software prototype for menu design under the Laws. Diet planning is considered as an art but consideration should be given to the need for a set of strict rules to design adequate menus. Thus, we model the "Laws of Nutrition" as a formal basis and standard framework for this task. Copyright © 2016 The Authors. Published by Elsevier Ltd.. All rights reserved.

Computer-Assisted Update of a Consumer Health Vocabulary Through Mining of Social Network Data

PubMed Central

2011-01-01

Background Consumer health vocabularies (CHVs) have been developed to aid consumer health informatics applications. This purpose is best served if the vocabulary evolves with consumers’ language. Objective Our objective was to create a computer assisted update (CAU) system that works with live corpora to identify new candidate terms for inclusion in the open access and collaborative (OAC) CHV. Methods The CAU system consisted of three main parts: a Web crawler and an HTML parser, a candidate term filter that utilizes natural language processing tools including term recognition methods, and a human review interface. In evaluation, the CAU system was applied to the health-related social network website PatientsLikeMe.com. The system’s utility was assessed by comparing the candidate term list it generated to a list of valid terms hand extracted from the text of the crawled webpages. Results The CAU system identified 88,994 unique terms 1- to 7-grams (“n-grams” are n consecutive words within a sentence) in 300 crawled PatientsLikeMe.com webpages. The manual review of the crawled webpages identified 651 valid terms not yet included in the OAC CHV or the Unified Medical Language System (UMLS) Metathesaurus, a collection of vocabularies amalgamated to form an ontology of medical terms, (ie, 1 valid term per 136.7 candidate n-grams). The term filter selected 774 candidate terms, of which 237 were valid terms, that is, 1 valid term among every 3 or 4 candidates reviewed. Conclusion The CAU system is effective for generating a list of candidate terms for human review during CHV development. PMID:21586386

Augmenting Oracle Text with the UMLS for enhanced searching of free-text medical reports.

PubMed

Ding, Jing; Erdal, Selnur; Dhaval, Rakesh; Kamal, Jyoti

2007-10-11

The intrinsic complexity of free-text medical reports imposes great challenges for information retrieval systems. We have developed a prototype search engine for retrieving clinical reports that leverages the powerful indexing and querying capabilities of Oracle Text, and the rich biomedical domain knowledge and semantic structures that are captured in the UMLS Metathesaurus.

"UML Quiz": Automatic Conversion of Web-Based E-Learning Content in Mobile Applications

ERIC Educational Resources Information Center

von Franqué, Alexander; Tellioglu, Hilda

2014-01-01

Many educational institutions use Learning Management Systems to provide e-learning content to their students. This often includes quizzes that can help students to prepare for exams. However, the content is usually web-optimized and not very usable on mobile devices. In this work a native mobile application ("UML Quiz") that imports…

From Informal Safety-Critical Requirements to Property-Driven Formal Validation

NASA Technical Reports Server (NTRS)

Cimatti, Alessandro; Roveri, Marco; Susi, Angelo; Tonetta, Stefano

2008-01-01

Most of the efforts in formal methods have historically been devoted to comparing a design against a set of requirements. The validation of the requirements themselves, however, has often been disregarded, and it can be considered a largely open problem, which poses several challenges. The first challenge is given by the fact that requirements are often written in natural language, and may thus contain a high degree of ambiguity. Despite the progresses in Natural Language Processing techniques, the task of understanding a set of requirements cannot be automatized, and must be carried out by domain experts, who are typically not familiar with formal languages. Furthermore, in order to retain a direct connection with the informal requirements, the formalization cannot follow standard model-based approaches. The second challenge lies in the formal validation of requirements. On one hand, it is not even clear which are the correctness criteria or the high-level properties that the requirements must fulfill. On the other hand, the expressivity of the language used in the formalization may go beyond the theoretical and/or practical capacity of state-of-the-art formal verification. In order to solve these issues, we propose a new methodology that comprises of a chain of steps, each supported by a specific tool. The main steps are the following. First, the informal requirements are split into basic fragments, which are classified into categories, and dependency and generalization relationships among them are identified. Second, the fragments are modeled using a visual language such as UML. The UML diagrams are both syntactically restricted (in order to guarantee a formal semantics), and enriched with a highly controlled natural language (to allow for modeling static and temporal constraints). Third, an automatic formal analysis phase iterates over the modeled requirements, by combining several, complementary techniques: checking consistency; verifying whether the requirements entail some desirable properties; verify whether the requirements are consistent with selected scenarios; diagnosing inconsistencies by identifying inconsistent cores; identifying vacuous requirements; constructing multiple explanations by enabling the fault-tree analysis related to particular fault models; verifying whether the specification is realizable.

Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems.

PubMed

Williams, Richard A; Timmis, Jon; Qwarnstrom, Eva E

2016-01-01

Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model. We present a domain model of the IL-1 stimulated NF-κB signalling pathway, which unambiguously defines the spatial, temporal and stochastic requirements for our future computational model. Through the development of this model, we observe that, in isolation, UML is not sufficient for the purpose of creating a domain model, and that a number of descriptive and multivariate statistical techniques provide complementary perspectives, in particular when modelling the heterogeneity of dynamics at the single-cell level. We believe this approach of using UML to define the structure and interactions within a complex system, along with statistics to define the stochastic and dynamic nature of complex systems, is crucial for ensuring that conceptual models of complex dynamical biosystems, which are developed using UML, are fit for purpose, and unambiguously define the functional requirements for the resultant computational model.

Statistical Techniques Complement UML When Developing Domain Models of Complex Dynamical Biosystems

PubMed Central

Timmis, Jon; Qwarnstrom, Eva E.

2016-01-01

Computational modelling and simulation is increasingly being used to complement traditional wet-lab techniques when investigating the mechanistic behaviours of complex biological systems. In order to ensure computational models are fit for purpose, it is essential that the abstracted view of biology captured in the computational model, is clearly and unambiguously defined within a conceptual model of the biological domain (a domain model), that acts to accurately represent the biological system and to document the functional requirements for the resultant computational model. We present a domain model of the IL-1 stimulated NF-κB signalling pathway, which unambiguously defines the spatial, temporal and stochastic requirements for our future computational model. Through the development of this model, we observe that, in isolation, UML is not sufficient for the purpose of creating a domain model, and that a number of descriptive and multivariate statistical techniques provide complementary perspectives, in particular when modelling the heterogeneity of dynamics at the single-cell level. We believe this approach of using UML to define the structure and interactions within a complex system, along with statistics to define the stochastic and dynamic nature of complex systems, is crucial for ensuring that conceptual models of complex dynamical biosystems, which are developed using UML, are fit for purpose, and unambiguously define the functional requirements for the resultant computational model. PMID:27571414

A UML-based ontology for describing hospital information system architectures.

PubMed

Winter, A; Brigl, B; Wendt, T

2001-01-01

To control the heterogeneity inherent to hospital information systems the information management needs appropriate hospital information systems modeling methods or techniques. This paper shows that, for several reasons, available modeling approaches are not able to answer relevant questions of information management. To overcome this major deficiency we offer an UML-based ontology for describing hospital information systems architectures. This ontology views at three layers: the domain layer, the logical tool layer, and the physical tool layer, and defines the relevant components. The relations between these components, especially between components of different layers make the answering of our information management questions possible.

Business Process Modelling is an Essential Part of a Requirements Analysis. Contribution of EFMI Primary Care Working Group.

PubMed

de Lusignan, S; Krause, P; Michalakidis, G; Vicente, M Tristan; Thompson, S; McGilchrist, M; Sullivan, F; van Royen, P; Agreus, L; Desombre, T; Taweel, A; Delaney, B

2012-01-01

To perform a requirements analysis of the barriers to conducting research linking of primary care, genetic and cancer data. We extended our initial data-centric approach to include socio-cultural and business requirements. We created reference models of core data requirements common to most studies using unified modelling language (UML), dataflow diagrams (DFD) and business process modelling notation (BPMN). We conducted a stakeholder analysis and constructed DFD and UML diagrams for use cases based on simulated research studies. We used research output as a sensitivity analysis. Differences between the reference model and use cases identified study specific data requirements. The stakeholder analysis identified: tensions, changes in specification, some indifference from data providers and enthusiastic informaticians urging inclusion of socio-cultural context. We identified requirements to collect information at three levels: micro- data items, which need to be semantically interoperable, meso- the medical record and data extraction, and macro- the health system and socio-cultural issues. BPMN clarified complex business requirements among data providers and vendors; and additional geographical requirements for patients to be represented in both linked datasets. High quality research output was the norm for most repositories. Reference models provide high-level schemata of the core data requirements. However, business requirements' modelling identifies stakeholder issues and identifies what needs to be addressed to enable participation.

Orthographic Software Modelling: A Novel Approach to View-Based Software Engineering

NASA Astrophysics Data System (ADS)

Atkinson, Colin

The need to support multiple views of complex software architectures, each capturing a different aspect of the system under development, has been recognized for a long time. Even the very first object-oriented analysis/design methods such as the Booch method and OMT supported a number of different diagram types (e.g. structural, behavioral, operational) and subsequent methods such as Fusion, Kruchten's 4+1 views and the Rational Unified Process (RUP) have added many more views over time. Today's leading modeling languages such as the UML and SysML, are also oriented towards supporting different views (i.e. diagram types) each able to portray a different facets of a system's architecture. More recently, so called enterprise architecture frameworks such as the Zachman Framework, TOGAF and RM-ODP have become popular. These add a whole set of new non-functional views to the views typically emphasized in traditional software engineering environments.

Preliminary design of a universal Martian lander

NASA Astrophysics Data System (ADS)

Norman, Timothy L.; Gaskin, David E.; Adkins, Sean; Gunawan, Mary; Johnson, Raquel; Macdonnell, David; Parlock, Andrew; Sarick, John; Bodwell, Charles; Hashimoto, Kouichi

In the next 25 years, mankind will be undertaking yet another giant leap forward in the exploration of the solar system: a manned mission to Mars. This journey will provide important information on the composition and history of both Mars and the Solar System. A manned mission will also provide the opportunity to study how humans can adapt to long term space flight conditions and the Martian environment. As part of the NASA/USRA program, nineteen West Virginia University students conducted a preliminary design of a manned Universal Martian Lander (UML). The UML's design will provide a 'universal' platform, consisting of four modules for living and laboratory experiments and a liquid-fuel propelled Manned Ascent Return Vehicle (MARV). The distinguishing feature of the UML is the 'universal' design of the modules which can be connected to form a network of laboratories and living quarters for future missions thereby reducing development and production costs. The WVU design considers descent to Mars from polar orbit, a six month surface stay, and ascent for rendezvous. The design begins with an unmanned UML landing at Elysium Mons followed by the manned UML landing nearby. During the six month surface stay, the eight modules will be assembled to form a Martian base where scientific experiments will be performed. The mission will also incorporate hydroponic plant growth into a Controlled Ecological Life Support System (CELSS) for water recycling, food production, and to counteract psychological effects of living on Mars. In situ fuel production for the MARV will be produced from gases in the Martian atmosphere. Following surface operations, the eight member crew will use the MARV to return to the Martian Transfer Vehicle (MTV) for the journey home to Earth.

Preliminary design of a universal Martian lander

NASA Technical Reports Server (NTRS)

Norman, Timothy L.; Gaskin, David E.; Adkins, Sean; Gunawan, Mary; Johnson, Raquel; Macdonnell, David; Parlock, Andrew; Sarick, John; Bodwell, Charles; Hashimoto, Kouichi

1993-01-01

In the next 25 years, mankind will be undertaking yet another giant leap forward in the exploration of the solar system: a manned mission to Mars. This journey will provide important information on the composition and history of both Mars and the Solar System. A manned mission will also provide the opportunity to study how humans can adapt to long term space flight conditions and the Martian environment. As part of the NASA/USRA program, nineteen West Virginia University students conducted a preliminary design of a manned Universal Martian Lander (UML). The UML's design will provide a 'universal' platform, consisting of four modules for living and laboratory experiments and a liquid-fuel propelled Manned Ascent Return Vehicle (MARV). The distinguishing feature of the UML is the 'universal' design of the modules which can be connected to form a network of laboratories and living quarters for future missions thereby reducing development and production costs. The WVU design considers descent to Mars from polar orbit, a six month surface stay, and ascent for rendezvous. The design begins with an unmanned UML landing at Elysium Mons followed by the manned UML landing nearby. During the six month surface stay, the eight modules will be assembled to form a Martian base where scientific experiments will be performed. The mission will also incorporate hydroponic plant growth into a Controlled Ecological Life Support System (CELSS) for water recycling, food production, and to counteract psychological effects of living on Mars. In situ fuel production for the MARV will be produced from gases in the Martian atmosphere. Following surface operations, the eight member crew will use the MARV to return to the Martian Transfer Vehicle (MTV) for the journey home to Earth.

The caBIG® Life Science Business Architecture Model

PubMed Central

Boyd, Lauren Becnel; Hunicke-Smith, Scott P.; Stafford, Grace A.; Freund, Elaine T.; Ehlman, Michele; Chandran, Uma; Dennis, Robert; Fernandez, Anna T.; Goldstein, Stephen; Steffen, David; Tycko, Benjamin; Klemm, Juli D.

2011-01-01

Motivation: Business Architecture Models (BAMs) describe what a business does, who performs the activities, where and when activities are performed, how activities are accomplished and which data are present. The purpose of a BAM is to provide a common resource for understanding business functions and requirements and to guide software development. The cancer Biomedical Informatics Grid (caBIG®) Life Science BAM (LS BAM) provides a shared understanding of the vocabulary, goals and processes that are common in the business of LS research. Results: LS BAM 1.1 includes 90 goals and 61 people and groups within Use Case and Activity Unified Modeling Language (UML) Diagrams. Here we report on the model's current release, LS BAM 1.1, its utility and usage, and plans for future use and continuing development for future releases. Availability and Implementation: The LS BAM is freely available as UML, PDF and HTML (https://wiki.nci.nih.gov/x/OFNyAQ). Contact: lbboyd@bcm.edu; laurenbboyd@gmail.com Supplementary information: Supplementary data) are avaliable at Bioinformatics online. PMID:21450709

A Wittgenstein Approach to the Learning of OO-modeling

NASA Astrophysics Data System (ADS)

Holmboe, Christian

2004-12-01

The paper uses Ludwig Wittgenstein's theories about the relationship between thought, language, and objects of the world to explore the assumption that OO-thinking resembles natural thinking. The paper imports from research in linguistic philosophy to computer science education research. I show how UML class diagrams (i.e., an artificial context-free language) correspond to the logically perfect languages described in Tractatus Logico-Philosophicus. In Philosophical Investigations Wittgenstein disputes his previous theories by showing that natural languages are not constructed by rules of mathematical logic, but are language games where the meaning of a word is constructed through its use in social contexts. Contradicting the claim that OO-thinking is easy to learn because of its similarity to natural thinking, I claim that OO-thinking is difficult to learn because of its differences from natural thinking. The nature of these differences is not currently well known or appreciated. I suggest how explicit attention to the nature and implications of different language games may improve the teaching and learning of OO-modeling as well as programming.

Assessment of disease named entity recognition on a corpus of annotated sentences.

PubMed

Jimeno, Antonio; Jimenez-Ruiz, Ernesto; Lee, Vivian; Gaudan, Sylvain; Berlanga, Rafael; Rebholz-Schuhmann, Dietrich

2008-04-11

In recent years, the recognition of semantic types from the biomedical scientific literature has been focused on named entities like protein and gene names (PGNs) and gene ontology terms (GO terms). Other semantic types like diseases have not received the same level of attention. Different solutions have been proposed to identify disease named entities in the scientific literature. While matching the terminology with language patterns suffers from low recall (e.g., Whatizit) other solutions make use of morpho-syntactic features to better cover the full scope of terminological variability (e.g., MetaMap). Currently, MetaMap that is provided from the National Library of Medicine (NLM) is the state of the art solution for the annotation of concepts from UMLS (Unified Medical Language System) in the literature. Nonetheless, its performance has not yet been assessed on an annotated corpus. In addition, little effort has been invested so far to generate an annotated dataset that links disease entities in text to disease entries in a database, thesaurus or ontology and that could serve as a gold standard to benchmark text mining solutions. As part of our research work, we have taken a corpus that has been delivered in the past for the identification of associations of genes to diseases based on the UMLS Metathesaurus and we have reprocessed and re-annotated the corpus. We have gathered annotations for disease entities from two curators, analyzed their disagreement (0.51 in the kappa-statistic) and composed a single annotated corpus for public use. Thereafter, three solutions for disease named entity recognition including MetaMap have been applied to the corpus to automatically annotate it with UMLS Metathesaurus concepts. The resulting annotations have been benchmarked to compare their performance. The annotated corpus is publicly available at ftp://ftp.ebi.ac.uk/pub/software/textmining/corpora/diseases and can serve as a benchmark to other systems. In addition, we found that dictionary look-up already provides competitive results indicating that the use of disease terminology is highly standardized throughout the terminologies and the literature. MetaMap generates precise results at the expense of insufficient recall while our statistical method obtains better recall at a lower precision rate. Even better results in terms of precision are achieved by combining at least two of the three methods leading, but this approach again lowers recall. Altogether, our analysis gives a better understanding of the complexity of disease annotations in the literature. MetaMap and the dictionary based approach are available through the Whatizit web service infrastructure (Rebholz-Schuhmann D, Arregui M, Gaudan S, Kirsch H, Jimeno A: Text processing through Web services: Calling Whatizit. Bioinformatics 2008, 24:296-298).

A study of actions in operative notes.

PubMed

Wang, Yan; Pakhomov, Serguei; Burkart, Nora E; Ryan, James O; Melton, Genevieve B

2012-01-01

Operative notes contain rich information about techniques, instruments, and materials used in procedures. To assist development of effective information extraction (IE) techniques for operative notes, we investigated the sublanguage used to describe actions within the operative report 'procedure description' section. Deep parsing results of 362,310 operative notes with an expanded Stanford parser using the SPECIALIST Lexicon resulted in 200 verbs (92% coverage) including 147 action verbs. Nominal action predicates for each action verb were gathered from WordNet, SPECIALIST Lexicon, New Oxford American Dictionary and Stedman's Medical Dictionary. Coverage gaps were seen in existing lexical, domain, and semantic resources (Unified Medical Language System (UMLS) Metathesaurus, SPECIALIST Lexicon, WordNet and FrameNet). Our findings demonstrate the need to construct surgical domain-specific semantic resources for IE from operative notes.

The Development of Web-GIS to support Resort Based Management for Conservation and Biodiversity in Indonesia

NASA Astrophysics Data System (ADS)

Vatresia, A.; Regen, R.

2016-12-01

Biodiversity loss is a global issue, but it is the pressing concern in mega-diverse countries, such as Indonesia. The lack of the data standardisation and remote area spread on 17.504 islands made it hard to organise and to manage without the aid of any technology on it. In this paper, we develop an application for forest rangers to capture the data of biodiversity and conservation in Indonesia that will integrate with web technology to manage the data. All of the processes was supported by the Ministry of Environmental and Forestry in Indonesia as the user of the system. This development was based on the latest law and policy in Indonesia to monitor the performance of conservation activity and biodiversity in Indonesia. It was developed by using Java and PHP programming language. The method we used is System Development Life Cycling (SDLC) and Unified Modelling Language (UML) 2.0 as the design model and the guidance to perform the system. The application was tested by using the method of the black box and the white box methodology that showed the system was rated as a GOOD application by the user. The result of the testing was also showed that all of the function in the system could be use for improving the performance of the user.

Model-based testing with UML applied to a roaming algorithm for bluetooth devices.

PubMed

Dai, Zhen Ru; Grabowski, Jens; Neukirchen, Helmut; Pals, Holger

2004-11-01

In late 2001, the Object Management Group issued a Request for Proposal to develop a testing profile for UML 2.0. In June 2003, the work on the UML 2.0 Testing Profile was finally adopted by the OMG. Since March 2004, it has become an official standard of the OMG. The UML 2.0 Testing Profile provides support for UML based model-driven testing. This paper introduces a methodology on how to use the testing profile in order to modify and extend an existing UML design model for test issues. The application of the methodology will be explained by applying it to an existing UML Model for a Bluetooth device.

Analysis of the possibility of SysML and BPMN application in formal data acquisition system description

NASA Astrophysics Data System (ADS)

Ćwikła, G.; Gwiazda, A.; Banaś, W.; Monica, Z.; Foit, K.

2017-08-01

The article presents the study of possible application of selected methods of complex description, that can be used as a support of the Manufacturing Information Acquisition System (MIAS) methodology, describing how to design a data acquisition system, allowing for collecting and processing real-time data on the functioning of a production system, necessary for management of a company. MIAS can allow conversion into Cyber-Physical Production System. MIAS is gathering and pre-processing data on the state of production system, including e.g. realisation of production orders, state of machines, materials and human resources. Systematised approach and model-based development is proposed for improving the quality of the design of MIAS methodology-based complex systems supporting data acquisition in various types of companies. Graphical specification can be the baseline for any model-based development in specified areas. The possibility of application of SysML and BPMN, both being UML-based languages, representing different approaches to modelling of requirements, architecture and implementation of the data acquisition system, as a tools supporting description of required features of MIAS, were considered.

Conceptual Modeling in the Time of the Revolution: Part II

NASA Astrophysics Data System (ADS)

Mylopoulos, John

Conceptual Modeling was a marginal research topic at the very fringes of Computer Science in the 60s and 70s, when the discipline was dominated by topics focusing on programs, systems and hardware architectures. Over the years, however, the field has moved to centre stage and has come to claim a central role both in Computer Science research and practice in diverse areas, such as Software Engineering, Databases, Information Systems, the Semantic Web, Business Process Management, Service-Oriented Computing, Multi-Agent Systems, Knowledge Management, and more. The transformation was greatly aided by the adoption of standards in modeling languages (e.g., UML), and model-based methodologies (e.g., Model-Driven Architectures) by the Object Management Group (OMG) and other standards organizations. We briefly review the history of the field over the past 40 years, focusing on the evolution of key ideas. We then note some open challenges and report on-going research, covering topics such as the representation of variability in conceptual models, capturing model intentions, and models of laws.

Heterogeneous but “Standard” Coding Systems for Adverse Events: Issues in Achieving Interoperability between Apples and Oranges

PubMed Central

Richesson, Rachel L.; Fung, Kin Wah; Krischer, Jeffrey P.

2008-01-01

Monitoring adverse events (AEs) is an important part of clinical research and a crucial target for data standards. The representation of adverse events themselves requires the use of controlled vocabularies with thousands of needed clinical concepts. Several data standards for adverse events currently exist, each with a strong user base. The structure and features of these current adverse event data standards (including terminologies and classifications) are different, so comparisons and evaluations are not straightforward, nor are strategies for their harmonization. Three different data standards - the Medical Dictionary for Regulatory Activities (MedDRA) and the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT) terminologies, and Common Terminology Criteria for Adverse Events (CTCAE) classification - are explored as candidate representations for AEs. This paper describes the structural features of each coding system, their content and relationship to the Unified Medical Language System (UMLS), and unsettled issues for future interoperability of these standards. PMID:18406213

Data-Flow Based Model Analysis

NASA Technical Reports Server (NTRS)

Saad, Christian; Bauer, Bernhard

2010-01-01

The concept of (meta) modeling combines an intuitive way of formalizing the structure of an application domain with a high expressiveness that makes it suitable for a wide variety of use cases and has therefore become an integral part of many areas in computer science. While the definition of modeling languages through the use of meta models, e.g. in Unified Modeling Language (UML), is a well-understood process, their validation and the extraction of behavioral information is still a challenge. In this paper we present a novel approach for dynamic model analysis along with several fields of application. Examining the propagation of information along the edges and nodes of the model graph allows to extend and simplify the definition of semantic constraints in comparison to the capabilities offered by e.g. the Object Constraint Language. Performing a flow-based analysis also enables the simulation of dynamic behavior, thus providing an "abstract interpretation"-like analysis method for the modeling domain.

Space Telecommunications Radio System Software Architecture Concepts and Analysis

NASA Technical Reports Server (NTRS)

Handler, Louis M.; Hall, Charles S.; Briones, Janette C.; Blaser, Tammy M.

2008-01-01

The Space Telecommunications Radio System (STRS) project investigated various Software Defined Radio (SDR) architectures for Space. An STRS architecture has been selected that separates the STRS operating environment from its various waveforms and also abstracts any specialized hardware to limit its effect on the operating environment. The design supports software evolution where new functionality is incorporated into the radio. Radio hardware functionality has been moving from hardware based ASICs into firmware and software based processors such as FPGAs, DSPs and General Purpose Processors (GPPs). Use cases capture the requirements of a system by describing how the system should interact with the users or other systems (the actors) to achieve a specific goal. The Unified Modeling Language (UML) is used to illustrate the Use Cases in a variety of ways. The Top Level Use Case diagram shows groupings of the use cases and how the actors are involved. The state diagrams depict the various states that a system or object may be in and the transitions between those states. The sequence diagrams show the main flow of activity as described in the use cases.

A review method for UML requirements analysis model employing system-side prototyping.

PubMed

Ogata, Shinpei; Matsuura, Saeko

2013-12-01

User interface prototyping is an effective method for users to validate the requirements defined by analysts at an early stage of a software development. However, a user interface prototype system offers weak support for the analysts to verify the consistency of the specifications about internal aspects of a system such as business logic. As the result, the inconsistency causes a lot of rework costs because the inconsistency often makes the developers impossible to actualize the system based on the specifications. For verifying such consistency, functional prototyping is an effective method for the analysts, but it needs a lot of costs and more detailed specifications. In this paper, we propose a review method so that analysts can verify the consistency among several different kinds of diagrams in UML efficiently by employing system-side prototyping without the detailed model. The system-side prototype system does not have any functions to achieve business logic, but visualizes the results of the integration among the diagrams in UML as Web pages. The usefulness of our proposal was evaluated by applying our proposal into a development of Library Management System (LMS) for a laboratory. This development was conducted by a group. As the result, our proposal was useful for discovering the serious inconsistency caused by the misunderstanding among the members of the group.

Lessons learned from a pilot implementation of the UMLS information sources map.

PubMed

Miller, P L; Frawley, S J; Wright, L; Roderer, N K; Powsner, S M

1995-01-01

To explore the software design issues involved in implementing an operational information sources map (ISM) knowledge base (KB) and system of navigational tools that can help medical users access network-based information sources relevant to a biomedical question. A pilot biomedical ISM KB and associated client-server software (ISM/Explorer) have been developed to help students, clinicians, researchers, and staff access network-based information sources, as part of the National Library of Medicine's (NLM) multi-institutional Unified Medical Language System (UMLS) project. The system allows the user to specify and constrain a search for a biomedical question of interest. The system then returns a list of sources matching the search. At this point the user may request 1) further information about a source, 2) that the list of sources be regrouped by different criteria to allow the user to get a better overall appreciation of the set of retrieved sources as a whole, or 3) automatic connection to a source. The pilot system operates in client-server mode and currently contains coded information for 121 sources. It is in routine use from approximately 40 workstations at the Yale School of Medicine. The lessons that have been learned are that: 1) it is important to make access to different versions of a source as seamless as possible, 2) achieving seamless, cross-platform access to heterogeneous sources is difficult, 3) significant differences exist between coding the subject content of an electronic information resource versus that of an article or a book, 4) customizing the ISM to multiple institutions entails significant complexities, and 5) there are many design trade-offs between specifying searches and viewing sets of retrieved sources that must be taken into consideration. An ISM KB and navigational tools have been constructed. In the process, much has been learned about the complexities of development and evaluation in this new environment, which are different from those for Gopher, wide area information servers (WAIS), World-Wide-Web (WWW), and MOSAIC resources.

Accessible Modelling of Complexity in Health (AMoCH) and associated data flows: asthma as an exemplar.

PubMed

Liyanage, Harshana; Luzi, Daniela; De Lusignan, Simon; Pecoraro, Fabrizio; McNulty, Richard; Tamburis, Oscar; Krause, Paul; Rigby, Michael; Blair, Mitch

2016-04-18

Background Modelling is an important part of information science. Models are abstractions of reality. We use models in the following contexts: (1) to describe the data and information flows in clinical practice to information scientists, (2) to compare health systems and care pathways, (3) to understand how clinical cases are recorded in record systems and (4) to model health care business models.Asthma is an important condition associated with a substantial mortality and morbidity. However, there are difficulties in determining who has the condition, making both its incidence and prevalence uncertain.Objective To demonstrate an approach for modelling complexity in health using asthma prevalence and incidence as an exemplar.Method The four steps in our process are:1. Drawing a rich picture, following Checkland's soft systems methodology;2. Constructing data flow diagrams (DFDs);3. Creating Unified Modelling Language (UML) use case diagrams to describe the interaction of the key actors with the system;4. Activity diagrams, either UML activity diagram or business process modelling notation diagram.Results Our rich picture flagged the complexity of factors that might impact on asthma diagnosis. There was consensus that the principle issue was that there were undiagnosed and misdiagnosed cases as well as correctly diagnosed. Genetic predisposition to atopy; exposure to environmental triggers; impact of respiratory health on earnings or ability to attend education or participate in sport, charities, pressure groups and the pharmaceutical industry all increased the likelihood of a diagnosis of asthma. Stigma and some factors within the health system diminished the likelihood of a diagnosis. The DFDs and other elements focused on better case finding.Conclusions This approach flagged the factors that might impact on the reported prevalence or incidence of asthma. The models suggested that applying selection criteria may improve the specificity of new or confirmed diagnosis.

Sculpting the UMLS Refined Semantic Network.

PubMed

He, Zhe; Morrey, C Paul; Perl, Yehoshua; Elhanan, Gai; Chen, Ling; Chen, Yan; Geller, James

2014-01-01

The Refined Semantic Network (RSN) for the UMLS was previously introduced to complement the UMLS Semantic Network (SN). The RSN partitions the UMLS Metathesaurus (META) into disjoint groups of concepts. Each such group is semantically uniform. However, the RSN was initially an order of magnitude larger than the SN, which is undesirable since to be useful, a semantic network should be compact. Most semantic types in the RSN represent combinations of semantic types in the UMLS SN. Such a "combination semantic type" is called Intersection Semantic Type (IST). Many ISTs are assigned to very few concepts. Moreover, when reviewing those concepts, many semantic type assignment inconsistencies were found. After correcting those inconsistencies many ISTs, among them some that contradicted UMLS rules, disappeared, which made the RSN smaller. The authors performed a longitudinal study with the goal of reducing the size of the RSN to become compact. This goal was achieved by correcting inconsistencies and errors in the IST assignments in the UMLS, which additionally helped identify and correct ambiguities, inconsistencies, and errors in source terminologies widely used in the realm of public health. In this paper, we discuss the process and steps employed in this longitudinal study and the intermediate results for different stages. The sculpting process includes removing redundant semantic type assignments, expanding semantic type assignments, and removing illegitimate ISTs by auditing ISTs of small extents. However, the emphasis of this paper is not on the auditing methodologies employed during the process, since they were introduced in earlier publications, but on the strategy of employing them in order to transform the RSN into a compact network. For this paper we also performed a comprehensive audit of 168 "small ISTs" in the 2013AA version of the UMLS to finalize the longitudinal study. Over the years it was found that the editors of the UMLS introduced some new inconsistencies that resulted in the reintroduction of unwarranted ISTs that had already been eliminated as a result of their previous corrections. Because of that, the transformation of the RSN into a compact network covering all necessary categories for the UMLS was slowed down. The corrections suggested by an audit of the 2013AA version of the UMLS achieve a compact RSN of equal magnitude as the UMLS SN. The number of ISTs has been reduced to 336. We also demonstrate how auditing the semantic type assignments of UMLS concepts can expose other modeling errors in the UMLS source terminologies, e.g., SNOMED CT, LOINC, and RxNORM that are important for health informatics. Such errors would otherwise stay hidden. It is hoped that the UMLS curators will implement all required corrections and use the RSN along with the SN when maintaining and extending the UMLS. When used correctly, the RSN will support the prevention of the accidental introduction of inconsistent semantic type assignments into the UMLS. Furthermore, this way the RSN will support the exposure of other hidden errors and inconsistencies in health informatics terminologies, which are sources of the UMLS. Notably, the development of the RSN materializes the deeper, more refined Semantic Network for the UMLS that its designers envisioned originally but had not implemented.

Feature-based component model for design of embedded systems

NASA Astrophysics Data System (ADS)

Zha, Xuan Fang; Sriram, Ram D.

2004-11-01

An embedded system is a hybrid of hardware and software, which combines software's flexibility and hardware real-time performance. Embedded systems can be considered as assemblies of hardware and software components. An Open Embedded System Model (OESM) is currently being developed at NIST to provide a standard representation and exchange protocol for embedded systems and system-level design, simulation, and testing information. This paper proposes an approach to representing an embedded system feature-based model in OESM, i.e., Open Embedded System Feature Model (OESFM), addressing models of embedded system artifacts, embedded system components, embedded system features, and embedded system configuration/assembly. The approach provides an object-oriented UML (Unified Modeling Language) representation for the embedded system feature model and defines an extension to the NIST Core Product Model. The model provides a feature-based component framework allowing the designer to develop a virtual embedded system prototype through assembling virtual components. The framework not only provides a formal precise model of the embedded system prototype but also offers the possibility of designing variation of prototypes whose members are derived by changing certain virtual components with different features. A case study example is discussed to illustrate the embedded system model.

Representing Medical Knowledge in the Form of Structured Text: The Development of Current Disease Descriptions*

PubMed Central

Nelson, Stuart J.; Sherertz, David D.; Erlbaum, Mark S.; Tuttle, Mark S.

1989-01-01

As part of the Unified Medical Language System (UMLS) initiative, some 900 diseases have been described using “structured text.” Structured text is words and short phrases entered under labelled contexts. Vocabulary is not controlled. The contexts comprise a template for the disease description. The structured text is both manipulable by machine and readable by humans. Use of the template was natural, and only a few problems arose in using the template. Instructions to disease description composers must be explicit in definitions of the contexts. Diseases to be described are chosen, after clustering related diseases, according to the distinctions that physicians practicing in the area under question believe are important. Limiting disease descriptions to primitive observations and to entities otherwise described within the corpus appears to be both feasible and desirable.

Tailoring vocabularies for NLP in sub-domains: a method to detect unused word sense.

PubMed

Figueroa, Rosa L; Zeng-Treitler, Qing; Goryachev, Sergey; Wiechmann, Eduardo P

2009-11-14

We developed a method to help tailor a comprehensive vocabulary system (e.g. the UMLS) for a sub-domain (e.g. clinical reports) in support of natural language processing (NLP). The method detects unused sense in a sub-domain by comparing the relational neighborhood of a word/term in the vocabulary with the semantic neighborhood of the word/term in the sub-domain. The semantic neighborhood of the word/term in the sub-domain is determined using latent semantic analysis (LSA). We trained and tested the unused sense detection on two clinical text corpora: one contains discharge summaries and the other outpatient visit notes. We were able to detect unused senses with precision from 79% to 87%, recall from 48% to 74%, and an area under receiver operation curve (AUC) of 72% to 87%.

Auto-Coding UML Statecharts for Flight Software

NASA Technical Reports Server (NTRS)

Benowitz, Edward G; Clark, Ken; Watney, Garth J.

2006-01-01

Statecharts have been used as a means to communicate behaviors in a precise manner between system engineers and software engineers. Hand-translating a statechart to code, as done on some previous space missions, introduces the possibility of errors in the transformation from chart to code. To improve auto-coding, we have developed a process that generates flight code from UML statecharts. Our process is being used for the flight software on the Space Interferometer Mission (SIM).

Framework for Design of Traceability System on Organic Rice Certification

NASA Astrophysics Data System (ADS)

Purwandoko, P. B.; Seminar, K. B.; Sutrisno; Sugiyanta

2018-05-01

Nowadays, the preferences of organic products such as organic rice have been increased. It because of the people awareness of the healthy and eco-friendly food product consumption has grown. Therefore, it is very important to ensure organic quality of the product that will be produced. Certification is a series of process that holds to ensure the quality of products meets all criteria of organic standards. Currently, there is a problem that traceability information system for organic rice certification has been not available. The current system still conducts manually caused the loss of information during storage process. This paper aimed at developing a traceability framework on organic rice certification process. First, the main discussed issues are organic certification process. Second, unified modeling language (UML) is used to build the model of user requirement in order to develop traceability system for all actors in the certification process. Furthermore, the information captured model along certification process will be explained in this paper. The model shows the information flow that has to be recorded for each actor. Finally, the challenges in the implementation system will be discussed in this paper.

A systematic approach for analysis and design of secure health information systems.

PubMed

Blobel, B; Roger-France, F

2001-06-01

A toolset using object-oriented techniques including the nowadays popular unified modelling language (UML) approach has been developed to facilitate the different users' views for security analysis and design of health care information systems. Paradigm and concepts used are based on the component architecture of information systems and on a general layered security model. The toolset was developed in 1996/1997 within the ISHTAR project funded by the European Commission as well as through international standardisation activities. Analysing and systematising real health care scenarios, only six and nine use case types could be found in the health and the security-related view, respectively. By combining these use case types, the analysis and design of any thinkable system architecture can be simplified significantly. Based on generic schemes, the environment needed for both communication and application security can be established by appropriate sets of security services and mechanisms. Because of the importance and the basic character of electronic health care record (EHCR) systems, the understanding of the approach is facilitated by (incomplete) examples for this application.

Ontology-guided organ detection to retrieve web images of disease manifestation: towards the construction of a consumer-based health image library.

PubMed

Chen, Yang; Ren, Xiaofeng; Zhang, Guo-Qiang; Xu, Rong

2013-01-01

Visual information is a crucial aspect of medical knowledge. Building a comprehensive medical image base, in the spirit of the Unified Medical Language System (UMLS), would greatly benefit patient education and self-care. However, collection and annotation of such a large-scale image base is challenging. To combine visual object detection techniques with medical ontology to automatically mine web photos and retrieve a large number of disease manifestation images with minimal manual labeling effort. As a proof of concept, we first learnt five organ detectors on three detection scales for eyes, ears, lips, hands, and feet. Given a disease, we used information from the UMLS to select affected body parts, ran the pretrained organ detectors on web images, and combined the detection outputs to retrieve disease images. Compared with a supervised image retrieval approach that requires training images for every disease, our ontology-guided approach exploits shared visual information of body parts across diseases. In retrieving 2220 web images of 32 diseases, we reduced manual labeling effort to 15.6% while improving the average precision by 3.9% from 77.7% to 81.6%. For 40.6% of the diseases, we improved the precision by 10%. The results confirm the concept that the web is a feasible source for automatic disease image retrieval for health image database construction. Our approach requires a small amount of manual effort to collect complex disease images, and to annotate them by standard medical ontology terms.

Biomedical Ontologies in Action: Role in Knowledge Management, Data Integration and Decision Support

PubMed Central

Bodenreider, O.

2008-01-01

Summary Objectives To provide typical examples of biomedical ontologies in action, emphasizing the role played by biomedical ontologies in knowledge management, data integration and decision support. Methods Biomedical ontologies selected for their practical impact are examined from a functional perspective. Examples of applications are taken from operational systems and the biomedical literature, with a bias towards recent journal articles. Results The ontologies under investigation in this survey include SNOMED CT, the Logical Observation Identifiers, Names, and Codes (LOINC), the Foundational Model of Anatomy, the Gene Ontology, RxNorm, the National Cancer Institute Thesaurus, the International Classification of Diseases, the Medical Subject Headings (MeSH) and the Unified Medical Language System (UMLS). The roles played by biomedical ontologies are classified into three major categories: knowledge management (indexing and retrieval of data and information, access to information, mapping among ontologies); data integration, exchange and semantic interoperability; and decision support and reasoning (data selection and aggregation, decision support, natural language processing applications, knowledge discovery). Conclusions Ontologies play an important role in biomedical research through a variety of applications. While ontologies are used primarily as a source of vocabulary for standardization and integration purposes, many applications also use them as a source of computable knowledge. Barriers to the use of ontologies in biomedical applications are discussed. PMID:18660879

Effect of different fermentation strategies on β-mannanase production in fed-batch bioreactor system.

PubMed

Germec, Mustafa; Yatmaz, Ercan; Karahalil, Ercan; Turhan, İrfan

2017-05-01

Mannanases, one of the important enzyme group for industry, are produced by numerous filamentous fungi, especially Aspergillus species with different fermentation methods. The aim of this study was to show the best fermentation method of β-mannanase production for fungal growth in fermenter. Therefore, different fermentation strategies in fed-batch fermentation (suspended, immobilized cell, biofilm and microparticle-enhanced bioreactor) were applied for β-mannanase production from glucose medium (GM) and carob extract medium (CEM) by using recombinant Aspergillus sojae. The highest β-mannanase activities were obtained from microparticle-enhanced bioreactor strategy. It was found to be 347.47 U/mL by adding 10 g/L of Al 2 O 3 to GM and 439.13 U/mL by adding 1 g/L of talcum into CEM. The maximum β-mannanase activities for suspended, immobilization, and biofilm reactor remained at 72.55 U/mL in GM, 148.81 U/mL in CEM, and 194.09 U/mL in GM, respectively. The reason for that is the excessive, and irregular shaped growth and bulk formation, inadequate oxygen transfer or substrate diffusion in bioreactor. Consequently, the enzyme activity was significantly enhanced by addition of microparticles compared to other fed-batch fermentation strategies. Also, repeatable β-mannanase activities were obtained by controlling of the cell morphology by adding microparticle inside the fermenter.

Sculpting the UMLS Refined Semantic Network

PubMed Central

Morrey, C. Paul; Perl, Yehoshua; Elhanan, Gai; Chen, Ling; Chen, Yan; Geller, James

2014-01-01

Background The Refined Semantic Network (RSN) for the UMLS was previously introduced to complement the UMLS Semantic Network (SN). The RSN partitions the UMLS Metathesaurus (META) into disjoint groups of concepts. Each such group is semantically uniform. However, the RSN was initially an order of magnitude larger than the SN, which is undesirable since to be useful, a semantic network should be compact. Most semantic types in the RSN represent combinations of semantic types in the UMLS SN. Such a “combination semantic type” is called Intersection Semantic Type (IST). Many ISTs are assigned to very few concepts. Moreover, when reviewing those concepts, many semantic type assignment inconsistencies were found. After correcting those inconsistencies many ISTs, among them some that contradicted UMLS rules, disappeared, which made the RSN smaller. Objective The authors performed a longitudinal study with the goal of reducing the size of the RSN to become compact. This goal was achieved by correcting inconsistencies and errors in the IST assignments in the UMLS, which additionally helped identify and correct ambiguities, inconsistencies, and errors in source terminologies widely used in the realm of public health. Methods In this paper, we discuss the process and steps employed in this longitudinal study and the intermediate results for different stages. The sculpting process includes removing redundant semantic type assignments, expanding semantic type assignments, and removing illegitimate ISTs by auditing ISTs of small extents. However, the emphasis of this paper is not on the auditing methodologies employed during the process, since they were introduced in earlier publications, but on the strategy of employing them in order to transform the RSN into a compact network. For this paper we also performed a comprehensive audit of 168 “small ISTs” in the 2013AA version of the UMLS to finalize the longitudinal study. Results Over the years it was found that the editors of the UMLS introduced some new inconsistencies that resulted in the reintroduction of unwarranted ISTs that had already been eliminated as a result of their previous corrections. Because of that, the transformation of the RSN into a compact network covering all necessary categories for the UMLS was slowed down. The corrections suggested by an audit of the 2013AA version of the UMLS achieve a compact RSN of equal magnitude as the UMLS SN. The number of ISTs has been reduced to 336. We also demonstrate how auditing the semantic type assignments of UMLS concepts can expose other modeling errors in the UMLS source terminologies, e.g., SNOMED CT, LOINC, and RxNORM that are important for health informatics. Such errors would otherwise stay hidden. Conclusions It is hoped that the UMLS curators will implement all required corrections and use the RSN along with the SN when maintaining and extending the UMLS. When used correctly, the RSN will support the prevention of the accidental introduction of inconsistent semantic type assignments into the UMLS. Furthermore, this way the RSN will support the exposure of other hidden errors and inconsistencies in health informatics terminologies, which are sources of the UMLS. Notably, the development of the RSN materializes the deeper, more refined Semantic Network for the UMLS that its designers envisioned originally but had not implemented. PMID:25422719

Modeling traceability information and functionality requirement in export-oriented tilapia chain.

PubMed

Zhang, Xiaoshuan; Feng, Jianying; Xu, Mark; Hu, Jinyou

2011-05-01

Tilapia has been named as the 'food fish of the 21st century' and has become the most important farmed fish. China is the world leader in tilapia production and export. Identifying information and functional requirements is critical in developing an efficient traceability system because traceability has become a fundamental prerequisite for exporting aquaculture products. This paper examines the export-oriented tilapia chains and information flow in the chains, and identifies the key actors, information requirements and information-capturing points. Unified Modeling Language (UML) technology is adopted to describe the information and functionality requirement for chain traceability. The barriers of traceability system adoption are also identified. The results show that the traceability data consist of four categories that must be recorded by each link in the chain. The functionality requirement is classified into four categories from the fundamental information record to decisive quality control; the top three barriers to the traceability system adoption are: high costs of implementing the system, lack of experienced and professional staff; and low level of government involvement and support. Copyright © 2011 Society of Chemical Industry.

Requirements' Role in Mobilizing and Enabling Design Conversation

NASA Astrophysics Data System (ADS)

Bergman, Mark

Requirements play a critical role in a design conversation of systems and products. Product and system design exists at the crossroads of problems, solutions and requirements. Requirements contextualize problems and solutions, pointing the way to feasible outcomes. These are captured with models and detailed specifications. Still, stakeholders need to be able to understand one-another using shared design representations in order to mobilize bias and transform knowledge towards legitimized, desired results. Many modern modeling languages, including UML, as well as detailed, logic-based specifications are beyond the comprehension of key stakeholders. Hence, they inhibit, rather than promote design conversation. Improved design boundary objects (DBO), especially design requirements boundary objects (DRBO), need to be created and refined to improve the communications between principals. Four key features of design boundary objects that improve and promote design conversation are discussed in detail. A systems analysis and design case study is presented which demonstrates these features in action. It describes how a small team of analysts worked with key stakeholders to mobilize and guide a complex system design discussion towards an unexpected, yet desired outcome within a short time frame.

Logic-based assessment of the compatibility of UMLS ontology sources

PubMed Central

2011-01-01

Background The UMLS Metathesaurus (UMLS-Meta) is currently the most comprehensive effort for integrating independently-developed medical thesauri and ontologies. UMLS-Meta is being used in many applications, including PubMed and ClinicalTrials.gov. The integration of new sources combines automatic techniques, expert assessment, and auditing protocols. The automatic techniques currently in use, however, are mostly based on lexical algorithms and often disregard the semantics of the sources being integrated. Results In this paper, we argue that UMLS-Meta’s current design and auditing methodologies could be significantly enhanced by taking into account the logic-based semantics of the ontology sources. We provide empirical evidence suggesting that UMLS-Meta in its 2009AA version contains a significant number of errors; these errors become immediately apparent if the rich semantics of the ontology sources is taken into account, manifesting themselves as unintended logical consequences that follow from the ontology sources together with the information in UMLS-Meta. We then propose general principles and specific logic-based techniques to effectively detect and repair such errors. Conclusions Our results suggest that the methodologies employed in the design of UMLS-Meta are not only very costly in terms of human effort, but also error-prone. The techniques presented here can be useful for both reducing human effort in the design and maintenance of UMLS-Meta and improving the quality of its contents. PMID:21388571

Biomedical Terminology Mapper for UML projects.

PubMed

Thibault, Julien C; Frey, Lewis

2013-01-01

As the biomedical community collects and generates more and more data, the need to describe these datasets for exchange and interoperability becomes crucial. This paper presents a mapping algorithm that can help developers expose local implementations described with UML through standard terminologies. The input UML class or attribute name is first normalized and tokenized, then lookups in a UMLS-based dictionary are performed. For the evaluation of the algorithm 142 UML projects were extracted from caGrid and automatically mapped to National Cancer Institute (NCI) terminology concepts. Resulting mappings at the UML class and attribute levels were compared to the manually curated annotations provided in caGrid. Results are promising and show that this type of algorithm could speed-up the tedious process of mapping local implementations to standard biomedical terminologies.

Biomedical Terminology Mapper for UML projects

PubMed Central

Thibault, Julien C.; Frey, Lewis

As the biomedical community collects and generates more and more data, the need to describe these datasets for exchange and interoperability becomes crucial. This paper presents a mapping algorithm that can help developers expose local implementations described with UML through standard terminologies. The input UML class or attribute name is first normalized and tokenized, then lookups in a UMLS-based dictionary are performed. For the evaluation of the algorithm 142 UML projects were extracted from caGrid and automatically mapped to National Cancer Institute (NCI) terminology concepts. Resulting mappings at the UML class and attribute levels were compared to the manually curated annotations provided in caGrid. Results are promising and show that this type of algorithm could speed-up the tedious process of mapping local implementations to standard biomedical terminologies. PMID:24303278

A passage retrieval method based on probabilistic information retrieval model and UMLS concepts in biomedical question answering.

PubMed

Sarrouti, Mourad; Ouatik El Alaoui, Said

2017-04-01

Passage retrieval, the identification of top-ranked passages that may contain the answer for a given biomedical question, is a crucial component for any biomedical question answering (QA) system. Passage retrieval in open-domain QA is a longstanding challenge widely studied over the last decades. However, it still requires further efforts in biomedical QA. In this paper, we present a new biomedical passage retrieval method based on Stanford CoreNLP sentence/passage length, probabilistic information retrieval (IR) model and UMLS concepts. In the proposed method, we first use our document retrieval system based on PubMed search engine and UMLS similarity to retrieve relevant documents to a given biomedical question. We then take the abstracts from the retrieved documents and use Stanford CoreNLP for sentence splitter to make a set of sentences, i.e., candidate passages. Using stemmed words and UMLS concepts as features for the BM25 model, we finally compute the similarity scores between the biomedical question and each of the candidate passages and keep the N top-ranked ones. Experimental evaluations performed on large standard datasets, provided by the BioASQ challenge, show that the proposed method achieves good performances compared with the current state-of-the-art methods. The proposed method significantly outperforms the current state-of-the-art methods by an average of 6.84% in terms of mean average precision (MAP). We have proposed an efficient passage retrieval method which can be used to retrieve relevant passages in biomedical QA systems with high mean average precision. Copyright © 2017 Elsevier Inc. All rights reserved.

White organic light-emitting diodes with ultra-thin mixed emitting layer

NASA Astrophysics Data System (ADS)

Jeon, T.; Forget, S.; Chenais, S.; Geffroy, B.; Tondelier, D.; Bonnassieux, Y.; Ishow, E.

2012-02-01

White light can be obtained from Organic Light Emitting Diodes by mixing three primary colors, (i.e. red, green and blue) or two complementary colors in the emissive layer. In order to improve the efficiency and stability of the devices, a host-guest system is generally used as an emitting layer. However, the color balance to obtain white light is difficult to control and optimize because the spectrum is very sensitive to doping concentration (especially when a small amount of material is used). We use here an ultra-thin mixed emitting layer (UML) deposited by thermal evaporation to fabricate white organic light emitting diodes (WOLEDs) without co-evaporation. The UML was inserted in the hole-transporting layer consisting of 4, 4'-bis[N-(1-naphtyl)-N-phenylamino]biphenyl (α-NPB) instead of using a conventional doping process. The UML was formed from a single evaporation boat containing a mixture of two dipolar starbust triarylamine molecules (fvin and fcho) presenting very similar structures and thermal properties and emitting in complementary spectral regions (orange and blue respectively) and mixed according to their weight ratio. The composition of the UML specifically allows for fine tuning of the emission color despite its very thin thickness down to 1 nm. Competitive energy transfer processes from fcho and the host interface toward fvin are key parameters to control the relative intensity between red and blue emission. White light with very good CIE 1931 color coordinate (0.34, 0.34) was obtained by simply adjusting the UML film composition.

Conceptual Model of Clinical Governance Information System for Statistical Indicators by Using UML in Two Sample Hospitals.

PubMed

Jeddi, Fatemeh Rangraz; Farzandipoor, Mehrdad; Arabfard, Masoud; Hosseini, Azam Haj Mohammad

2014-04-01

The purpose of this study was investigating situation and presenting a conceptual model for clinical governance information system by using UML in two sample hospitals. However, use of information is one of the fundamental components of clinical governance; but unfortunately, it does not pay much attention to information management. A cross sectional study was conducted in October 2012- May 2013. Data were gathered through questionnaires and interviews in two sample hospitals. Face and content validity of the questionnaire has been confirmed by experts. Data were collected from a pilot hospital and reforms were carried out and Final questionnaire was prepared. Data were analyzed by descriptive statistics and SPSS 16 software. With the scenario derived from questionnaires, UML diagrams are presented by using Rational Rose 7 software. The results showed that 32.14 percent Indicators of the hospitals were calculated. Database was not designed and 100 percent of the hospital's clinical governance was required to create a database. Clinical governance unit of hospitals to perform its mission, do not have access to all the needed indicators. Defining of Processes and drawing of models and creating of database are essential for designing of information systems.

Conceptual Model of Clinical Governance Information System for Statistical Indicators by Using UML in Two Sample Hospitals.

PubMed

Jeddi, Fatemeh Rangraz; Farzandipoor, Mehrdad; Arabfard, Masoud; Hosseini, Azam Haj Mohammad

2016-04-01

The purpose of this study was investigating situation and presenting a conceptual model for clinical governance information system by using UML in two sample hospitals. However, use of information is one of the fundamental components of clinical governance; but unfortunately, it does not pay much attention to information management. A cross sectional study was conducted in October 2012- May 2013. Data were gathered through questionnaires and interviews in two sample hospitals. Face and content validity of the questionnaire has been confirmed by experts. Data were collected from a pilot hospital and reforms were carried out and Final questionnaire was prepared. Data were analyzed by descriptive statistics and SPSS 16 software. With the scenario derived from questionnaires, UML diagrams are presented by using Rational Rose 7 software. The results showed that 32.14 percent Indicators of the hospitals were calculated. Database was not designed and 100 percent of the hospital's clinical governance was required to create a database. Clinical governance unit of hospitals to perform its mission, do not have access to all the needed indicators. Defining of Processes and drawing of models and creating of database are essential for designing of information systems.

Creating Shareable Clinical Decision Support Rules for a Pharmacogenomics Clinical Guideline Using Structured Knowledge Representation.

PubMed

Linan, Margaret K; Sottara, Davide; Freimuth, Robert R

2015-01-01

Pharmacogenomics (PGx) guidelines contain drug-gene relationships, therapeutic and clinical recommendations from which clinical decision support (CDS) rules can be extracted, rendered and then delivered through clinical decision support systems (CDSS) to provide clinicians with just-in-time information at the point of care. Several tools exist that can be used to generate CDS rules that are based on computer interpretable guidelines (CIG), but none have been previously applied to the PGx domain. We utilized the Unified Modeling Language (UML), the Health Level 7 virtual medical record (HL7 vMR) model, and standard terminologies to represent the semantics and decision logic derived from a PGx guideline, which were then mapped to the Health eDecisions (HeD) schema. The modeling and extraction processes developed here demonstrate how structured knowledge representations can be used to support the creation of shareable CDS rules from PGx guidelines.

A model for indexing medical documents combining statistical and symbolic knowledge.

PubMed

Avillach, Paul; Joubert, Michel; Fieschi, Marius

2007-10-11

To develop and evaluate an information processing method based on terminologies, in order to index medical documents in any given documentary context. We designed a model using both symbolic general knowledge extracted from the Unified Medical Language System (UMLS) and statistical knowledge extracted from a domain of application. Using statistical knowledge allowed us to contextualize the general knowledge for every particular situation. For each document studied, the extracted terms are ranked to highlight the most significant ones. The model was tested on a set of 17,079 French standardized discharge summaries (SDSs). The most important ICD-10 term of each SDS was ranked 1st or 2nd by the method in nearly 90% of the cases. The use of several terminologies leads to more precise indexing. The improvement achieved in the models implementation performances as a result of using semantic relationships is encouraging.

A Model for Indexing Medical Documents Combining Statistical and Symbolic Knowledge.

PubMed Central

Avillach, Paul; Joubert, Michel; Fieschi, Marius

2007-01-01

OBJECTIVES: To develop and evaluate an information processing method based on terminologies, in order to index medical documents in any given documentary context. METHODS: We designed a model using both symbolic general knowledge extracted from the Unified Medical Language System (UMLS) and statistical knowledge extracted from a domain of application. Using statistical knowledge allowed us to contextualize the general knowledge for every particular situation. For each document studied, the extracted terms are ranked to highlight the most significant ones. The model was tested on a set of 17,079 French standardized discharge summaries (SDSs). RESULTS: The most important ICD-10 term of each SDS was ranked 1st or 2nd by the method in nearly 90% of the cases. CONCLUSIONS: The use of several terminologies leads to more precise indexing. The improvement achieved in the model’s implementation performances as a result of using semantic relationships is encouraging. PMID:18693792

Knowledge-based approaches to the maintenance of a large controlled medical terminology.

PubMed Central

Cimino, J J; Clayton, P D; Hripcsak, G; Johnson, S B

1994-01-01

OBJECTIVE: Develop a knowledge-based representation for a controlled terminology of clinical information to facilitate creation, maintenance, and use of the terminology. DESIGN: The Medical Entities Dictionary (MED) is a semantic network, based on the Unified Medical Language System (UMLS), with a directed acyclic graph to represent multiple hierarchies. Terms from four hospital systems (laboratory, electrocardiography, medical records coding, and pharmacy) were added as nodes in the network. Additional knowledge about terms, added as semantic links, was used to assist in integration, harmonization, and automated classification of disparate terminologies. RESULTS: The MED contains 32,767 terms and is in active clinical use. Automated classification was successfully applied to terms for laboratory specimens, laboratory tests, and medications. One benefit of the approach has been the automated inclusion of medications into multiple pharmacologic and allergenic classes that were not present in the pharmacy system. Another benefit has been the reduction of maintenance efforts by 90%. CONCLUSION: The MED is a hybrid of terminology and knowledge. It provides domain coverage, synonymy, consistency of views, explicit relationships, and multiple classification while preventing redundancy, ambiguity (homonymy) and misclassification. PMID:7719786

Building a knowledge base of severe adverse drug events based on AERS reporting data using semantic web technologies.

PubMed

Jiang, Guoqian; Wang, Liwei; Liu, Hongfang; Solbrig, Harold R; Chute, Christopher G

2013-01-01

A semantically coded knowledge base of adverse drug events (ADEs) with severity information is critical for clinical decision support systems and translational research applications. However it remains challenging to measure and identify the severity information of ADEs. The objective of the study is to develop and evaluate a semantic web based approach for building a knowledge base of severe ADEs based on the FDA Adverse Event Reporting System (AERS) reporting data. We utilized a normalized AERS reporting dataset and extracted putative drug-ADE pairs and their associated outcome codes in the domain of cardiac disorders. We validated the drug-ADE associations using ADE datasets from SIDe Effect Resource (SIDER) and the UMLS. We leveraged the Common Terminology Criteria for Adverse Event (CTCAE) grading system and classified the ADEs into the CTCAE in the Web Ontology Language (OWL). We identified and validated 2,444 unique Drug-ADE pairs in the domain of cardiac disorders, of which 760 pairs are in Grade 5, 775 pairs in Grade 4 and 2,196 pairs in Grade 3.

EMSE at TREC 2015 Clinical Decision Support Track

DTIC Science & Technology

2015-11-20

pseudo relevant documents, semantic ressources of UMLS , and a hybrid approach called SMERA that combines LSI and UMLS based approaches. Only three of...approach to query expansion uses ontologies ( UMLS ) and a lo- cal approach based on pseudo relevant feedback documents using LSI. A brief description of...pseudo relevance feedback documents, and a semantic method based on UMLS concepts. The LSI-based method was used only to expand summary terms that can’t

Piecewise synonyms for enhanced UMLS source terminology integration.

PubMed

Huang, Kuo-Chuan; Geller, James; Halper, Michael; Cimino, James J

2007-10-11

The UMLS contains more than 100 source vocabularies and is growing via the integration of others. When integrating a new source, the source terms already in the UMLS must first be found. The easiest approach to this is simple string matching. However, string matching usually does not find all concepts that should be found. A new methodology, based on the notion of piecewise synonyms, for enhancing the process of concept discovery in the UMLS is presented. This methodology is supported by first creating a general synonym dictionary based on the UMLS. Each multi-word source term is decomposed into its component words, allowing for the generation of separate synonyms for each word from the general synonym dictionary. The recombination of these synonyms into new terms creates an expanded pool of matching candidates for terms from the source. The methodology is demonstrated with respect to an existing UMLS source. It shows a 34% improvement over simple string matching.

The Preliminary Design of a Universal Martian Lander

NASA Technical Reports Server (NTRS)

Norman, Timothy L.; Gaskin, David; Adkins, Sean; MacDonnell, David; Ross, Enoch; Hashimoto, Kouichi; Miller, Loran; Sarick, John; Hicks, Jonathan; Parlock, Andrew;

CUILESS2016: a clinical corpus applying compositional normalization of text mentions.

PubMed

Osborne, John D; Neu, Matthew B; Danila, Maria I; Solorio, Thamar; Bethard, Steven J

2018-01-10

Traditionally text mention normalization corpora have normalized concepts to single ontology identifiers ("pre-coordinated concepts"). Less frequently, normalization corpora have used concepts with multiple identifiers ("post-coordinated concepts") but the additional identifiers have been restricted to a defined set of relationships to the core concept. This approach limits the ability of the normalization process to express semantic meaning. We generated a freely available corpus using post-coordinated concepts without a defined set of relationships that we term "compositional concepts" to evaluate their use in clinical text. We annotated 5397 disorder mentions from the ShARe corpus to SNOMED CT that were previously normalized as "CUI-less" in the "SemEval-2015 Task 14" shared task because they lacked a pre-coordinated mapping. Unlike the previous normalization method, we do not restrict concept mappings to a particular set of the Unified Medical Language System (UMLS) semantic types and allow normalization to occur to multiple UMLS Concept Unique Identifiers (CUIs). We computed annotator agreement and assessed semantic coverage with this method. We generated the largest clinical text normalization corpus to date with mappings to multiple identifiers and made it freely available. All but 8 of the 5397 disorder mentions were normalized using this methodology. Annotator agreement ranged from 52.4% using the strictest metric (exact matching) to 78.2% using a hierarchical agreement that measures the overlap of shared ancestral nodes. Our results provide evidence that compositional concepts can increase semantic coverage in clinical text. To our knowledge we provide the first freely available corpus of compositional concept annotation in clinical text.

Unambiguous UML Composite Structures: The OMEGA2 Experience

NASA Astrophysics Data System (ADS)

Ober, Iulian; Dragomir, Iulia

Starting from version 2.0, UML introduced hierarchical composite structures, which are a very expressive way of defining complex software architectures, but which have a very loosely defined semantics in the standard. In this paper we propose a set of consistency rules that ensure UML composite structures are unambiguous and can be given a precise semantics. Our primary application of the static consistency rules defined in this paper is within the OMEGA UML profile [6], but these rules are general and applicable to other hierarchical component models based on the same concepts, such as MARTE GCM or SysML. The rule set has been formalized in OCL and is currently used in the OMEGA UML compiler.

Does serum CA125 have clinical value for follow-up monitoring of postoperative patients with epithelial ovarian cancer? Results of a 12-year study.

PubMed

Guo, Na; Peng, Zhilan

2017-03-11

The detection of CA125 has been used in the follow up of ovarian cancer. At present, some scholars believe that serum CA125 has no clinical value for the follow-up monitoring the recurrence for postoperative patients with epithelial ovarian cancer, but in our clinical follow-up found that when the serum CA125 value is <35 U/ml, postoperative patients of epithelial ovarian carcinoma had already showed recurrent lesions in some ecological and imaging examinations or in laparotomy exploration and biopsy, and we given the patients timely treatment, the prognosis were improved. Retrospective analysis the values of serum CA125 of 342 postoperative patients of epithelial ovarian carcinoma, consisting of 296 non-recurrent and 46 recurrent cases, as well as 3175 cases of menopausal women and 603 cases of postoperative patients of gynecological malignant tumor for the follow-up from January 2005 to December 2016. The median value of CA125 for non-recurrent patients of epithelial ovarian carcinoma is 8.9 U/ml, the median value of CA125 for non-recurrent patients of epithelial ovarian carcinoma is 29.7 U/ml; for menopausal women, 8.1 U/ml; and for postoperative patients of gynecological malignant tumor, 7.2 U/ml, whereas the mean ± standard deviation is 9.0 ± 1.9 U/ml, 31.3 ± 16.2U/ml, 8.0 ± 1.1 U/ml, and 6.8 ± 2.1 U/ml, respectively. If the value of the CA125 for postoperative patients of epithelial ovarian carcinoma between 10 and 35 U/ml indicates a relative risk of recurrence. When the value of CA125 is higher than 10 U/ml and continuously increased, need to be vigilant and should be combined with imaging examination (PET-CT). This result may improve the prognosis for recurrent patients because of the early detection of recurrent lesions and early retreatment.

Elevated soluble MUC1 levels and decreased anti-MUC1 antibody levels in patients with multiple myeloma.

PubMed

Treon, S P; Maimonis, P; Bua, D; Young, G; Raje, N; Mollick, J; Chauhan, D; Tai, Y T; Hideshima, T; Shima, Y; Hilgers, J; von Mensdorff-Pouilly, S; Belch, A R; Pilarski, L M; Anderson, K C

2000-11-01

Soluble MUC1 (sMUC1) levels are elevated in many MUC1(+) cancers. We and others have shown that MUC1 is expressed on multiple myeloma (MM) plasma cells and B cells. In this study, we measured sMUC1 levels in bone marrow (BM) plasma from 71 MM patients and 21 healthy donors (HDs), and in peripheral blood (PB) plasma from 42 MM patients and 13 HDs using an immunoassay that detects the CA27.29 epitope of MUC1. sMUC1 levels were found to be significantly greater (mean 31.76 U/mL, range 5.69 to 142.48 U/mL) in MM patient BM plasma versus HD BM plasma (mean 9.68 U/mL, range 0.65 to 39.83 U/mL) (P <. 001). Importantly, BM plasma sMUC1 levels were related to tumor burden because sMUC1 levels were significantly higher for MM patients with active disease (34.62 U/mL, range 5.69 to 142.48 U/mL) versus MM patients with minimal residual disease (16.16 U/mL, range 5.7 to 56.68 U/mL) (P =.0026). sMUC1 levels were also elevated in the PB plasma of MM patients (32.79 U/mL, range 4.15 to 148.84 U/mL) versus HDs (18.47 U/mL, range 8.84 to 42.49) (P =.0052). Lastly, circulating immunglobulin M (IgM) and IgG antibodies to MUC1 were measured in 114 MM patients and 31 HDs, because natural antibodies to MUC1 have been detected in patients with other MUC1-bearing malignancies. These studies demonstrated lower levels of circulating IgM (P <.001) and IgG (P =.078) antibodies to MUC1 in MM patients compared with HDs. Our data therefore show that in MM patients, sMUC1 levels are elevated and correlate with disease burden, whereas anti-MUC1 antibody levels are decreased.

Old torsion Balance Observations - too old for modern Exploration?

NASA Astrophysics Data System (ADS)

Götze, H.-J.

2003-04-01

Gravity gradiometry is a new gravity measurement technology that could fundamentally change the game of subsurface modelling and enhance geological interpretations: at fully inertial stabilized platforms they provide observed components of the E&{uml;o}tv&{uml;o}s tensor for 3D interpretations in mining and oil exploration and other fields of pure and applied geophysics. Although gravity gradiometry was among the first geophysical methods used successfully in applied Geophysics (E&{uml;o}tv&{uml;o}s torsion balance), the technology fell from favour in the 1930s. From this time measurements, done by torsion balances (Drehwaagen), are presented here which were observed to detect salt domes in the Northwest German basin. The data were digitized from old copies, then reprocessed and recalculated to draw Bouguer anomaly maps. However, the second derivatives of the gravity potential provide also independent data which can be used to constrain forward modelling. 3D modelling of Vxz, Vyz and other components of the E&{uml;o}tv&{uml;o}s tensor provide better insight into the geometry of the salt dome structure than modelling of the Bouguer gravity field. In addition to this first example results from gravity data processing by applying curvature techniques and again 3D forward modelling of second derivatives of the potential of density domains in the uppermost crust in the area of the Dead Sea Transform (Jordan) is presented here. The 3D modelling is conducted by the program package IGMAS which supply possibilities to calculate potential, gravity, its components and the Eötvös tensor components. Based on results so far one can conclude that the knowledge of the "second derivatives of the potential" could fundamentally change the role of gravity field measurements in the process of underground investigations not only for resource exploration but for investigations along large faults systems.

Remodeling of legacy systems in health care using UML.

PubMed

Garde, Sebastian; Knaup, Petra; Herold, Ralf

2002-01-01

Research projects in the field of Medical Informatics often involve the development of application systems. Usually they are developed over a longer period of time, so that at a certain point of time a systematically planned reimplementation is necessary. The first step of reimplementation should be a systematic and comprehensive remodeling. When using UML for this task a systematic approach for remodeling activities is missing. Therefore, we developed a method for remodeling of legacy systems (Qumquad) and applied it to DOSPO, a documentation and therapy planning system for pediatric oncology. Qumquad helps to systematically carry out three steps: the modeling of the current actual state of the application system, the systematic identification of weak points and the development of a target concept for reimplementation considering the identified weak points. Results show that this approach is valuable and feasible and could be applied to various application systems in health care.

Uncompacted myelin lamellae in peripheral nerve biopsy.

PubMed

Vital, Claude; Vital, Anne; Bouillot, Sandrine; Favereaux, Alexandre; Lagueny, Alain; Ferrer, Xavier; Brechenmacher, Christiane; Petry, Klaus G

2003-01-01

Since 1979, the authors have studied 49 peripheral nerve biopsies presenting uncompacted myelin lamellae (UML). Based on the ultrastructural pattern of UML they propose a 3-category classification. The first category includes cases displaying regular UML, which was observed in 43 cases; it was more frequent in 9 cases with polyneuropathy organomegaly endocrinopathy m-protein skin changes (POEMS) syndrome as well as in 1 case of Charcot-Marie-Tooth 1B with a novel point mutation in the P0 gene. The second category consists of cases showing irregular UML, observed in 4 cases with IgM monoclonal gammopathy and anti-myelin-associated glycoprotein (MAG) activity. This group included 1 benign case and 3 B-cell malignant lymphomas. The third category is complex UML, which was present in 2 unrelated patients with an Arg 98 His missense mutation in the P0 protein gene. Irregular and complex UML are respectively related to MAG and P0, which play a crucial role in myelin lamellae compaction and adhesion.

Conceptual Model of Clinical Governance Information System for Statistical Indicators by Using UML in Two Sample Hospitals

PubMed Central

Jeddi, Fatemeh Rangraz; Farzandipoor, Mehrdad; Arabfard, Masoud; Hosseini, Azam Haj Mohammad

2016-01-01

Objective: The purpose of this study was investigating situation and presenting a conceptual model for clinical governance information system by using UML in two sample hospitals. Background: However, use of information is one of the fundamental components of clinical governance; but unfortunately, it does not pay much attention to information management. Material and Methods: A cross sectional study was conducted in October 2012- May 2013. Data were gathered through questionnaires and interviews in two sample hospitals. Face and content validity of the questionnaire has been confirmed by experts. Data were collected from a pilot hospital and reforms were carried out and Final questionnaire was prepared. Data were analyzed by descriptive statistics and SPSS 16 software. Results: With the scenario derived from questionnaires, UML diagrams are presented by using Rational Rose 7 software. The results showed that 32.14 percent Indicators of the hospitals were calculated. Database was not designed and 100 percent of the hospital’s clinical governance was required to create a database. Conclusion: Clinical governance unit of hospitals to perform its mission, do not have access to all the needed indicators. Defining of Processes and drawing of models and creating of database are essential for designing of information systems. PMID:27147804

Conceptual Model of Clinical Governance Information System for Statistical Indicators by Using UML in Two Sample Hospitals

PubMed Central

Jeddi, Fatemeh Rangraz; Farzandipoor, Mehrdad; Arabfard, Masoud; Hosseini, Azam Haj Mohammad

2014-01-01

Objective: The purpose of this study was investigating situation and presenting a conceptual model for clinical governance information system by using UML in two sample hospitals. Background: However, use of information is one of the fundamental components of clinical governance; but unfortunately, it does not pay much attention to information management. Material and Methods: A cross sectional study was conducted in October 2012- May 2013. Data were gathered through questionnaires and interviews in two sample hospitals. Face and content validity of the questionnaire has been confirmed by experts. Data were collected from a pilot hospital and reforms were carried out and Final questionnaire was prepared. Data were analyzed by descriptive statistics and SPSS 16 software. Results: With the scenario derived from questionnaires, UML diagrams are presented by using Rational Rose 7 software. The results showed that 32.14 percent Indicators of the hospitals were calculated. Database was not designed and 100 percent of the hospital’s clinical governance was required to create a database. Conclusion: Clinical governance unit of hospitals to perform its mission, do not have access to all the needed indicators. Defining of Processes and drawing of models and creating of database are essential for designing of information systems. PMID:24825933

Design of a web portal for interdisciplinary image retrieval from multiple online image resources.

PubMed

Kammerer, F J; Frankewitsch, T; Prokosch, H-U

2009-01-01

Images play an important role in medicine. Finding the desired images within the multitude of online image databases is a time-consuming and frustrating process. Existing websites do not meet all the requirements for an ideal learning environment for medical students. This work intends to establish a new web portal providing a centralized access point to a selected number of online image databases. A back-end system locates images on given websites and extracts relevant metadata. The images are indexed using UMLS and the MetaMap system provided by the US National Library of Medicine. Specially developed functions allow to create individual navigation structures. The front-end system suits the specific needs of medical students. A navigation structure consisting of several medical fields, university curricula and the ICD-10 was created. The images may be accessed via the given navigation structure or using different search functions. Cross-references are provided by the semantic relations of the UMLS. Over 25,000 images were identified and indexed. A pilot evaluation among medical students showed good first results concerning the acceptance of the developed navigation structures and search features. The integration of the images from different sources into the UMLS semantic network offers a quick and an easy-to-use learning environment.

Assessing the role of a medication-indication resource in the treatment relation extraction from clinical text

PubMed Central

Bejan, Cosmin Adrian; Wei, Wei-Qi; Denny, Joshua C

2015-01-01

Objective To evaluate the contribution of the MEDication Indication (MEDI) resource and SemRep for identifying treatment relations in clinical text. Materials and methods We first processed clinical documents with SemRep to extract the Unified Medical Language System (UMLS) concepts and the treatment relations between them. Then, we incorporated MEDI into a simple algorithm that identifies treatment relations between two concepts if they match a medication-indication pair in this resource. For a better coverage, we expanded MEDI using ontology relationships from RxNorm and UMLS Metathesaurus. We also developed two ensemble methods, which combined the predictions of SemRep and the MEDI algorithm. We evaluated our selected methods on two datasets, a Vanderbilt corpus of 6864 discharge summaries and the 2010 Informatics for Integrating Biology and the Bedside (i2b2)/Veteran's Affairs (VA) challenge dataset. Results The Vanderbilt dataset included 958 manually annotated treatment relations. A double annotation was performed on 25% of relations with high agreement (Cohen's κ = 0.86). The evaluation consisted of comparing the manual annotated relations with the relations identified by SemRep, the MEDI algorithm, and the two ensemble methods. On the first dataset, the best F1-measure results achieved by the MEDI algorithm and the union of the two resources (78.7 and 80, respectively) were significantly higher than the SemRep results (72.3). On the second dataset, the MEDI algorithm achieved better precision and significantly lower recall values than the best system in the i2b2 challenge. The two systems obtained comparable F1-measure values on the subset of i2b2 relations with both arguments in MEDI. Conclusions Both SemRep and MEDI can be used to extract treatment relations from clinical text. Knowledge-based extraction with MEDI outperformed use of SemRep alone, but superior performance was achieved by integrating both systems. The integration of knowledge-based resources such as MEDI into information extraction systems such as SemRep and the i2b2 relation extractors may improve treatment relation extraction from clinical text. PMID:25336593

On Using SysML, DoDAF 2.0 and UPDM to Model the Architecture for the NOAA's Joint Polar Satellite System (JPSS) Ground System (GS)

NASA Technical Reports Server (NTRS)

Hayden, Jeffrey L.; Jeffries, Alan

2012-01-01

The JPSS Ground System is a lIexible system of systems responsible for telemetry, tracking & command (TT &C), data acquisition, routing and data processing services for a varied lIeet of satellites to support weather prediction, modeling and climate modeling. To assist in this engineering effort, architecture modeling tools are being employed to translate the former NPOESS baseline to the new JPSS baseline, The paper will focus on the methodology for the system engineering process and the use of these architecture modeling tools within that process, The Department of Defense Architecture Framework version 2,0 (DoDAF 2.0) viewpoints and views that are being used to describe the JPSS GS architecture are discussed. The Unified Profile for DoOAF and MODAF (UPDM) and Systems Modeling Language (SysML), as ' provided by extensions to the MagicDraw UML modeling tool, are used to develop the diagrams and tables that make up the architecture model. The model development process and structure are discussed, examples are shown, and details of handling the complexities of a large System of Systems (SoS), such as the JPSS GS, with an equally complex modeling tool, are described

Enhancing acronym/abbreviation knowledge bases with semantic information.

PubMed

Torii, Manabu; Liu, Hongfang

2007-10-11

In the biomedical domain, a terminology knowledge base that associates acronyms/abbreviations (denoted as SFs) with the definitions (denoted as LFs) is highly needed. For the construction such terminology knowledge base, we investigate the feasibility to build a system automatically assigning semantic categories to LFs extracted from text. Given a collection of pairs (SF,LF) derived from text, we i) assess the coverage of LFs and pairs (SF,LF) in the UMLS and justify the need of a semantic category assignment system; and ii) automatically derive name phrases annotated with semantic category and construct a system using machine learning. Utilizing ADAM, an existing collection of (SF,LF) pairs extracted from MEDLINE, our system achieved an f-measure of 87% when assigning eight UMLS-based semantic groups to LFs. The system has been incorporated into a web interface which integrates SF knowledge from multiple SF knowledge bases. Web site: http://gauss.dbb.georgetown.edu/liblab/SFThesurus.

Model-Driven Configuration of SELinux Policies

NASA Astrophysics Data System (ADS)

Agreiter, Berthold; Breu, Ruth

The need for access control in computer systems is inherent. However, the complexity to configure such systems is constantly increasing which affects the overall security of a system negatively. We think that it is important to define security requirements on a non-technical level while taking the application domain into respect in order to have a clear and separated view on security configuration (i.e. unblurred by technical details). On the other hand, security functionality has to be tightly integrated with the system and its development process in order to provide comprehensive means of enforcement. In this paper, we propose a systematic approach based on model-driven security configuration to leverage existing operating system security mechanisms (SELinux) for realising access control. We use UML models and develop a UML profile to satisfy these needs. Our goal is to exploit a comprehensive protection mechanism while rendering its security policy manageable by a domain specialist.

Improved production of an enzyme that hydrolyses raw yam starch by Penicillium sp. S-22 using fed-batch fermentation.

PubMed

Sun, Hai-Yan; Ge, Xiang-Yang; Zhang, Wei-Guo

2006-11-01

A newly isolated strain, Penicillium sp. S-22, was used to produce an enzyme that hydrolyses raw yam starch [raw yam starch digesting enzyme (RYSDE)]. The enzyme activity and overall enzyme productivity were respectively 16 U/ml and 0.19 U/ml h in the batch culture. The enzyme activity increased to 85 U/ml by feeding of partially hydrolyzed raw yam starch. When a mixture containing partially hydrolyzed raw yam starch and peptone was fed by a pH-stat strategy, the enzyme activity reached 366 U/ml, 23-fold of that obtained in the batch culture, and the overall productivity reached 3.4 U/ml h, which was 18-fold of that in the batch culture.

Co-occurrence graphs for word sense disambiguation in the biomedical domain.

PubMed

Duque, Andres; Stevenson, Mark; Martinez-Romo, Juan; Araujo, Lourdes

2018-05-01

Word sense disambiguation is a key step for many natural language processing tasks (e.g. summarization, text classification, relation extraction) and presents a challenge to any system that aims to process documents from the biomedical domain. In this paper, we present a new graph-based unsupervised technique to address this problem. The knowledge base used in this work is a graph built with co-occurrence information from medical concepts found in scientific abstracts, and hence adapted to the specific domain. Unlike other unsupervised approaches based on static graphs such as UMLS, in this work the knowledge base takes the context of the ambiguous terms into account. Abstracts downloaded from PubMed are used for building the graph and disambiguation is performed using the personalized PageRank algorithm. Evaluation is carried out over two test datasets widely explored in the literature. Different parameters of the system are also evaluated to test robustness and scalability. Results show that the system is able to outperform state-of-the-art knowledge-based systems, obtaining more than 10% of accuracy improvement in some cases, while only requiring minimal external resources. Copyright © 2018 Elsevier B.V. All rights reserved.

Meta-manager: a requirements analysis.

PubMed

Cook, J F; Rozenblit, J W; Chacko, A K; Martinez, R; Timboe, H L

1999-05-01

The digital imaging network-picture-archiving and communications system (DIN-PACS) will be implemented in ten sites within the Great Plains Regional Medical Command (GPRMC). This network of PACS and teleradiology technology over a shared T1 network has opened the door for round the clock radiology coverage of all sites. However, the concept of a virtual radiology environment poses new issues for military medicine. A new workflow management system must be developed. This workflow management system will allow us to efficiently resolve these issues including quality of care, availability, severe capitation, and quality of the workforce. The design process of this management system must employ existing technology, operate over various telecommunication networks and protocols, be independent of platform operating systems, be flexible and scaleable, and involve the end user at the outset in the design process for which it is developed. Using the unified modeling language (UML), the specifications for this new business management system were created in concert between the University of Arizona and the GPRMC. These specifications detail a management system operating through a common object request brokered architecture (CORBA) environment. In this presentation, we characterize the Meta-Manager management system including aspects of intelligence, interfacility routing, fail-safe operations, and expected improvements in patient care and efficiency.

DICOM static and dynamic representation through unified modeling language

NASA Astrophysics Data System (ADS)

Martinez-Martinez, Alfonso; Jimenez-Alaniz, Juan R.; Gonzalez-Marquez, A.; Chavez-Avelar, N.

2004-04-01

The DICOM standard, as all standards, specifies in generic way the management in network and storage media environments of digital medical images and their related information. However, understanding the specifications for particular implementation is not a trivial work. Thus, this work is about understanding and modelling parts of the DICOM standard using Object Oriented methodologies, as part of software development processes. This has offered different static and dynamic views, according with the standard specifications, and the resultant models have been represented through the Unified Modelling Language (UML). The modelled parts are related to network conformance claim: Network Communication Support for Message Exchange, Message Exchange, Information Object Definitions, Service Class Specifications, Data Structures and Encoding, and Data Dictionary. The resultant models have given a better understanding about DICOM parts and have opened the possibility of create a software library to develop DICOM conformable PACS applications.

A Journey in Standard Development: The Core Manufacturing Simulation Data (CMSD) Information Model.

PubMed

Lee, Yung-Tsun Tina

2015-01-01

This report documents a journey "from research to an approved standard" of a NIST-led standard development activity. That standard, Core Manufacturing Simulation Data (CMSD) information model, provides neutral structures for the efficient exchange of manufacturing data in a simulation environment. The model was standardized under the auspices of the international Simulation Interoperability Standards Organization (SISO). NIST started the research in 2001 and initiated the standardization effort in 2004. The CMSD standard was published in two SISO Products. In the first Product, the information model was defined in the Unified Modeling Language (UML) and published in 2010 as SISO-STD-008-2010. In the second Product, the information model was defined in Extensible Markup Language (XML) and published in 2013 as SISO-STD-008-01-2012. Both SISO-STD-008-2010 and SISO-STD-008-01-2012 are intended to be used together.

Coverage criteria for test case generation using UML state chart diagram

NASA Astrophysics Data System (ADS)

Salman, Yasir Dawood; Hashim, Nor Laily; Rejab, Mawarny Md; Romli, Rohaida; Mohd, Haslina

2017-10-01

To improve the effectiveness of test data generation during the software test, many studies have focused on the automation of test data generation from UML diagrams. One of these diagrams is the UML state chart diagram. Test cases are generally evaluated according to coverage criteria. However, combinations of multiple criteria are required to achieve better coverage. Different studies used various number and types of coverage criteria in their methods and approaches. The objective of this paper to propose suitable coverage criteria for test case generation using UML state chart diagram especially in handling loops. In order to achieve this objective, this work reviewed previous studies to present the most practical coverage criteria combinations, including all-states, all-transitions, all-transition-pairs, and all-loop-free-paths coverage. Calculation to determine the coverage percentage of the proposed coverage criteria were presented together with an example has they are applied on a UML state chart diagram. This finding would be beneficial in the area of test case generating especially in handling loops in UML state chart diagram.

Characterization of protease from bacillus sp. on medium containing FeCl3 exposed to magnetic field 0.2 mt

NASA Astrophysics Data System (ADS)

Sumardi; Agustrina, Rochmah; Nugroho Ekowati, Christina; Selvie Pasaribu, Yovita

2018-03-01

This purpose of this research is to determine the character of the protease enzymes from Bacillus sp. on media content of FeCl3 exposed to 0.2 mT magnetic field. The data obtained were analyzed descriptively. The result showed that protease enzyme without Fe resulted in the highest activity at pH 8, temperature. 30°C with the addition of activator Mn2+, and Vmax of 0.28 U/ml, and Km of 4.60 U/ml. The protease enzyme on media without magnetic field exposure and containing Fe yielded the highest activity at pH 8, temperature 30°C with the addition of activator Mn2+, and Vmax of 0.33 U/ml, and Km of 5.64 U/ml. The protease enzyme on medium with magnetic field exposure and use Fe as inductors have the highest activity at pH 9, the temperature of 55° C with the addition of activator Mn2+, and Vmax of 0.35 U/ml, and Km 10.04 U/ml.

Characterizing the reliability of a bioMEMS-based cantilever sensor

NASA Astrophysics Data System (ADS)

Bhalerao, Kaustubh D.

2004-12-01

The cantilever-based BioMEMS sensor represents one instance from many competing ideas of biosensor technology based on Micro Electro Mechanical Systems. The advancement of BioMEMS from laboratory-scale experiments to applications in the field will require standardization of their components and manufacturing procedures as well as frameworks to evaluate their performance. Reliability, the likelihood with which a system performs its intended task, is a compact mathematical description of its performance. The mathematical and statistical foundation of systems-reliability has been applied to the cantilever-based BioMEMS sensor. The sensor is designed to detect one aspect of human ovarian cancer, namely the over-expression of the folate receptor surface protein (FR-alpha). Even as the application chosen is clinically motivated, the objective of this study was to demonstrate the underlying systems-based methodology used to design, develop and evaluate the sensor. The framework development can be readily extended to other BioMEMS-based devices for disease detection and will have an impact in the rapidly growing $30 bn industry. The Unified Modeling Language (UML) is a systems-based framework for design and development of object-oriented information systems which has potential application for use in systems designed to interact with biological environments. The UML has been used to abstract and describe the application of the biosensor, to identify key components of the biosensor, and the technology needed to link them together in a coherent manner. The use of the framework is also demonstrated in computation of system reliability from first principles as a function of the structure and materials of the biosensor. The outcomes of applying the systems-based framework to the study are the following: (1) Characterizing the cantilever-based MEMS device for disease (cell) detection. (2) Development of a novel chemical interface between the analyte and the sensor that provides a degree of selectivity towards the disease. (3) Demonstrating the performance and measuring the reliability of the biosensor prototype, and (4) Identification of opportunities in technological development in order to further refine the proposed biosensor. Application of the methodology to design develop and evaluate the reliability of BioMEMS devices will be beneficial in the streamlining the growth of the BioMEMS industry, while providing a decision-support tool in comparing and adopting suitable technologies from available competing options.

Nutrient utilisation and particulate organic matter changes during summer in the upper mixed layer (Ross Sea, Antarctica)

NASA Astrophysics Data System (ADS)

Catalano, G.; Povero, P.; Fabiano, M.; Benedetti, F.; Goffart, A.

1997-01-01

The relationships among vertical stability, estimated nutrient utilisation and particulate organic matter in the Ross Sea are analysed from data collected during two cruises in the summers of 1987-1988 and 1989-1990. In the upper mixed layer (UML), identified through the vertical stability E( Z(UML)), nutrient consumption is calculated as the difference between the "diluted" nutrient value and the mean calculated from the integrated value in the UML. The nutrient utilisation ratio and E( Z(UML)) are linearly related for E( Z(UML))≤25, whereas for values > 25, the distribution pattern is more scattered and independent of E( Z(UML)). For E( Z(UML))≥25, utilisation values were ≥4, 0.4 and 10 mmol m -3 for nitrate, phosphate and silicate, respectively. Significant relationships between nutrient depletion and both particulate organic carbon (POC) and particulate protein/particulate carbohydrate ratios (PPRT/PCHO) are found. The analysis of particulate matter distribution vs nutrient utilisation shows that the stations could be divided into two groups having different characteristics. The first group includes coastal stations, where high nutrient utilisation, POC and PPRT/PCHO are typical of areas with high production. In the second group (pelagic stations), nutrient utilisation, POC and PPRT/PCHO are lower. The vertical stability can be used to discriminate among the factors that influence primary production.

Semantic transference for enriching multilingual biomedical knowledge resources.

PubMed

Pérez, María; Berlanga, Rafael

2015-12-01

Biomedical knowledge resources (KRs) are mainly expressed in English, and many applications using them suffer from the scarcity of knowledge in non-English languages. The goal of the present work is to take maximum profit from existing multilingual biomedical KRs lexicons to enrich their non-English counterparts. We propose to combine different automatic methods to generate pair-wise language alignments. More specifically, we use two well-known translation methods (GIZA++ and Moses), and we propose a new ad hoc method specially devised for multilingual KRs. Then, resulting alignments are used to transfer semantics between KRs across their languages. Transference quality is ensured by checking the semantic coherence of the generated alignments. Experiments have been carried out over the Spanish, French and German UMLS Metathesaurus counterparts. As a result, the enriched Spanish KR can grow up to 1,514,217 concepts (originally 286,659), the French KR up to 1,104,968 concepts (originally 83,119), and the German KR up to 1,136,020 concepts (originally 86,842). Copyright © 2015 Elsevier Inc. All rights reserved.

A future Outlook: Web based Simulation of Hydrodynamic models

NASA Astrophysics Data System (ADS)

Islam, A. S.; Piasecki, M.

2003-12-01

Despite recent advances to present simulation results as 3D graphs or animation contours, the modeling user community still faces some shortcomings when trying to move around and analyze data. Typical problems include the lack of common platforms with standard vocabulary to exchange simulation results from different numerical models, insufficient descriptions about data (metadata), lack of robust search and retrieval tools for data, and difficulties to reuse simulation domain knowledge. This research demonstrates how to create a shared simulation domain in the WWW and run a number of models through multi-user interfaces. Firstly, meta-datasets have been developed to describe hydrodynamic model data based on geographic metadata standard (ISO 19115) that has been extended to satisfy the need of the hydrodynamic modeling community. The Extended Markup Language (XML) is used to publish this metadata by the Resource Description Framework (RDF). Specific domain ontology for Web Based Simulation (WBS) has been developed to explicitly define vocabulary for the knowledge based simulation system. Subsequently, this knowledge based system is converted into an object model using Meta Object Family (MOF). The knowledge based system acts as a Meta model for the object oriented system, which aids in reusing the domain knowledge. Specific simulation software has been developed based on the object oriented model. Finally, all model data is stored in an object relational database. Database back-ends help store, retrieve and query information efficiently. This research uses open source software and technology such as Java Servlet and JSP, Apache web server, Tomcat Servlet Engine, PostgresSQL databases, Protégé ontology editor, RDQL and RQL for querying RDF in semantic level, Jena Java API for RDF. Also, we use international standards such as the ISO 19115 metadata standard, and specifications such as XML, RDF, OWL, XMI, and UML. The final web based simulation product is deployed as Web Archive (WAR) files which is platform and OS independent and can be used by Windows, UNIX, or Linux. Keywords: Apache, ISO 19115, Java Servlet, Jena, JSP, Metadata, MOF, Linux, Ontology, OWL, PostgresSQL, Protégé, RDF, RDQL, RQL, Tomcat, UML, UNIX, Windows, WAR, XML

CoLeMo: A Collaborative Learning Environment for UML Modelling

ERIC Educational Resources Information Center

Chen, Weiqin; Pedersen, Roger Heggernes; Pettersen, Oystein

2006-01-01

This paper presents the design, implementation, and evaluation of a distributed collaborative UML modelling environment, CoLeMo. CoLeMo is designed for students studying UML modelling. It can also be used as a platform for collaborative design of software. We conducted formative evaluations and a summative evaluation to improve the environment and…

Feasibility of feature-based indexing, clustering, and search of clinical trials: A case study of breast cancer trials from ClinicalTrials.gov

PubMed Central

Boland, Mary Regina; Miotto, Riccardo; Gao, Junfeng; Weng, Chunhua

2013-01-01

Summary Background When standard therapies fail, clinical trials provide experimental treatment opportunities for patients with drug-resistant illnesses or terminal diseases. Clinical Trials can also provide free treatment and education for individuals who otherwise may not have access to such care. To find relevant clinical trials, patients often search online; however, they often encounter a significant barrier due to the large number of trials and in-effective indexing methods for reducing the trial search space. Objectives This study explores the feasibility of feature-based indexing, clustering, and search of clinical trials and informs designs to automate these processes. Methods We decomposed 80 randomly selected stage III breast cancer clinical trials into a vector of eligibility features, which were organized into a hierarchy. We clustered trials based on their eligibility feature similarities. In a simulated search process, manually selected features were used to generate specific eligibility questions to filter trials iteratively. Results We extracted 1,437 distinct eligibility features and achieved an inter-rater agreement of 0.73 for feature extraction for 37 frequent features occurring in more than 20 trials. Using all the 1,437 features we stratified the 80 trials into six clusters containing trials recruiting similar patients by patient-characteristic features, five clusters by disease-characteristic features, and two clusters by mixed features. Most of the features were mapped to one or more Unified Medical Language System (UMLS) concepts, demonstrating the utility of named entity recognition prior to mapping with the UMLS for automatic feature extraction. Conclusions It is feasible to develop feature-based indexing and clustering methods for clinical trials to identify trials with similar target populations and to improve trial search efficiency. PMID:23666475

Feasibility of feature-based indexing, clustering, and search of clinical trials. A case study of breast cancer trials from ClinicalTrials.gov.

PubMed

Boland, M R; Miotto, R; Gao, J; Weng, C

2013-01-01

When standard therapies fail, clinical trials provide experimental treatment opportunities for patients with drug-resistant illnesses or terminal diseases. Clinical Trials can also provide free treatment and education for individuals who otherwise may not have access to such care. To find relevant clinical trials, patients often search online; however, they often encounter a significant barrier due to the large number of trials and in-effective indexing methods for reducing the trial search space. This study explores the feasibility of feature-based indexing, clustering, and search of clinical trials and informs designs to automate these processes. We decomposed 80 randomly selected stage III breast cancer clinical trials into a vector of eligibility features, which were organized into a hierarchy. We clustered trials based on their eligibility feature similarities. In a simulated search process, manually selected features were used to generate specific eligibility questions to filter trials iteratively. We extracted 1,437 distinct eligibility features and achieved an inter-rater agreement of 0.73 for feature extraction for 37 frequent features occurring in more than 20 trials. Using all the 1,437 features we stratified the 80 trials into six clusters containing trials recruiting similar patients by patient-characteristic features, five clusters by disease-characteristic features, and two clusters by mixed features. Most of the features were mapped to one or more Unified Medical Language System (UMLS) concepts, demonstrating the utility of named entity recognition prior to mapping with the UMLS for automatic feature extraction. It is feasible to develop feature-based indexing and clustering methods for clinical trials to identify trials with similar target populations and to improve trial search efficiency.

Expanding the Extent of a UMLS Semantic Type via Group Neighborhood Auditing

PubMed Central

Chen, Yan; Gu, Huanying; Perl, Yehoshua; Halper, Michael; Xu, Junchuan

2009-01-01

Objective Each Unified Medical Language System (UMLS) concept is assigned one or more semantic types (ST). A dynamic methodology for aiding an auditor in finding concepts that are missing the assignment of a given ST, S is presented. Design The first part of the methodology exploits the previously introduced Refined Semantic Network and accompanying refined semantic types (RST) to help narrow the search space for offending concepts. The auditing is focused in a neighborhood surrounding the extent of an RST, T (of S) called an envelope, consisting of parents and children of concepts in the extent. The audit moves outward as long as missing assignments are discovered. In the second part, concepts not reached previously are processed and reassigned T as needed during the processing of S's other RSTs. The set of such concepts is expanded in a similar way to that in the first part. Measurements The number of errors discovered is reported. To measure the methodology's efficiency, “error hit rates” (i.e., errors found in concepts examined) are computed. Results The methodology was applied to three STs: Experimental Model of Disease (EMD), Environmental Effect of Humans, and Governmental or Regulatory Activity. The EMD experienced the most drastic change. For its RST “EMD ∩ Neoplastic Process” (RST “EMD”) with only 33 (31) original concepts, 915 (134) concepts were found by the first (second) part to be missing the EMD assignment. Changes to the other two STs were smaller. Conclusion The results show that the proposed auditing methodology can help to effectively and efficiently identify concepts lacking the assignment of a particular semantic type. PMID:19567802

Technical Data Exchange Software Tools Adapted to Distributed Microsatellite Design

NASA Astrophysics Data System (ADS)

Pache, Charly

2002-01-01

One critical issue concerning distributed design of satellites, is the collaborative work it requires. In particular, the exchange of data between each group responsible for each subsystem can be complex and very time-consuming. The goal of this paper is to present a design collaborative tool, the SSETI Design Model (SDM), specifically developed for enabling satellite distributed design. SDM is actually used in the ongoing Student Space Exploration &Technology (SSETI) initiative (www.sseti.net). SSETI is lead by European Space Agency (ESA) outreach office (http://www.estec.esa.nl/outreach), involving student groups from all over Europe for design, construction and launch of a microsatellite. The first part of this paper presents the current version of the SDM tool, a collection of Microsoft Excel linked worksheets, one for each subsystem. An overview of the project framework/structure is given, explaining the different actors, the flows between them, as well as the different types of data and the links - formulas - between data sets. Unified Modeling Language (UML) diagrams give an overview of the different parts . Then the SDM's functionalities, developed in VBA scripts (Visual Basic for Application), are introduced, as well as the interactive features, user interfaces and administration tools. The second part discusses the capabilities and limitations of SDM current version. Taking into account these capabilities and limitations, the third part outlines the next version of SDM, a web-oriented, database-driven evolution of the current version. This new approach will enable real-time data exchange and processing between the different actors of the mission. Comprehensive UML diagrams will guide the audience through the entire modeling process of such a system. Tradeoffs simulation capabilities, security, reliability, hardware and software issues will also be thoroughly discussed.

Effects of Inteferons on Human B-cell Differentiation in vitro

PubMed Central

Kim, Samyong; Stoetter, Hans; Heimpel, Herrman

1987-01-01

The effects of interferons (IFN) on in vitro differentiation of B-lymphocytes were studied. Peripheral lymphocytes from normal subjects were cultivated under polyclonal activator pokeweed mitogen (PWN) or Epstein-Barr virus (EBV) stimulation. The secreted Ig in the culture supernatants were measured for IgM by ELISA method. To determine the cellular level of IFN action T-cell enriched fraction (Te) or B-cell enriched fraction (Be) were preincubated with IFN prior to recombination culture. IFN had modulatory activities on Ig production; at low to moderately high doses (10–1000 U/ml of IFN-alpha or 12–120 U/ml of IFN-gamma) stimulating when IFN was added until 48 hr after the start of the culture, while after 72 hr from culture start IFN suppressed Ig production. Preincubation of Be-cells with moderately high doses of IFN (120 U/ml of IFN-gamma or 1000 U/ml of IFN-alpha) prior to PWM-stimulation suppressed Ig production. Likewise, in EBV-stimulated culture, high dose IFN suppressed Ig production. But low dose of IFN enhanced ig production in EBV-stimulated culture. Preincubation of Te-cells with IFN prior to PWM-stimulation with Be-cells enhanced the Ig production. The T-cell subset analysis at the end of these culture showed enhanced ratio of T-helper cell relative to T-suppressor cells, suggesting increased T-helper cell proliferation after incubation with IFN. Thus, it is concluded that IFNs have modulatory activities on B-cell differentiation. The mechanism seems to be direct effects on B-cells (in PWM and EBV system) as well as through T-helper cell mediation (PWM system). The IFN-gamma showed more potent (2-to 6-fold) stimulatory activities than IFN-alpha. PMID:2484953

A Survey of UML Based Regression Testing

NASA Astrophysics Data System (ADS)

Fahad, Muhammad; Nadeem, Aamer

Regression testing is the process of ensuring software quality by analyzing whether changed parts behave as intended, and unchanged parts are not affected by the modifications. Since it is a costly process, a lot of techniques are proposed in the research literature that suggest testers how to build regression test suite from existing test suite with minimum cost. In this paper, we discuss the advantages and drawbacks of using UML diagrams for regression testing and analyze that UML model helps in identifying changes for regression test selection effectively. We survey the existing UML based regression testing techniques and provide an analysis matrix to give a quick insight into prominent features of the literature work. We discuss the open research issues like managing and reducing the size of regression test suite, prioritization of the test cases that would be helpful during strict schedule and resources that remain to be addressed for UML based regression testing.

The information system of pregnant womans' health nutritious based on android (Case study: Puskesmas Mopah Merauke)

NASA Astrophysics Data System (ADS)

Letsoin, Sri Murniani Angelina; Kolyaan, Yuliana; Cahyadi, Dedy

2017-02-01

The cause of maternal mortality can be divided into two, the direct cause and indirect cause. One of the indirect causes is too difficult to reach health services and the lack of pregnancy knowledge. On the other hand, Android smartphone development of communications technology has increased compared to users of other devices, e.g. blackberry, which has dropped from 11.5% to 4.8% while the android market share has grown from 46.9% up to 68.1%. This increasing is being an opportunity for the software developers to design some software based on Android. The aim of this study was to facilitate the pregnant women to find out some information about the nutritional health, abstinence, calculate gestational age and nutrition based on the period of pregnancy. The information system was designed by using UML, the Eclipse IDE with the java programming language, MySQL as the database. The testing results showed that the nutrition information system based on android could help pregnant women to obtain health nutrition information such as nutrition, calories, dietary restrictions that should be avoided during the first month to the nine month of pregnancy, and the calculation of gestation.

Design, Development, and Initial Evaluation of a Terminology for Clinical Decision Support and Electronic Clinical Quality Measurement.

PubMed

Lin, Yanhua; Staes, Catherine J; Shields, David E; Kandula, Vijay; Welch, Brandon M; Kawamoto, Kensaku

2015-01-01

When coupled with a common information model, a common terminology for clinical decision support (CDS) and electronic clinical quality measurement (eCQM) could greatly facilitate the distributed development and sharing of CDS and eCQM knowledge resources. To enable such scalable knowledge authoring and sharing, we systematically developed an extensible and standards-based terminology for CDS and eCQM in the context of the HL7 Virtual Medical Record (vMR) information model. The development of this terminology entailed three steps: (1) systematic, physician-curated concept identification from sources such as the Health Information Technology Standards Panel (HITSP) and the SNOMED-CT CORE problem list; (2) concept de-duplication leveraging the Unified Medical Language System (UMLS) MetaMap and Metathesaurus; and (3) systematic concept naming using standard terminologies and heuristic algorithms. This process generated 3,046 concepts spanning 68 domains. Evaluation against representative CDS and eCQM resources revealed approximately 50-70% concept coverage, indicating the need for continued expansion of the terminology.

Ontology-based vector space model and fuzzy query expansion to retrieve knowledge on medical computational problem solutions.

PubMed

Bratsas, Charalampos; Koutkias, Vassilis; Kaimakamis, Evangelos; Bamidis, Panagiotis; Maglaveras, Nicos

2007-01-01

Medical Computational Problem (MCP) solving is related to medical problems and their computerized algorithmic solutions. In this paper, an extension of an ontology-based model to fuzzy logic is presented, as a means to enhance the information retrieval (IR) procedure in semantic management of MCPs. We present herein the methodology followed for the fuzzy expansion of the ontology model, the fuzzy query expansion procedure, as well as an appropriate ontology-based Vector Space Model (VSM) that was constructed for efficient mapping of user-defined MCP search criteria and MCP acquired knowledge. The relevant fuzzy thesaurus is constructed by calculating the simultaneous occurrences of terms and the term-to-term similarities derived from the ontology that utilizes UMLS (Unified Medical Language System) concepts by using Concept Unique Identifiers (CUI), synonyms, semantic types, and broader-narrower relationships for fuzzy query expansion. The current approach constitutes a sophisticated advance for effective, semantics-based MCP-related IR.

An information sources map for Occupational and Environmental Medicine: guidance to network-based information through domain-specific indexing.

PubMed Central

Silverstein, S. M.; Miller, P. L.; Cullen, M. R.

1993-01-01

This paper describes a prototype information sources map (ISM), an on-line information source finder, for Occupational and Environmental Medicine (OEM). The OEM ISM was built as part of the Unified Medical Language System (UMLS) project of the National Library of Medicine. It allows a user to identify sources of on-line information appropriate to a specific OEM question, and connect to the sources. In the OEM ISM we explore a domain-specific method of indexing information source contents, and also a domain-specific user interface. The indexing represents a domain expert's opinion of the specificity of an information source in helping to answer specific types of domain questions. For each information source, an index field represents whether a source might provide useful information in an occupational, industrial, or environmental category. Additional fields represent the degree of specificity of a source in individual question types in each category. The paper discusses the development, design, and implementation of the prototype OEM ISM. PMID:8130548

Graph-based signal integration for high-throughput phenotyping

PubMed Central

2012-01-01

Background Electronic Health Records aggregated in Clinical Data Warehouses (CDWs) promise to revolutionize Comparative Effectiveness Research and suggest new avenues of research. However, the effectiveness of CDWs is diminished by the lack of properly labeled data. We present a novel approach that integrates knowledge from the CDW, the biomedical literature, and the Unified Medical Language System (UMLS) to perform high-throughput phenotyping. In this paper, we automatically construct a graphical knowledge model and then use it to phenotype breast cancer patients. We compare the performance of this approach to using MetaMap when labeling records. Results MetaMap's overall accuracy at identifying breast cancer patients was 51.1% (n=428); recall=85.4%, precision=26.2%, and F1=40.1%. Our unsupervised graph-based high-throughput phenotyping had accuracy of 84.1%; recall=46.3%, precision=61.2%, and F1=52.8%. Conclusions We conclude that our approach is a promising alternative for unsupervised high-throughput phenotyping. PMID:23320851

Design, Development, and Initial Evaluation of a Terminology for Clinical Decision Support and Electronic Clinical Quality Measurement

PubMed Central

Lin, Yanhua; Staes, Catherine J; Shields, David E; Kandula, Vijay; Welch, Brandon M; Kawamoto, Kensaku

2015-01-01

When coupled with a common information model, a common terminology for clinical decision support (CDS) and electronic clinical quality measurement (eCQM) could greatly facilitate the distributed development and sharing of CDS and eCQM knowledge resources. To enable such scalable knowledge authoring and sharing, we systematically developed an extensible and standards-based terminology for CDS and eCQM in the context of the HL7 Virtual Medical Record (vMR) information model. The development of this terminology entailed three steps: (1) systematic, physician-curated concept identification from sources such as the Health Information Technology Standards Panel (HITSP) and the SNOMED-CT CORE problem list; (2) concept de-duplication leveraging the Unified Medical Language System (UMLS) MetaMap and Metathesaurus; and (3) systematic concept naming using standard terminologies and heuristic algorithms. This process generated 3,046 concepts spanning 68 domains. Evaluation against representative CDS and eCQM resources revealed approximately 50–70% concept coverage, indicating the need for continued expansion of the terminology. PMID:26958220

Anatomical entity mention recognition at literature scale

PubMed Central

Pyysalo, Sampo; Ananiadou, Sophia

2014-01-01

Motivation: Anatomical entities ranging from subcellular structures to organ systems are central to biomedical science, and mentions of these entities are essential to understanding the scientific literature. Despite extensive efforts to automatically analyze various aspects of biomedical text, there have been only few studies focusing on anatomical entities, and no dedicated methods for learning to automatically recognize anatomical entity mentions in free-form text have been introduced. Results: We present AnatomyTagger, a machine learning-based system for anatomical entity mention recognition. The system incorporates a broad array of approaches proposed to benefit tagging, including the use of Unified Medical Language System (UMLS)- and Open Biomedical Ontologies (OBO)-based lexical resources, word representations induced from unlabeled text, statistical truecasing and non-local features. We train and evaluate the system on a newly introduced corpus that substantially extends on previously available resources, and apply the resulting tagger to automatically annotate the entire open access scientific domain literature. The resulting analyses have been applied to extend services provided by the Europe PubMed Central literature database. Availability and implementation: All tools and resources introduced in this work are available from http://nactem.ac.uk/anatomytagger. Contact: sophia.ananiadou@manchester.ac.uk Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:24162468

Tannase enzyme production by entrapped cells of Aspergillus niger FETL FT3 in submerged culture system.

PubMed

Darah, I; Sumathi, G; Jain, K; Lim, S H

2011-09-01

The ability of immobilized cell cultures of Aspergillus niger FETL FT3 to produce extracellular tannase was investigated. The production of enzyme was increased by entrapping the fungus in scouring mesh cubes compared to free cells. Using optimized parameters of six scouring mesh cubes and inoculum size of 1 × 10(6) spores/mL, the tannase production of 3.98 U/mL was obtained from the immobilized cells compared to free cells (2.81 U/mL). It was about 41.64% increment. The immobilized cultures exhibited significant tannase production stability of two repeated runs.

KEYNOTE 2 : Rebuilding the Tower of Babel - Better Communication with Standards

DTIC Science & Technology

2013-02-01

and a member of the Object Management Group (OMG) SysML specification team. He has been developing multi-national complex systems for almost 35 years...critical systems development, virtual team management, systems development, and software development with UML, SysML and Architectural Frameworks

Five Year Results of US Intergroup/RTOG 9704 With Postoperative CA 19-9 {<=}90 U/mL and Comparison to the CONKO-001 Trial

DOE Office of Scientific and Technical Information (OSTI.GOV)

Berger, Adam C., E-mail: adam.berger@jefferson.edu; Winter, Kathryn; Hoffman, John P.

2012-11-01

Purpose: Radiation Therapy Oncology Group (RTOG) trial 9704 was the largest randomized trial to use adjuvant chemoradiation therapy for patients with pancreatic cancer. This report analyzes 5-year survival by serum level of tumor marker CA 19-9 of {<=}90 vs >90 U/mL and compares results to the those of the CONKO-001 trial. Methods and Materials: CA 19-9 expression was analyzed as a dichotomized variable ({<=}90 vs >90 U/mL). Cox proportional hazard models were used to identify the impact of the CA 19-9 value on overall survival (OS). Actuarial estimates of OS were calculated using the Kaplan-Meier method. Results: Both univariate (hazardmore » ratio [HR] = 3.2; 95% confidence interval [CI], 2.3-4.3, P<.0001) and multivariate (HR = 3.1; 95% CI, 2.2-4.2, P<.0001) analyses demonstrated a statistically significant decrease in OS for CA 19-9 serum level of {>=}90 U/mL. For patients in the gemcitabine (Gem) treatment arm with CA 19-9 <90 U/mL, median survival was 21 months. For patients with CA 19-9 {>=}90 U/mL, this number dropped to 10 months. In patients with pancreatic head tumors in the Gem treatment arm with RT quality assurance per protocol and CA 19-9 of <90 U/mL, median survival and 5-year rate were 24 months and 34%. In comparison, the median survival and 5-year OS rate for patients in the Gem arm of the CONKO trial were 22 months and 21%. Conclusions: This analysis demonstrates that patients with postresection CA 19-9 values {>=}90 U/mL had a significantly worse survival. Patients with pancreatic head tumors treated with Gem with CA 19-9 serum level of <90 U/mL and per protocol RT had favorable survival compared to that seen in the CONKO trial. CA 19-9 is a stratification factor for the current RTOG adjuvant pancreas trial (0848).« less

Novel marine actinobacteria from emerald Andaman & Nicobar Islands: a prospective source for industrial and pharmaceutical byproducts

PubMed Central

2013-01-01

Background Andaman and Nicobar Islands situated in the eastern part of Bay of Bengal are one of the distinguished biodiversity hotspot. Even though number of studies carried out on the marine flora and fauna, the studies on actinobacteria from Andaman and Nicobar Islands are meager. The aim of the present study was to screen the actinobacteria for their characterization and identify the potential sources for industrial and pharmaceutical byproducts. Results A total of 26 actinobacterial strains were isolated from the marine sediments collected from various sites of Port Blair Bay where no collection has been characterized previously. Isolates were categorized under the genera: Saccharopolyspora, Streptomyces, Nocardiopsis, Streptoverticillium, Microtetraspora, Actinopolyspora, Actinokineospora and Dactylosporangium. Majority of the isolates were found to produce industrially important enzymes such as amylase, protease, gelatinase, lipase, DNase, cellulase, urease and phosphatase, and also exhibited substantial antibacterial activity against human pathogens. 77% of isolates exhibited significant hemolytic activity. Among 26 isolates, three strains (NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26) were found to generate appreciable extent of surfactant, amylase, cellulase and protease enzyme. NIOT-VKKMA02 produced surfactant using kerosene as carbon source and emulsified upto E24–63.6%. Moreover, NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26 synthesized 13.27 U/ml, 9.85 U/ml and 8.03 U/ml amylase; 7.75 U/ml, 5.01 U/ml and 2.08 U/ml of cellulase and 11.34 U/ml, 6.89 U/ml and 3.51 U/ml of protease enzyme, respectively. Conclusions High diversity of marine actinobacteria was isolated and characterized in this work including undescribed species and species not previously reported from emerald Andaman and Nicobar Islands, including Streptomyces griseus, Streptomyces venezuelae and Saccharopolyspora salina. The enhanced salt, pH and temperature tolerance of the actinobacterial isolates along with their capacity to secrete commercially valuable primary and secondary metabolites emerges as an attractive feature of these organisms. These results are reported for the first time from these emerald Islands and expand the scope to functionally characterize novel marine actinobacteria and their metabolites for the potential novel molecules of commercial interest. PMID:23800234

Novel marine actinobacteria from emerald Andaman & Nicobar Islands: a prospective source for industrial and pharmaceutical byproducts.

PubMed

Meena, Balakrishnan; Rajan, Lawrance Anbu; Vinithkumar, Nambali Valsalan; Kirubagaran, Ramalingam

2013-06-22

Andaman and Nicobar Islands situated in the eastern part of Bay of Bengal are one of the distinguished biodiversity hotspot. Even though number of studies carried out on the marine flora and fauna, the studies on actinobacteria from Andaman and Nicobar Islands are meager. The aim of the present study was to screen the actinobacteria for their characterization and identify the potential sources for industrial and pharmaceutical byproducts. A total of 26 actinobacterial strains were isolated from the marine sediments collected from various sites of Port Blair Bay where no collection has been characterized previously. Isolates were categorized under the genera: Saccharopolyspora, Streptomyces, Nocardiopsis, Streptoverticillium, Microtetraspora, Actinopolyspora, Actinokineospora and Dactylosporangium. Majority of the isolates were found to produce industrially important enzymes such as amylase, protease, gelatinase, lipase, DNase, cellulase, urease and phosphatase, and also exhibited substantial antibacterial activity against human pathogens. 77% of isolates exhibited significant hemolytic activity. Among 26 isolates, three strains (NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26) were found to generate appreciable extent of surfactant, amylase, cellulase and protease enzyme. NIOT-VKKMA02 produced surfactant using kerosene as carbon source and emulsified upto E(24)-63.6%. Moreover, NIOT-VKKMA02, NIOT-VKKMA22 and NIOT-VKKMA26 synthesized 13.27 U/ml, 9.85 U/ml and 8.03 U/ml amylase; 7.75 U/ml, 5.01 U/ml and 2.08 U/ml of cellulase and 11.34 U/ml, 6.89 U/ml and 3.51 U/ml of protease enzyme, respectively. High diversity of marine actinobacteria was isolated and characterized in this work including undescribed species and species not previously reported from emerald Andaman and Nicobar Islands, including Streptomyces griseus, Streptomyces venezuelae and Saccharopolyspora salina. The enhanced salt, pH and temperature tolerance of the actinobacterial isolates along with their capacity to secrete commercially valuable primary and secondary metabolites emerges as an attractive feature of these organisms. These results are reported for the first time from these emerald Islands and expand the scope to functionally characterize novel marine actinobacteria and their metabolites for the potential novel molecules of commercial interest.

An Agent-Based Data Mining System for Ontology Evolution

NASA Astrophysics Data System (ADS)

Hadzic, Maja; Dillon, Darshan

We have developed an evidence-based mental health ontological model that represents mental health in multiple dimensions. The ongoing addition of new mental health knowledge requires a continual update of the Mental Health Ontology. In this paper, we describe how the ontology evolution can be realized using a multi-agent system in combination with data mining algorithms. We use the TICSA methodology to design this multi-agent system which is composed of four different types of agents: Information agent, Data Warehouse agent, Data Mining agents and Ontology agent. We use UML 2.1 sequence diagrams to model the collaborative nature of the agents and a UML 2.1 composite structure diagram to model the structure of individual agents. The Mental Heath Ontology has the potential to underpin various mental health research experiments of a collaborative nature which are greatly needed in times of increasing mental distress and illness.

Immunogenicity and safety of the Vi-CRM197 conjugate vaccine against typhoid fever in adults, children, and infants in south and southeast Asia: results from two randomised, observer-blind, age de-escalation, phase 2 trials.

PubMed

Bhutta, Zulfiqar A; Capeding, Maria Rosario; Bavdekar, Ashish; Marchetti, Elisa; Ariff, Shabina; Soofi, Sajid B; Anemona, Alessandra; Habib, Muhammad A; Alberto, Edison; Juvekar, Sanjay; Khan, Rana M Qasim; Marhaba, Rachid; Ali, Noshad; Malubay, Nelia; Kawade, Anand; Saul, Allan; Martin, Laura B; Podda, Audino

2014-02-01

Typhoid vaccination is a public health priority in developing countries where young children are greatly affected by typhoid fever. Because present vaccines are not recommended for children younger than 2 years, the Novartis Vaccines Institute for Global Health developed a conjugate vaccine (Vi-CRM197) for infant immunisation. We aimed to assess the immunogenicity and safety of Vi-CRM197 in participants of various ages in endemic countries in south and southeast Asia. We did two randomised, observer-blind, age de-escalation, phase 2 trials at two sites in Pakistan and India (study A), and at one site in the Philippines (study B), between March 2, 2011, and Aug 9, 2012. Adults aged 18-45 years, children aged 24-59 months, older infants aged 9-12 months, and infants aged 6-8 weeks were randomly assigned (1:1) with a computer-generated randomisation list (block size of four) to receive either 5 μg Vi-CRM197 or 25 μg Vi-polysaccharide vaccine (or 13-valent pneumococcal conjugate vaccine in children younger than 2 years). Both infant populations received Vi-CRM197 concomitantly with vaccines of the Expanded Programme on Immunization (EPI), according to WHO schedule. With the exception of designated study site personnel responsible for vaccine preparation, study investigators, those assessing outcomes, and data analysts were masked to treatment allocation. We specified no a-priori null hypothesis for the immunogenicity or safety objectives and all analyses were descriptive. Analyses were by modified intention-to-treat. These studies are registered with ClinicalTrials.gov, numbers NCT01229176 and NCT01437267. 320 participants were enrolled and vaccinated in the two trials: 200 in study A (all age groups) and 120 in study B (children and infants only), of whom 317 (99%) were included in the modified intention-to-treat analysis. One dose of Vi-CRM197 significantly increased concentrations of anti-Vi antibody in adults (from 113 U/mL [95% CI 67-190] to 208 U/mL [117-369]), children (201 U/mL [138-294] to 368 U/mL [234-580]), and older infants (179 U/mL [129-250] to 249 U/mL [130-477]). However, in children and older infants, a second dose of conjugate vaccine had no incremental effect on antibody titres and, at all ages, concentrations of antibodies increased substantially 6 months after vaccination (from 55 U/mL [33-94] to 63 U/mL [35-114] in adults, from 23 U/mL [15-34] to 51 U/mL [34-76] in children, and from 21 U/mL [14-31] to 22 U/mL [14-33] in older infants). Immune response in infants aged 6-8 weeks was lower than that in older participants and, 6 months after third vaccination, antibody concentrations were significantly higher than pre-vaccination concentrations in Filipino (21 U/mL [16-28] vs 2.88 U/mL [1.95-4.25]), but not Pakistani (3.76 U/mL [2.77-5.08] vs 2.77 U/mL [2.1-3.66]), infants. Vi-CRM197 was safe and well tolerated and did not induce any significant interference with EPI vaccines. No deaths or vaccine-related serious adverse events were reported throughout the studies. Vi-CRM197 is safe and immunogenic in endemic populations of all ages. Given at 9 months of age, concomitantly with measles vaccine, Vi-CRM197 shows a promise for potential inclusion in EPI schedules of countries endemic for typhoid. An apparent absence of booster response and a reduction in antibody titres 6 months after immunisation should be further investigated, but data show that an immunogenic typhoid vaccine can be safely delivered to infants during EPI visits recommended by WHO. Sclavo Vaccines Association and Regione Toscana. Copyright © 2014 Elsevier Ltd. All rights reserved.

The User Knows What to Call It: Incorporating Patient Voice Through User-Contributed Tags on a Participatory Platform About Health Management

PubMed Central

Carriere, Rachel M; Kaplan, Samantha Jan

2017-01-01

Background Body listening, described as the act of paying attention to the body’s signals and cues, can be an important component of long-term health management. Objective The aim of this study was to introduce and evaluate the Body Listening Project, an innovative effort to engage the public in the creation of a public resource—to leverage collective wisdom in the health domain. This project involved a website where people could contribute their experiences of and dialogue with others concerning body listening and self-management. This article presents an analysis of the tags contributed, with a focus on the value of these tags for knowledge organization and incorporation into consumer-friendly health information retrieval systems. Methods First, we performed content analysis of the tags contributed, identifying a set of categories and refining the relational structure of the categories to develop a preliminary classification scheme, the Body Listening and Self-Management Taxonomy. Second, we compared the concepts in the Body Listening and Self-Management Taxonomy with concepts that were automatically identified from an extant health knowledge resource, the Unified Medical Language System (UMLS), to better characterize the information that participants contributed. Third, we employed visualization techniques to explore the concept space of the tags. A correlation matrix, based on the extent to which categories tended to be assigned to the same tags, was used to study the interrelatedness of the taxonomy categories. Then a network visualization was used to investigate structural relationships among the categories in the taxonomy. Results First, we proposed a taxonomy called the Body Listening and Self-Management Taxonomy, with four meta-level categories: (1) health management strategies, (2) concepts and states, (3) influencers, and (4) health-related information behavior. This taxonomy could inform future efforts to organize knowledge and content of this subject matter. Second, we compared the categories from this taxonomy with the UMLS concepts that were identified. Though the UMLS offers benefits such as speed and breadth of coverage, the Body Listening and Self-Management Taxonomy is more consumer-centric. Third, the correlation matrix and network visualization demonstrated that there are natural areas of ambiguity and semantic relatedness in the meanings of the concepts in the Body Listening and Self-Management Taxonomy. Use of these visualizations can be helpful in practice settings, to help library and information science practitioners understand and resolve potential challenges in classification; in research, to characterize the structure of the conceptual space of health management; and in the development of consumer-centric health information retrieval systems. Conclusions A participatory platform can be employed to collect data concerning patient experiences of health management, which can in turn be used to develop new health knowledge resources or augment existing ones, as well as be incorporated into consumer-centric health information systems. PMID:28882809

The User Knows What to Call It: Incorporating Patient Voice Through User-Contributed Tags on a Participatory Platform About Health Management.

PubMed

Chen, Annie T; Carriere, Rachel M; Kaplan, Samantha Jan

2017-09-07

Body listening, described as the act of paying attention to the body's signals and cues, can be an important component of long-term health management. The aim of this study was to introduce and evaluate the Body Listening Project, an innovative effort to engage the public in the creation of a public resource-to leverage collective wisdom in the health domain. This project involved a website where people could contribute their experiences of and dialogue with others concerning body listening and self-management. This article presents an analysis of the tags contributed, with a focus on the value of these tags for knowledge organization and incorporation into consumer-friendly health information retrieval systems. First, we performed content analysis of the tags contributed, identifying a set of categories and refining the relational structure of the categories to develop a preliminary classification scheme, the Body Listening and Self-Management Taxonomy. Second, we compared the concepts in the Body Listening and Self-Management Taxonomy with concepts that were automatically identified from an extant health knowledge resource, the Unified Medical Language System (UMLS), to better characterize the information that participants contributed. Third, we employed visualization techniques to explore the concept space of the tags. A correlation matrix, based on the extent to which categories tended to be assigned to the same tags, was used to study the interrelatedness of the taxonomy categories. Then a network visualization was used to investigate structural relationships among the categories in the taxonomy. First, we proposed a taxonomy called the Body Listening and Self-Management Taxonomy, with four meta-level categories: (1) health management strategies, (2) concepts and states, (3) influencers, and (4) health-related information behavior. This taxonomy could inform future efforts to organize knowledge and content of this subject matter. Second, we compared the categories from this taxonomy with the UMLS concepts that were identified. Though the UMLS offers benefits such as speed and breadth of coverage, the Body Listening and Self-Management Taxonomy is more consumer-centric. Third, the correlation matrix and network visualization demonstrated that there are natural areas of ambiguity and semantic relatedness in the meanings of the concepts in the Body Listening and Self-Management Taxonomy. Use of these visualizations can be helpful in practice settings, to help library and information science practitioners understand and resolve potential challenges in classification; in research, to characterize the structure of the conceptual space of health management; and in the development of consumer-centric health information retrieval systems. A participatory platform can be employed to collect data concerning patient experiences of health management, which can in turn be used to develop new health knowledge resources or augment existing ones, as well as be incorporated into consumer-centric health information systems. ©Annie T Chen, Rachel M Carriere, Samantha Jan Kaplan. Originally published in the Journal of Medical Internet Research (http://www.jmir.org), 07.09.2017.

Bacillus sp. Acting as Dual Role for Corrosion Induction and Corrosion Inhibition with Carbon Steel (CS)

PubMed Central

Karn, Santosh K.; Fang, Guan; Duan, Jizhou

2017-01-01

Present work investigated the role of five different bacteria species as a corrosion inducer as well as corrosion inhibitor with carbon steel (CS). We observed the ability of different bacteria species on the metal surface attachment, biofilm formation, and determined Peroxidase, Catalase enzyme activity in the detached biofilm from the CS surface. We found that each strain has diverse conduct for surface attachment like DS1 3.3, DS2 2.5, DS3 4.3, DS4 4.0, and DS5 4.71 log cfu/cm2 and for biofilm 8.3 log cfu/cm2. The enzyme Peroxidase, Catalase was found in huge concentration inside the biofilm Peroxidase was maximum for DS4 36.0 U/ml and least for DS3 19.54 U/ml. Whereas, Catalase was highest for DS4, DS5 70.14 U/ml and least 57.2 U/ml for DS2. Scanning electron microscopy (SEM) was conducted to examine the biofilm and electrochemical impedance spectroscopy (EIS) were utilized to observe corrosion in the presence of bacteria. The electrochemical results confirmed that DS1, DS3, DS4, and DS5 strains have statistically significant MIC-factors (Microbially Influenced Corrosion) of 5.46, 8.51, 2.36, and 1.04, while DS2 protective effect factor of 0.89. Weight reduction results with carbon steel likewise supports that corrosion was initiated by DS1 and DS3, while DS2 and DS5 have no any impact though with DS4 we watched less weight reduction however assumed no role in the corrosion. We established the relation of Peroxidase enzyme activity of the isolates. DS1, DS3 and having Peroxidase in the range 22.18, 19.54 U/ml which induce the corrosion whereas DS2 and DS5 having 28.57 and 27.0 U/ml has no any effect and DS4 36 U/ml has inhibitory effect, increasing concentration inhibiting the corrosion. For Catalase DS1, DS3 have 67.28, 61.57 U/ml which induce corrosion while DS2 and DS5 57.71 and 59.14 U/ml also has no effect whereas DS4 70.14 U/ml can inhibit corrosion. Results clearly express that in a specific range both enzymes can induce the corrosion. Our goals are to pursuit and locate the potential role of the enzyme in corrosion induction and inhibition. There is still further work is proceeded for the more profound perception. PMID:29114242

New Insulin Glargine 300 U/mL for the Treatment of Type 1 and Type 2 Diabetes Mellitus.

PubMed

Goldman, Jennifer; White, John R

2015-10-01

To describe the studies evaluating the efficacy and safety of new insulin glargine 300 U/mL (Gla-300) as a basal insulin in the treatment of type 1 (T1DM) and type 2 (T2DM) diabetes mellitus. A literature search of MEDLINE was conducted (January 2008-June 2015) using the terms U300, Gla-300, and insulin glargine 300 units/mL and supplemented with congress abstracts published in 2014 and 2015. All English language studies assessing the efficacy and/or safety of Gla-300 were evaluated. The efficacy and safety of once-daily Gla-300 has been compared with insulin glargine 100 U/mL (Gla-100) in the EDITION trials, 6 phase-3, multinational, open-label studies in T1DM and T2DM. Across these studies, Gla-300 consistently demonstrated glycemic control comparable to Gla-100; a mean (standard error) change in glycated hemoglobin A1c of -1.02% (0.03) with both Gla-100 (n = 1235) and Gla-300 (n = 1239) was seen in a patient-level meta-analysis. Gla-300 was associated with comparable or reduced nocturnal hypoglycemia compared with Gla-100; the relative risk for nocturnal hypoglycemia with Gla-300 versus Gla-100 was 0.75 (95% CI = 0.68 to 0.83) in a patient-level meta-analysis. There is also some evidence for less weight gain with Gla-300 compared with Gla-100, despite a higher insulin dose. Gla-300 was well tolerated, with the number of adverse events being comparable to that with Gla-100. These results suggest that Gla-300 may have a place as an alternative, long-acting basal insulin for patients with T1DM or T2DM, with the possibility for improved tolerability. © The Author(s) 2015.

Metadata mapping and reuse in caBIG.

PubMed

Kunz, Isaac; Lin, Ming-Chin; Frey, Lewis

2009-02-05

This paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facilitate the building domain models. This is examined in the context of an existing system, the National Cancer Institute (NCI)'s cancer Biomedical Informatics Grid (caBIG). The goal is to demonstrate the deployment of open source tools that can be used to effectively map models and enable the reuse of existing information objects and CDEs in the development of new models for translational research applications. This effort is intended to help developers reuse appropriate CDEs to enable interoperability of their systems when developing within the caBIG framework or other frameworks that use metadata repositories. The Dice (di-grams) and Dynamic algorithms are compared and both algorithms have similar performance matching UML model class-attributes to CDE class object-property pairs. With algorithms used, the baselines for automatically finding the matches are reasonable for the data models examined. It suggests that automatic mapping of UML models and CDEs is feasible within the caBIG framework and potentially any framework that uses a metadata repository. This work opens up the possibility of using mapping algorithms to reduce cost and time required to map local data models to a reference data model such as those used within caBIG. This effort contributes to facilitating the development of interoperable systems within caBIG as well as other metadata frameworks. Such efforts are critical to address the need to develop systems to handle enormous amounts of diverse data that can be leveraged from new biomedical methodologies.

Production of xylanase and protease by Penicillium janthinellum CRC 87M-115 from different agricultural wastes.

PubMed

Oliveira, Luciana A; Porto, Ana L F; Tambourgi, Elias B

2006-04-01

Five agricultural wastes were evaluated in submerged fermentation for xylanolytic enzymes production by Penicillium janthinellum. The wastes were hydrolyzed in acid medium and the liquid fraction was used for cultivation. Corn cob (55.3 U/mL) and oat husk (54.8 U/mL) were the best inducers of xylanase. Sugar cane bagasse (23.0 U/mL) and corn husk (23.8 U/mL) were moderately good, while cassava peel was negligible. Protease production was very low in all agro-industrial residues. The maximum biomass yields were 1.30 and 1.17 g/L for cassava peel and corn husk after 180 h, respectively. Xylanolytic activity showed a cell growth associated profile.

Model-Driven Theme/UML

NASA Astrophysics Data System (ADS)

Carton, Andrew; Driver, Cormac; Jackson, Andrew; Clarke, Siobhán

Theme/UML is an existing approach to aspect-oriented modelling that supports the modularisation and composition of concerns, including crosscutting ones, in design. To date, its lack of integration with model-driven engineering (MDE) techniques has limited its benefits across the development lifecycle. Here, we describe our work on facilitating the use of Theme/UML as part of an MDE process. We have developed a transformation tool that adopts model-driven architecture (MDA) standards. It defines a concern composition mechanism, implemented as a model transformation, to support the enhanced modularisation features of Theme/UML. We evaluate our approach by applying it to the development of mobile, context-aware applications-an application area characterised by many non-functional requirements that manifest themselves as crosscutting concerns.

Domain-specific languages and diagram customization for a concurrent engineering environment

NASA Astrophysics Data System (ADS)

Cole, B.; Dubos, G.; Banazadeh, P.; Reh, J.; Case, K.; Wang, Y.; Jones, S.; Picha, F.

A major open question for advocates of Model-Based Systems Engineering (MBSE) is the question of how system and subsystem engineers will work together. The Systems Modeling Language (SysML), like any language intended for a large audience, is in tension between the desires for simplicity and for expressiveness. In order to be more expressive, many specialized language elements may be introduced, which will unfortunately make a complete understanding of the language a more daunting task. While this may be acceptable for systems modelers, it will increase the challenge of including subsystem engineers in the modeling effort. One possible answer to this situation is the use of Domain-Specific Languages (DSL), which are fully supported by the Unified Modeling Language (UML). SysML is in fact a DSL for systems engineering. The expressive power of a DSL can be enhanced through the use of diagram customization. Various domains have already developed their own schematic vocabularies. Within the space engineering community, two excellent examples are the propulsion and telecommunication subsystems. A return to simple box-and-line diagrams (e.g., the SysML Internal Block Diagram) are in many ways a step backward. In order allow subsystem engineers to contribute directly to the model, it is necessary to make a system modeling tool at least approximate in accessibility to drawing tools like Microsoft PowerPoint and Visio. The challenge is made more extreme in a concurrent engineering environment, where designs must often be drafted in an hour or two. In the case of the Jet Propulsion Laboratory's Team X concurrent design team, a subsystem is specified using a combination of PowerPoint for drawing and Excel for calculation. A pilot has been undertaken in order to meld the drawing portion and the production of master equipment lists (MELs) via a SysML authoring tool, MagicDraw. Team X currently interacts with its customers in a process of sharing presentations. There are severa- inefficiencies that arise from this situation. The first is that a customer team must wait two weeks to a month (which is 2-4 times the duration of most Team X studies themselves) for a finalized, detailed design description. Another is that this information must be re-entered by hand into the set of engineering artifacts and design tools that the mission concept team uses after a study is complete. Further, there is no persistent connection to Team X or institutionally shared formulation design tools and data after a given study, again reducing the direct reuse of designs created in a Team X study. This paper presents the underpinnings of subsystem DSLs as they were developed for this pilot. This includes specialized semantics for different domains as well as the process by which major categories of objects were derived in support of defining the DSLs. The feedback given to us by the domain experts on usability, along with a pilot study with the partial inclusion of these tools is also discussed.

Domain-Specific Languages and Diagram Customization for a Concurrent Engineering Environment

NASA Technical Reports Server (NTRS)

Cole, Bjorn; Dubos, Greg; Banazadeh, Payam; Reh, Jonathan; Case, Kelley; Wang, Yeou-Fang; Jones, Susan; Picha, Frank

2013-01-01

A major open question for advocates of Model-Based Systems Engineering (MBSE) is the question of how system and subsystem engineers will work together. The Systems Modeling Language (SysML), like any language intended for a large audience, is in tension between the desires for simplicity and for expressiveness. In order to be more expressive, many specialized language elements may be introduced, which will unfortunately make a complete understanding of the language a more daunting task. While this may be acceptable for systems modelers, it will increase the challenge of including subsystem engineers in the modeling effort. One possible answer to this situation is the use of Domain-Specific Languages (DSL), which are fully supported by the Unified Modeling Language (UML). SysML is in fact a DSL for systems engineering. The expressive power of a DSL can be enhanced through the use of diagram customization. Various domains have already developed their own schematic vocabularies. Within the space engineering community, two excellent examples are the propulsion and telecommunication subsystems. A return to simple box-and-line diagrams (e.g., the SysML Internal Block Diagram) are in many ways a step backward. In order allow subsystem engineers to contribute directly to the model, it is necessary to make a system modeling tool at least approximate in accessibility to drawing tools like Microsoft PowerPoint and Visio. The challenge is made more extreme in a concurrent engineering environment, where designs must often be drafted in an hour or two. In the case of the Jet Propulsion Laboratory's Team X concurrent design team, a subsystem is specified using a combination of PowerPoint for drawing and Excel for calculation. A pilot has been undertaken in order to meld the drawing portion and the production of master equipment lists (MELs) via a SysML authoring tool, MagicDraw. Team X currently interacts with its customers in a process of sharing presentations. There are several inefficiencies that arise from this situation. The first is that a customer team must wait two weeks to a month (which is 2-4 times the duration of most Team X studies themselves) for a finalized, detailed design description. Another is that this information must be re-entered by hand into the set of engineering artifacts and design tools that the mission concept team uses after a study is complete. Further, there is no persistent connection to Team X or institutionally shared formulation design tools and data after a given study, again reducing the direct reuse of designs created in a Team X study. This paper presents the underpinnings of subsystem DSLs as they were developed for this pilot. This includes specialized semantics for different domains as well as the process by which major categories of objects were derived in support of defining the DSLs. The feedback given to us by the domain experts on usability, along with a pilot study with the partial inclusion of these tools is also discussed.

Customer-experienced rapid prototyping

NASA Astrophysics Data System (ADS)

Zhang, Lijuan; Zhang, Fu; Li, Anbo

2008-12-01

In order to describe accurately and comprehend quickly the perfect GIS requirements, this article will integrate the ideas of QFD (Quality Function Deployment) and UML (Unified Modeling Language), and analyze the deficiency of prototype development model, and will propose the idea of the Customer-Experienced Rapid Prototyping (CE-RP) and describe in detail the process and framework of the CE-RP, from the angle of the characteristics of Modern-GIS. The CE-RP is mainly composed of Customer Tool-Sets (CTS), Developer Tool-Sets (DTS) and Barrier-Free Semantic Interpreter (BF-SI) and performed by two roles of customer and developer. The main purpose of the CE-RP is to produce the unified and authorized requirements data models between customer and software developer.

An integrated GIS-based data model for multimodal urban public transportation analysis and management

NASA Astrophysics Data System (ADS)

Chen, Shaopei; Tan, Jianjun; Ray, C.; Claramunt, C.; Sun, Qinqin

2008-10-01

Diversity is one of the main characteristics of transportation data collected from multiple sources or formats, which can be extremely complex and disparate. Moreover, these multimodal transportation data are usually characterised by spatial and temporal properties. Multimodal transportation network data modelling involves both an engineering and research domain that has attracted the design of a number of spatio-temporal data models in the geographic information system (GIS). However, the application of these specific models to multimodal transportation network is still a challenging task. This research addresses this challenge from both integrated multimodal data organization and object-oriented modelling perspectives, that is, how a complex urban transportation network should be organized, represented and modeled appropriately when considering a multimodal point of view, and using object-oriented modelling method. We proposed an integrated GIS-based data model for multimodal urban transportation network that lays a foundation to enhance the multimodal transportation network analysis and management. This modelling method organizes and integrates multimodal transit network data, and supports multiple representations for spatio-temporal objects and relationship as both visual and graphic views. The data model is expressed by using a spatio-temporal object-oriented modelling method, i.e., the unified modelling language (UML) extended to spatial and temporal plug-in for visual languages (PVLs), which provides an essential support to the spatio-temporal data modelling for transportation GIS.

Clinical, information and business process modeling to promote development of safe and flexible software.

PubMed

Liaw, Siaw-Teng; Deveny, Elizabeth; Morrison, Iain; Lewis, Bryn

2006-09-01

Using a factorial vignette survey and modeling methodology, we developed clinical and information models - incorporating evidence base, key concepts, relevant terms, decision-making and workflow needed to practice safely and effectively - to guide the development of an integrated rule-based knowledge module to support prescribing decisions in asthma. We identified workflows, decision-making factors, factor use, and clinician information requirements. The Unified Modeling Language (UML) and public domain software and knowledge engineering tools (e.g. Protégé) were used, with the Australian GP Data Model as the starting point for expressing information needs. A Web Services service-oriented architecture approach was adopted within which to express functional needs, and clinical processes and workflows were expressed in the Business Process Execution Language (BPEL). This formal analysis and modeling methodology to define and capture the process and logic of prescribing best practice in a reference implementation is fundamental to tackling deficiencies in prescribing decision support software.

Soluble CD30 levels in recipients undergoing heart transplantation do not predict post-transplant outcome.

PubMed

Ypsilantis, Efthymios; Key, Timothy; Bradley, J Andrew; Morgan, C Helen; Tsui, Stephen; Parameshwar, Jayan; Taylor, Craig J

2009-11-01

The pre-transplant serum level of soluble CD30 (sCD30), a proteolytic derivative of the lymphocyte surface receptor CD30, has been suggested as a biomarker for immunologic risk after organ transplantation. Pre-transplant serum sCD30 levels were determined in 200 consecutive adult heart transplant recipients undertaken at a single center. Transplant outcome (acute rejection in the first 12 months and patient survival up to 5 years post-transplant) was determined. Patients treated with a left ventricular assist device (LVAD) prior to transplantation (n = 28) had higher levels of sCD30 (median 64 U/ml, range 12 to 112 U/ml) than those (n = 172) with no LVAD (median 36 U/ml, range 1 to 158 U/ml, p < 0.0001). Recipients were categorized according to whether sCD30 levels were "low" (lower quartile, <24 U/ml, n = 50), "intermediate" (24 to 58 U/ml, n = 100) or "high" (upper quartile, >58 U/ml, n = 50). Neither acute rejection nor recipient survival differed according to sCD30 level, with values (mean +/- SEM) of 0.30 +/- 0.04, 0.23 +/- 0.03 and 0.30 +/- 0.05 acute rejection episodes per 100 days in the low, intermediate and high groups, respectively, with recipient survival rates at 1 year of 77.7%, 84.9% and 86% and at 5 years of 73.6%, 67.9% and 75.8%, respectively. Pre-transplant serum sCD30 level does not predict acute allograft rejection or recipient survival after heart transplantation, although sCD30 levels are increased by LVAD, possibly as a result of biomaterial-host immune interaction.

Value of soluble CD30 in liver transplantation.

PubMed

Fábrega, E; Unzueta, M G; Cobo, M; Casafont, F; Amado, J A; Romero, F P

2007-09-01

CD30 is a membrane glycoprotein that belongs to the tumor necrosis factor superfamily. It is expressed on activated T cells. After activation of CD30(+) T cells, a soluble form of CD30 (sCD30) released into the bloodstream, can be measured in the serum. The aim of our study was to investigate the time course of serum levels of sCD30 during hepatic allograft rejection. Serum levels of sCD30 were determined in 30 healthy subjects and 50 hepatic transplant recipients. These patients were divided into two groups: group I, 35 patients without rejection; and group II, 15 patients with acute rejection. Samples were collected on day 1 and 7 after transplantation and on the day of liver biopsy. The concentrations of sCD30 were similar in the rejection (40.4 +/- 16.5 U/mL) and nonrejection groups (43.0 +/- 18.2 U/mL) on postoperative day 1. We observed a significant increase in sCD30 levels in the rejection group on postoperative day 7 (76.3 +/- 61.8 U/mL vs 46.8 +/- 20.5 U/mL; P = .01). The difference increased when a diagnosis of acute rejection had been established: namely 133.0 +/- 113.5 U/mL versus 40.1 +/- 22.0 U/mL; (P = .001). These levels were also significantly higher during the entire postoperative period in all the patients, with or without rejection, than those observed in healthy controls (26.6 +/- 5.3 U/mL; P = .005). The release of circulating sCD30 is a prominent feature coinciding with the first episode of hepatic allograft rejection. So, monitoring of sCD30 levels may be useful for the early diagnosis of an acute rejection episode.

Evaluation of secretome of highly efficient lignocellulolytic Penicillium sp. Dal 5 isolated from rhizosphere of conifers.

PubMed

Rai, Rohit; Kaur, Baljit; Singh, Surender; Di Falco, Macros; Tsang, Adrian; Chadha, B S

2016-09-01

Penicillium sp. (Dal 5) isolated from rhizosphere of conifers from Dalhousie (Himachal Pradesh, India) was found to be an efficient cellulolytic strain. The culture under shake flask on CWR (cellulose, wheat bran and rice straw) medium produced appreciably higher levels of endoglucanase (35.69U/ml), β-glucosidase (4.20U/ml), cellobiohydrolase (2.86U/ml), FPase (1.2U/ml) and xylanase (115U/ml) compared to other Penicillium strains reported in literature. The mass spectroscopy analysis of Penicillium sp. Dal 5 secretome identified 108 proteins constituting an array of CAZymes including glycosyl hydrolases (GH) belonging to 24 different families, polysaccharide lyases (PL), carbohydrate esterases (CE), lytic polysaccharide mono-oxygenases (LPMO) in addition to swollenin and a variety of carbohydrate binding modules (CBM) indicating an elaborate genetic potential of this strain for hydrolysis of lignocellulosics. Further, the culture extract was evaluated for hydrolysis of alkali treated rice straw, wheat straw, bagasse and corn cob at 10% substrate loading rate. Copyright © 2016 Elsevier Ltd. All rights reserved.

Mapping Japanese medical terms to UMLS Metathesaurus.

PubMed

Onogi, Yuzo; Ohe, Kazuhiko; Tanaka, Masaaki; Nozoe, Atsutake; Sasaki, Tetsuro; Sato, Megumi; Kikuchi, Yuko; Shinohara, Tsuneki; Suzuki, Hiromichi; Kaihara, Shigekoto; Seyama, Yousuke

2004-01-01

This paper introduces and reports the results for a project to map Japanese medical terms to the UMLS Metathesaurus. The "Thesaurus for Medical and Health related Terms version 5" published in 2003 by the Japan Medical Abstracts Society and UMLS version 2002AC provided by NLM were used in this study. The goal was to judge the validity of the correlation between the Japanese and English terms that belong to the same MeSH concept. Fifteen medicine, nursing, and library science professionals, excluding JAMAS, used a custom designed Web interface to perform this task. About 10% of the concepts were judged as invalid, and the reasoning behind these failures were analyzed. Experience from this project can be used to estimate the manpower required to revise the Japanese thesaurus after future revisions to UMLS or MeSH.

Software Hardware Asset Reuse Enterprise (SHARE) Repository Framework Final Report: Component Specification and Ontology

DTIC Science & Technology

2009-08-19

SSDS Ship Self Defense System TSTS Total Ship Training System UDDI Universal Description, Discovery, and Integration UML Unified Modeling...34ContractorOrganization" type="ContractorOrganizationType"> <xs:annotation> <xs:documentation>Identifies a contractor organization resposible for the

Epstein-Barr virus is related with 5-aminosalicylic acid, tonsillectomy, and CD19(+) cells in Crohn's disease.

PubMed

Andreu-Ballester, Juan C; Gil-Borrás, Rafael; García-Ballesteros, Carlos; Catalán-Serra, Ignacio; Amigo, Victoria; Fernández-Fígares, Virgina; Cuéllar, Carmen

2015-04-21

To study anti-Epstein-Barr virus (EBV) IgG antibodies in Crohn's disease in relation to treatment, immune cells, and prior tonsillectomy/appendectomy. This study included 36 CD patients and 36 healthy individuals (controls), and evaluated different clinical scenarios (new patient, remission and active disease), previous mucosa-associated lymphoid tissue removal (tonsillectomy and appendectomy) and therapeutic regimens (5-aminosalicylic acid, azathioprine, anti-tumor necrosis factor, antibiotics, and corticosteroids). T and B cells subsets in peripheral blood were analyzed by flow cytometry (markers included: CD45, CD4, CD8, CD3, CD19, CD56, CD2, CD3, TCRαβ and TCRγδ) to relate with the levels of anti-EBV IgG antibodies, determined by enzyme-linked immunosorbent assay. The lowest anti-EBV IgG levels were observed in the group of patients that were not in a specific treatment (95.4 ± 53.9 U/mL vs 131.5 ± 46.2 U/mL, P = 0.038). The patients that were treated with 5-aminosalicylic acid showed the highest anti-EBV IgG values (144.3 U/mL vs 102.6 U/mL, P = 0.045). CD19(+) cells had the largest decrease in the group of CD patients that received treatment (138.6 vs 223.9, P = 0.022). The analysis of anti-EBV IgG with respect to the presence or absence of tonsillectomy showed the highest values in the tonsillectomy group of CD patients (169.2 ± 20.7 U/mL vs 106.1 ± 50.3 U/mL, P = 0.002). However, in the group of healthy controls, no differences were seen between those who had been tonsillectomized and subjects who had not been operated on (134.0 ± 52.5 U/mL vs 127.7 ± 48.1 U/mL, P = 0.523). High anti-EBV IgG levels in CD are associated with 5-aminosalicylic acid treatment, tonsillectomy, and decrease of CD19(+) cells.

Crude cellulase from oil palm empty fruit bunch by Trichoderma asperellum UPM1 and Aspergillus fumigatus UPM2 for fermentable sugars production.

PubMed

Ibrahim, M F; Razak, M N A; Phang, L Y; Hassan, M A; Abd-Aziz, S

2013-07-01

Cellulase is an enzyme that converts the polymer structure of polysaccharides into fermentable sugars. The high market demand for this enzyme together with the variety of applications in the industry has brought the research on cellulase into focus. In this study, crude cellulase was produced from oil palm empty fruit bunch (OPEFB) pretreated with 2% NaOH with autoclave, which was composed of 59.7% cellulose, 21.6% hemicellulose, and 12.3% lignin using Trichoderma asperellum UPM1 and Aspergillus fumigatus UPM2. Approximately 0.8 U/ml of FPase, 24.7 U/ml of CMCase and 5.0 U/ml of β-glucosidase were produced by T. asperellum UPM1 at a temperature of 35 °C and at an initial pH of 7.0. A 1.7 U/ml of FPase, 24.2 U/ml of CMCase, and 1.1 U/ml of β-glucosidase were produced by A. fumigatus UPM2 at a temperature of 45 °C and at initial pH of 6.0. The crude cellulase was best produced at 1% of substrate concentration for both T. asperellum UPM1 and A. fumigatus UPM2. The hydrolysis percentage of pretreated OPEFB using 5% of crude cellulase concentration from T. asperellum UPM1 and A. fumigatus UPM2 were 3.33% and 19.11%, with the reducing sugars concentration of 1.47 and 8.63 g/l, respectively.

Metadata mapping and reuse in caBIG™

PubMed Central

Kunz, Isaac; Lin, Ming-Chin; Frey, Lewis

2009-01-01

Background This paper proposes that interoperability across biomedical databases can be improved by utilizing a repository of Common Data Elements (CDEs), UML model class-attributes and simple lexical algorithms to facilitate the building domain models. This is examined in the context of an existing system, the National Cancer Institute (NCI)'s cancer Biomedical Informatics Grid (caBIG™). The goal is to demonstrate the deployment of open source tools that can be used to effectively map models and enable the reuse of existing information objects and CDEs in the development of new models for translational research applications. This effort is intended to help developers reuse appropriate CDEs to enable interoperability of their systems when developing within the caBIG™ framework or other frameworks that use metadata repositories. Results The Dice (di-grams) and Dynamic algorithms are compared and both algorithms have similar performance matching UML model class-attributes to CDE class object-property pairs. With algorithms used, the baselines for automatically finding the matches are reasonable for the data models examined. It suggests that automatic mapping of UML models and CDEs is feasible within the caBIG™ framework and potentially any framework that uses a metadata repository. Conclusion This work opens up the possibility of using mapping algorithms to reduce cost and time required to map local data models to a reference data model such as those used within caBIG™. This effort contributes to facilitating the development of interoperable systems within caBIG™ as well as other metadata frameworks. Such efforts are critical to address the need to develop systems to handle enormous amounts of diverse data that can be leveraged from new biomedical methodologies. PMID:19208192

Incremental checking of Master Data Management model based on contextual graphs

NASA Astrophysics Data System (ADS)

Lamolle, Myriam; Menet, Ludovic; Le Duc, Chan

2015-10-01

The validation of models is a crucial step in distributed heterogeneous systems. In this paper, an incremental validation method is proposed in the scope of a Model Driven Engineering (MDE) approach, which is used to develop a Master Data Management (MDM) field represented by XML Schema models. The MDE approach presented in this paper is based on the definition of an abstraction layer using UML class diagrams. The validation method aims to minimise the model errors and to optimisethe process of model checking. Therefore, the notion of validation contexts is introduced allowing the verification of data model views. Description logics specify constraints that the models have to check. An experimentation of the approach is presented through an application developed in ArgoUML IDE.

The Neighborhood Auditing Tool: a hybrid interface for auditing the UMLS.

PubMed

Morrey, C Paul; Geller, James; Halper, Michael; Perl, Yehoshua

2009-06-01

The UMLS's integration of more than 100 source vocabularies, not necessarily consistent with one another, causes some inconsistencies. The purpose of auditing the UMLS is to detect such inconsistencies and to suggest how to resolve them while observing the requirement of fully representing the content of each source in the UMLS. A software tool, called the Neighborhood Auditing Tool (NAT), that facilitates UMLS auditing is presented. The NAT supports "neighborhood-based" auditing, where, at any given time, an auditor concentrates on a single-focus concept and one of a variety of neighborhoods of its closely related concepts. Typical diagrammatic displays of concept networks have a number of shortcomings, so the NAT utilizes a hybrid diagram/text interface that features stylized neighborhood views which retain some of the best features of both the diagrammatic layouts and text windows while avoiding the shortcomings. The NAT allows an auditor to display knowledge from both the Metathesaurus (concept) level and the Semantic Network (semantic type) level. Various additional features of the NAT that support the auditing process are described. The usefulness of the NAT is demonstrated through a group of case studies. Its impact is tested with a study involving a select group of auditors.

NeuroNames: an ontology for the BrainInfo portal to neuroscience on the web.

PubMed

Bowden, Douglas M; Song, Evan; Kosheleva, Julia; Dubach, Mark F

2012-01-01

BrainInfo ( http://braininfo.org ) is a growing portal to neuroscientific information on the Web. It is indexed by NeuroNames, an ontology designed to compensate for ambiguities in neuroanatomical nomenclature. The 20-year old ontology continues to evolve toward the ideal of recognizing all names of neuroanatomical entities and accommodating all structural concepts about which neuroscientists communicate, including multiple concepts of entities for which neuroanatomists have yet to determine the best or 'true' conceptualization. To make the definitions of structural concepts unambiguous and terminologically consistent we created a 'default vocabulary' of unique structure names selected from existing terminology. We selected standard names by criteria designed to maximize practicality for use in verbal communication as well as computerized knowledge management. The ontology of NeuroNames accommodates synonyms and homonyms of the standard terms in many languages. It defines complex structures as models composed of primary structures, which are defined in unambiguous operational terms. NeuroNames currently relates more than 16,000 names in eight languages to some 2,500 neuroanatomical concepts. The ontology is maintained in a relational database with three core tables: Names, Concepts and Models. BrainInfo uses NeuroNames to index information by structure, to interpret users' queries and to clarify terminology on remote web pages. NeuroNames is a resource vocabulary of the NLM's Unified Medical Language System (UMLS, 2011) and the basis for the brain regions component of NIFSTD (NeuroLex, 2011). The current version has been downloaded to hundreds of laboratories for indexing data and linking to BrainInfo, which attracts some 400 visitors/day, downloading 2,000 pages/day.

An approach for software-driven and standard-based support of cross-enterprise tumor boards.

PubMed

Mangesius, Patrick; Fischer, Bernd; Schabetsberger, Thomas

2015-01-01

For tumor boards, the networking of different medical disciplines' expertise continues to gain importance. However, interdisciplinary tumor boards spread across several institutions are rarely supported by information technology tools today. The aim of this paper is to point out an approach for a tumor board management system prototype. For analyzing the requirements, an incremental process was used. The requirements were surveyed using Informal Conversational Interview and documented with Use Case Diagrams defined by the Unified Modeling Language (UML). Analyses of current EHR standards were conducted to evaluate technical requirements. Functional and technical requirements of clinical conference applications were evaluated and documented. In several steps, workflows were derived and application mockups were created. Although there is a vast amount of common understanding concerning how clinical conferences should be conducted and how their workflows should be structured, these are hardly standardized, neither on a functional nor on a technical level. This results in drawbacks for participants and patients. Using modern EHR technologies based on profiles such as IHE Cross Enterprise document sharing (XDS), these deficits could be overcome.

In their own words? A terminological analysis of e-mail to a cancer information service.

PubMed Central

Smith, Catherine Arnott; Stavri, P. Zoë; Chapman, Wendy Webber

2002-01-01

OBJECTIVE: To better understand the terms used by consumers to describe their health information needs and determine if this "consumer terminology"differs from those used by health care professionals. METHODS: Features and findings identified in 139 e-mail messages to the University of Pittsburgh Cancer Institute's Cancer Information and Referral Service were coded and matched against the 2001 Unified Medical Language System Metathesaurus. RESULTS:504 unique terms were identified. 185 (36%) were exact matches to concepts in the 2001 UMLS Metathesaurus (MTH). 179 (35%) were partial string matches; 119 (24%) were known synonyms for MTH concepts; and 2 (<1%) were lexical variants. Only 19,or 4% of the total terms, were not found to be present in the 2001 MT1H. CONCLUSION: 96% of the clinical findings and features mentioned in e-mail by correspondents who did not self-identify as healthcare professionals were described using terms from controlled healthcare terminologies. The notion of a paradigmatic "consumer" who uses a particular vocabulary specific to her "consumer" status may be ill-founded. PMID:12463914

A MATLAB toolbox for the efficient estimation of the psychometric function using the updated maximum-likelihood adaptive procedure.

PubMed

Shen, Yi; Dai, Wei; Richards, Virginia M

2015-03-01

A MATLAB toolbox for the efficient estimation of the threshold, slope, and lapse rate of the psychometric function is described. The toolbox enables the efficient implementation of the updated maximum-likelihood (UML) procedure. The toolbox uses an object-oriented architecture for organizing the experimental variables and computational algorithms, which provides experimenters with flexibility in experimental design and data management. Descriptions of the UML procedure and the UML Toolbox are provided, followed by toolbox use examples. Finally, guidelines and recommendations of parameter configurations are given.

Executable Architecture Modeling and Simulation Based on fUML

DTIC Science & Technology

2014-06-01

SoS behaviors. Wang et al.[9] use SysML sequence diagram to model the behaviors and translate the models into Colored Petri Nets (CPN). Staines T.S...Renzhong and Dagli C H. An executable system architecture approach to discrete events system modeling using SysML in conjunction with colored Petri

A model-based design and validation approach with OMEGA-UML and the IF toolset

NASA Astrophysics Data System (ADS)

Ben-hafaiedh, Imene; Constant, Olivier; Graf, Susanne; Robbana, Riadh

2009-03-01

Intelligent, embedded systems such as autonomous robots and other industrial systems are becoming increasingly more heterogeneous with respect to the platforms on which they are implemented, and thus the software architecture more complex to design and analyse. In this context, it is important to have well-defined design methodologies which should be supported by (1) high level design concepts allowing to master the design complexity, (2) concepts for the expression of non-functional requirements and (3) analysis tools allowing to verify or invalidate that the system under development will be able to conform to its requirements. We illustrate here such an approach for the design of complex embedded systems on hand of a small case study used as a running example for illustration purposes. We briefly present the important concepts of the OMEGA-RT UML profile, we show how we use this profile in a modelling approach, and explain how these concepts are used in the IFx verification toolbox to integrate validation into the design flow and make scalable verification possible.

14-3-3η Autoantibodies: Diagnostic Use in Early Rheumatoid Arthritis.

PubMed

Maksymowych, Walter P; Boire, Gilles; van Schaardenburg, Dirkjan; Wichuk, Stephanie; Turk, Samina; Boers, Maarten; Siminovitch, Katherine A; Bykerk, Vivian; Keystone, Ed; Tak, Paul Peter; van Kuijk, Arno W; Landewé, Robert; van der Heijde, Desiree; Murphy, Mairead; Marotta, Anthony

2015-09-01

To describe the expression and diagnostic use of 14-3-3η autoantibodies in early rheumatoid arthritis (RA). 14-3-3η autoantibody levels were measured using an electrochemiluminescent multiplexed assay in 500 subjects (114 disease-modifying antirheumatic drug-naive patients with early RA, 135 with established RA, 55 healthy, 70 autoimmune, and 126 other non-RA arthropathy controls). 14-3-3η protein levels were determined in an earlier analysis. Two-tailed Student t tests and Mann-Whitney U tests compared differences among groups. Receiver-operator characteristic (ROC) curves were generated and diagnostic performance was estimated by area under the curve (AUC), as well as specificity, sensitivity, and likelihood ratios (LR) for optimal cutoffs. Median serum 14-3-3η autoantibody concentrations were significantly higher (p < 0.0001) in patients with early RA (525 U/ml) when compared with healthy controls (235 U/ml), disease controls (274 U/ml), autoimmune disease controls (274 U/ml), patients with osteoarthritis (259 U/ml), and all controls (265 U/ml). ROC curve analysis comparing early RA with healthy controls demonstrated a significant (p < 0.0001) AUC of 0.90 (95% CI 0.85-0.95). At an optimal cutoff of ≥ 380 U/ml, the ROC curve yielded a sensitivity of 73%, a specificity of 91%, and a positive LR of 8.0. Adding 14-3-3η autoantibodies to 14-3-3η protein positivity enhanced the identification of patients with early RA from 59% to 90%; addition of 14-3-3η autoantibodies to anticitrullinated protein antibodies (ACPA) and/or rheumatoid factor (RF) increased identification from 72% to 92%. Seventy-two percent of RF- and ACPA-seronegative patients were positive for 14-3-3η autoantibodies. 14-3-3η autoantibodies, alone and in combination with the 14-3-3η protein, RF, and/or ACPA identified most patients with early RA.

High variation of individual soluble serum CD30 levels of pre-transplantation patients: sCD30 a feasible marker for prediction of kidney allograft rejection?

PubMed

Altermann, Wolfgang; Schlaf, Gerald; Rothhoff, Anita; Seliger, Barbara

2007-10-01

Previous studies have suggested that the pre-transplant levels of the soluble CD30 molecule (sCD30) represent a non-invasive tool which can be used as a biomarker for the prediction of kidney allograft rejections. In order to evaluate the feasibility of sCD30 for pre-transplantation monitoring the sera of potential kidney recipients (n = 652) were collected four times in a 3 months interval. Serum from healthy blood donors (n = 203) served as controls. The sCD30 concentrations of all samples were determined using a commercially available ELISA. This strategy allowed the detection of possible variations of individual sCD30 levels over time. Heterogeneous sCD30 concentrations were found in the samples obtained from individual putative kidney transplant recipients when quarterly measured over 1 year. Total 95% of serum samples obtained from healthy controls exhibited sCD30 values <30 U/ml, whereas most recipients displayed higher serum levels (>30 U/ml). Total 524 patients (80.4%) constantly exhibited serum concentrations of <100 U/ml during the period investigated, whereas 109 patients (16.7%) showed variations by exceeding the proposed 'cut off' of 100 U/ml for one to three times. The frequency of samples exhibiting sCD30 values >100 U/ml was significantly lower than that previously reported. The high degree of variation does not allow the stratification of patients into high and low immunological risk groups based on a single sCD30 value > 100 U/ml. Due to the heterogeneity of sCD30 levels during time course and the high values of SD, its implementation as a pre-transplant marker cannot be justified to generate special provisions for the organ allocation to patients with single sCD30 values > 100 U/ml.

Evaluation Methodology for UML and GML Application Schemas Quality

NASA Astrophysics Data System (ADS)

Chojka, Agnieszka

2014-05-01

INSPIRE Directive implementation in Poland has caused the significant increase of interest in making spatial data and services available, particularly among public administration and private institutions. This entailed a series of initiatives that aim to harmonise different spatial data sets, so to ensure their internal logical and semantic coherence. Harmonisation lets to reach the interoperability of spatial databases, then among other things enables joining them together. The process of harmonisation requires either working out new data structures or adjusting existing data structures of spatial databases to INSPIRE guidelines and recommendations. Data structures are described with the use of UML and GML application schemas. Although working out accurate and correct application schemas isn't an easy task. There should be considered many issues, for instance recommendations of ISO 19100 series of Geographic Information Standards, appropriate regulations for given problem or topic, production opportunities and limitations (software, tools). In addition, GML application schema is deeply connected with UML application schema, it should be its translation. Not everything that can be expressed in UML, though can be directly expressed in GML, and this can have significant influence on the spatial data sets interoperability, and thereby the ability to valid data exchange. For these reasons, the capability to examine and estimate UML and GML application schemas quality, therein also the capability to explore their entropy, would be very important. The principal subject of this research is to propose an evaluation methodology for UML and GML application schemas quality prepared in the Head Office of Geodesy and Cartography in Poland within the INSPIRE Directive implementation works.

Prediction of acute renal allograft rejection in early post-transplantation period by soluble CD30.

PubMed

Dong, Wang; Shunliang, Yang; Weizhen, Wu; Qinghua, Wang; Zhangxin, Zeng; Jianming, Tan; He, Wang

2006-06-01

To evaluate the feasibility of serum sCD30 for prediction of acute graft rejection, we analyzed clinical data of 231 patients, whose serum levels of sCD30 were detected by ELISA before and after transplantation. They were divided into three groups: acute rejection group (AR, n = 49), uncomplicated course group (UC, n = 171) and delayed graft function group (DGF, n = 11). Preoperative sCD30 levels of three groups were 183 +/- 74, 177 +/- 82 and 168 +/- 53 U/ml, respectively (P = 0.82). Significant decrease of sCD30 was detected in three groups on day 5 and 10 post-transplantation respectively (52 +/- 30 and 9 +/- 5 U/ml respectively, P < 0.001). Compared with Group UC and DGF, patients of Group AR had higher sCD30 values on day 5 post-transplantation (92 +/- 27 U/ml vs. 41 +/- 20 U/ml and 48 +/- 18 U/ml, P < 0.001). However, sCD30 levels on day 10 post-transplantation were virtually similar in patients of three groups (P = 0.43). Receiver operating characteristic (ROC) curve demonstrated that sCD30 level on day 5 post-transplantation could differentiate patients who subsequently suffered acute allograft rejection from others (area under ROC curve 0.95). According to ROC curve, 65 U/ml may be the optimal operational cut-off level to predict impending graft rejection (specificity 91.8%, sensitivity 87.1%). Measurement of soluble CD30 on day 5 post-transplantation might offer a noninvasive means to recognize patients at risk of impending acute graft rejection during early post-transplantation period.

Supporting Development of Satellite's Guidance Navigation and Control Software: A Product Line Approach

NASA Technical Reports Server (NTRS)

McComas, David; Stark, Michael; Leake, Stephen; White, Michael; Morisio, Maurizio; Travassos, Guilherme H.; Powers, Edward I. (Technical Monitor)

2000-01-01

The NASA Goddard Space Flight Center Flight Software Branch (FSB) is developing a Guidance, Navigation, and Control (GNC) Flight Software (FSW) product line. The demand for increasingly more complex flight software in less time while maintaining the same level of quality has motivated us to look for better FSW development strategies. The GNC FSW product line has been planned to address the core GNC FSW functionality very similar on many recent low/near Earth missions in the last ten years. Unfortunately these missions have not accomplished significant drops in development cost since a systematic approach towards reuse has not been adopted. In addition, new demands are continually being placed upon the FSW which means the FSB must become more adept at providing GNC FSW functionality's core so it can accommodate additional requirements. These domain features together with engineering concepts are influencing the specification, description and evaluation of FSW product line. Domain engineering is the foundation for emerging product line software development approaches. A product line is 'A family of products designed to take advantage of their common aspects and predicted variabilities'. In our product line approach, domain engineering includes the engineering activities needed to produce reusable artifacts for a domain. Application engineering refers to developing an application in the domain starting from reusable artifacts. The focus of this paper is regarding the software process, lessons learned and on how the GNC FSW product line manages variability. Existing domain engineering approaches do not enforce any specific notation for domain analysis or commonality and variability analysis. Usually, natural language text is the preferred tool. The advantage is the flexibility and adapt ability of natural language. However, one has to be ready to accept also its well-known drawbacks, such as ambiguity, inconsistency, and contradictions. While most domain analysis approaches are functionally oriented, the idea of applying the object-oriented approach in domain analysis is not new. Some authors propose to use UML as the notation underlying domain analysis. Our work is based on the same idea of merging UML and domain analysis. Further, we propose a few extensions to UML in order to express variability, and we define precisely their semantics so that a tool can support them. The extensions are designed to be implemented on the API of a popular industrial CASE tool, with obvious advantages in cost and availability of tool support. The paper outlines the product line processes and identifies where variability must be addressed. Then it describes the product line products with respect to how they accommodate variability. The Celestial Body subdomain is used as a working example. Our results to date are summarized and plans for the future are described.

Knowledge modeling in image-guided neurosurgery: application in understanding intraoperative brain shift

NASA Astrophysics Data System (ADS)

Cohen-Adad, Julien; Paul, Perrine; Morandi, Xavier; Jannin, Pierre

2006-03-01

During an image-guided neurosurgery procedure, the neuronavigation system is subject to inaccuracy because of anatomical deformations which induce a gap between the preoperative images and their anatomical reality. Thus, the objective of many research teams is to succeed in quantifying these deformations in order to update preoperative images. Anatomical intraoperative deformations correspond to a complex spatio-temporal phenomenon. Our objective is to identify the parameters implicated in these deformations and to use these parameters as constrains for systems dedicated to updating preoperative images. In order to identify these parameters of deformation we followed the iterative methodology used for cognitive system conception: identification, conceptualization, formalization, implementation and validation. A state of the art about cortical deformations has been established in order to identify relevant parameters probably involved in the deformations. As a first step, 30 parameters have been identified and described following an ontological approach. They were formalized into a Unified Modeling Language (UML) class diagram. We implemented that model into a web-based application in order to fill a database. Two surgical cases have been studied at this moment. After having entered enough surgical cases for data mining purposes, we expect to identify the most relevant and influential parameters and to gain a better ability to understand the deformation phenomenon. This original approach is part of a global system aiming at quantifying and correcting anatomical deformations.

An agent-based hydroeconomic model to evaluate water policies in Jordan

NASA Astrophysics Data System (ADS)

Yoon, J.; Gorelick, S.

2014-12-01

Modern water systems can be characterized by a complex network of institutional and private actors that represent competing sectors and interests. Identifying solutions to enhance water security in such systems calls for analysis that can adequately account for this level of complexity and interaction. Our work focuses on the development of a hierarchical, multi-agent, hydroeconomic model that attempts to realistically represent complex interactions between hydrologic and multi-faceted human systems. The model is applied to Jordan, one of the most water-poor countries in the world. In recent years, the water crisis in Jordan has escalated due to an ongoing drought and influx of refugees from regional conflicts. We adopt a modular approach in which biophysical modules simulate natural and engineering phenomena, and human modules represent behavior at multiple scales of decision making. The human modules employ agent-based modeling, in which agents act as autonomous decision makers at the transboundary, state, organizational, and user levels. A systematic nomenclature and conceptual framework is used to characterize model agents and modules. Concepts from the Unified Modeling Language (UML) are adopted to promote clear conceptualization of model classes and process sequencing, establishing a foundation for full deployment of the integrated model in a scalable object-oriented programming environment. Although the framework is applied to the Jordanian water context, it is generalizable to other regional human-natural freshwater supply systems.

A MATLAB toolbox for the efficient estimation of the psychometric function using the updated maximum-likelihood adaptive procedure

PubMed Central

Richards, V. M.; Dai, W.

2014-01-01

A MATLAB toolbox for the efficient estimation of the threshold, slope, and lapse rate of the psychometric function is described. The toolbox enables the efficient implementation of the updated maximum-likelihood (UML) procedure. The toolbox uses an object-oriented architecture for organizing the experimental variables and computational algorithms, which provides experimenters with flexibility in experimental design and data management. Descriptions of the UML procedure and the UML Toolbox are provided, followed by toolbox use examples. Finally, guidelines and recommendations of parameter configurations are given. PMID:24671826

Uncompacted Myelin Lamellae and Nodal Ion Channel Disruption in POEMS Syndrome.

PubMed

Hashimoto, Rina; Koike, Haruki; Takahashi, Mie; Ohyama, Ken; Kawagashira, Yuichi; Iijima, Masahiro; Sobue, Gen

2015-12-01

To elucidate the significance of uncompacted myelin lamellae (UML) and ion channel disruption at the nodes of Ranvier in the polyneuropathy, organomegaly, endocrinopathy, monoclonal gammopathy, and skin changes (POEMS) syndrome, we evaluated sural nerve biopsy specimens from 33 patients with POEMS syndrome and from 7 control patients. Uncompacted myelin lamellae distribution was assessed by electron microscopy and immunofluorescence microscopy. In the POEMS patient biopsies, UML were seen more frequently in small versus large myelinated fibers. Paranodes and Schmidt-Lanterman incisures, where normal physiologic UM is located, were frequently associated with UM. Widening of the nodes of Ranvier (i.e. segmental demyelination) was not associated with UML. There was axonal hollowing with neurofilament condensation at Schmidt-Lanterman incisures with abnormal UML, suggesting axonal damage at those sites in the POEMS patient biopsies. Myelin sheath irregularity was conspicuous in large myelinated fibers and was associated with abnormally widened bizarrely shaped Schmidt-Lanterman incisures. Indirect immunofluorescent studies revealed abnormalities of sodium (pan sodium) and potassium (KCNQ2) channels, even at nonwidened nodes of Ranvier. Thus, UML was not apparently associated with segmental demyelination but seemed to be associated with axonal damage. These observations suggest that nodal ion channel disruption may be associated with functional deficits in POEMS syndrome patient nerves.

Evaluation of the heat balance constituents of the upper mixed layer in the North Atlantic

NASA Astrophysics Data System (ADS)

Polonsky, A. B.; Sukhonos, P. A.

2016-11-01

Different physical mechanisms which cause interannual and interdecadal temperature anomalies in the upper mixed layer (UML) of the North Atlantic are investigated using the data of ORA-S3 reanalysis for the period of 1959-2011. It is shown that the annual mean heat budget in UML is mainly caused by the balance between advective heat transfer and horizontal turbulent mixing (estimated as a residual term in the equation of thermal balance). The local UML temperature change and contribution from the heat fluxes on the lower boundary of the UML to the heat budget of the upper layer are insignificant for the time scale under consideration. The contribution of the heat fluxes on the upper UML boundary to the low-frequency variability of the upper layer temperature in the whole North Atlantic area is substantially less than 30%. Areas like the northwestern part of the Northern Subtropical Anticyclonic Gyre (NSAG), where their contribution exceeds 30-60%, are exceptions. The typical time scales of advective heat transfer variability are revealed. In the NSAG area, an interannual variability associated with the North Atlantic Oscillation dominates, while in the North Atlantic subpolar gyre, an interdecadal variability of advective transfers with periods of more than 30 years prevails.

Semantic web data warehousing for caGrid.

PubMed

McCusker, James P; Phillips, Joshua A; González Beltrán, Alejandra; Finkelstein, Anthony; Krauthammer, Michael

2009-10-01

The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrating this information. Although the data models exposed on caGrid are semantically well annotated, it is currently up to the caGrid client to infer relationships between the different models and their classes. In this paper, we present a Semantic Web-based data warehouse (Corvus) for creating relationships among caGrid models. This is accomplished through the transformation of semantically-annotated caBIG Unified Modeling Language (UML) information models into Web Ontology Language (OWL) ontologies that preserve those semantics. We demonstrate the validity of the approach by Semantic Extraction, Transformation and Loading (SETL) of data from two caGrid data sources, caTissue and caArray, as well as alignment and query of those sources in Corvus. We argue that semantic integration is necessary for integration of data from distributed web services and that Corvus is a useful way of accomplishing this. Our approach is generalizable and of broad utility to researchers facing similar integration challenges.

A Prototype Symbolic Model of Canonical Functional Neuroanatomy of the Motor System

PubMed Central

Rubin, Daniel L.; Halle, Michael; Musen, Mark; Kikinis, Ron

2008-01-01

Recent advances in bioinformatics have opened entire new avenues for organizing, integrating and retrieving neuroscientific data, in a digital, machine-processable format, which can be at the same time understood by humans, using ontological, symbolic data representations. Declarative information stored in ontological format can be perused and maintained by domain experts, interpreted by machines, and serve as basis for a multitude of decision-support, computerized simulation, data mining, and teaching applications. We have developed a prototype symbolic model of canonical neuroanatomy of the motor system. Our symbolic model is intended to support symbolic lookup, logical inference and mathematical modeling by integrating descriptive, qualitative and quantitative functional neuroanatomical knowledge. Furthermore, we show how our approach can be extended to modeling impaired brain connectivity in disease states, such as common movement disorders. In developing our ontology, we adopted a disciplined modeling approach, relying on a set of declared principles, a high-level schema, Aristotelian definitions, and a frame-based authoring system. These features, along with the use of the Unified Medical Language System (UMLS) vocabulary, enable the alignment of our functional ontology with an existing comprehensive ontology of human anatomy, and thus allow for combining the structural and functional views of neuroanatomy for clinical decision support and neuroanatomy teaching applications. Although the scope of our current prototype ontology is limited to a particular functional system in the brain, it may be possible to adapt this approach for modeling other brain functional systems as well. PMID:18164666

[Standardization of terminology in laboratory medicine I].

PubMed

Yoon, Soo Young; Yoon, Jong Hyun; Min, Won Ki; Lim, Hwan Sub; Song, Junghan; Chae, Seok Lae; Lee, Chang Kyu; Kwon, Jung Ah; Lee, Kap No

2007-04-01

Standardization of medical terminology is essential for data transmission between health-care institutions or clinical laboratories and for maximizing the benefits of information technology. Purpose of our study was to standardize the medical terms used in the clinical laboratory, such as test names, units, terms used in result descriptions, etc. During the first year of the study, we developed a standard database of concept names for laboratory terms, which covered the terms used in government health care centers, their branch offices, and primary health care units. Laboratory terms were collected from the electronic data interchange (EDI) codes from National Health Insurance Corporation (NHIC), Logical Observation Identifier Names and Codes (LOINC) database, community health centers and their branch offices, and clinical laboratories of representative university medical centers. For standard expression, we referred to the English-Korean/ Korean-English medical dictionary of Korean Medical Association and the rules for foreign language translation. Programs for mapping between LOINC DB and EDI code and for translating English to Korean were developed. A Korean standard laboratory terminology database containing six axial concept names such as components, property, time aspect, system (specimen), scale type, and method type was established for 7,508 test observations. Short names and a mapping table for EDI codes and Unified Medical Language System (UMLS) were added. Synonym tables for concept names, words used in the database, and six axial terms were prepared to make it easier to find the standard terminology with common terms used in the field of laboratory medicine. Here we report for the first time a Korean standard laboratory terminology database for test names, result description terms, result units covering most laboratory tests in primary healthcare centers.

Towards automated traceability maintenance

PubMed Central

Mäder, Patrick; Gotel, Orlena

2012-01-01

Traceability relations support stakeholders in understanding the dependencies between artifacts created during the development of a software system and thus enable many development-related tasks. To ensure that the anticipated benefits of these tasks can be realized, it is necessary to have an up-to-date set of traceability relations between the established artifacts. This goal requires the creation of traceability relations during the initial development process. Furthermore, the goal also requires the maintenance of traceability relations over time as the software system evolves in order to prevent their decay. In this paper, an approach is discussed that supports the (semi-) automated update of traceability relations between requirements, analysis and design models of software systems expressed in the UML. This is made possible by analyzing change events that have been captured while working within a third-party UML modeling tool. Within the captured flow of events, development activities comprised of several events are recognized. These are matched with predefined rules that direct the update of impacted traceability relations. The overall approach is supported by a prototype tool and empirical results on the effectiveness of tool-supported traceability maintenance are provided. PMID:23471308

[Changes in levels of chorionic gonadotrophin (hCG) and its subunit alpha and beta in pregnancy complicated by diabetes (GDM)].

PubMed

Olszewski, J; Szczurowicz, A; Wójcikowski, C

1995-02-01

The aim of the study was estimation of endocrinological function of placenta in pregnancy complicated by GDM. The study were performed on a group 13 women with GDM and 14 women in normal pregnancy. All women with GDM were treat by diet and intensive insulinotherapy with self monitoring levels of glucose. In women with GDM level of fructosamine and HbAlc were significant higher but in normal range. In 28 and 36 week of pregnancy were determined levels of hCG, alpha hCG, beta hCG, in serum. Level of hCG in control group and in women with GDM were respectively 97.29 U/ml vs. 29.29 U/ml, p < 0.01 in 28 week of pregnancy and 77.23 U/ml vs. 37.93 U/ml, p < 0.05 in 36 week. Level of alpha hCG was lower and beta hCG was higher in group with GDM.

Administration of human recombinant activated protein C is not associated with pancreatic parenchymal haemorrhage in L-arginine-induced experimental acute pancreatitis.

PubMed

Jamdar, Saurabh; Babu, Benoy I; Nirmalan, Mahesh; Jeziorska, Maria; McMahon, Raymond F T; Siriwardena, Ajith K

2013-11-10

Microvascular thrombosis is a critical event in severe acute pancreatitis. Human recombinant activated protein C (Xigris®, Eli Lilly, Indianapolis, IN, USA) modulates the interplay between pro-inflammatory and pro-coagulant pathways and maintains microvascular patency. However, the anticoagulant properties of Xigris® may precipitate bleeding from the inflamed pancreas. This study tests the hypothesis that Xigris® can ameliorate experimental acute pancreatitis without causing pancreatic haemorrhage. Sprague Dawley rats were allocated as follows: Group 1: control (n=7); Group 2: acute pancreatitis (n=6); Group 3: administration of Xigris® 500 µg/kg body weight before induction of acute pancreatitis (n=6); and Group 4: Administration of Xigris® 500 µg/kg body weight 30 minutes after induction of acute pancreatitis (n=6). Acute pancreatitis was induced by intraperitoneal administration of L-arginine 300 mg/100 g body weight. Animals were sacrificed at 48 hours and biochemical, haematological, and histological markers of pancreatic haemorrhage and inflammation assessed. Median lipase in animals with acute pancreatitis was 10 U/mL (range: 7-16 U/mL) compared to 5.5 (range: 3-8 U/mL) in controls (P=0.028). Lipase was also elevated in animals given Xigris® both before (12 U/mL, range: 8-22 U/mL; P=0.031 vs. control group) and after (46 U/mL, range: 9-71 U/mL; P=0.015 vs. control group) induction of acute pancreatitis). Haemoglobin levels were similar among all groups (P=0.323). There was no histological evidence of pancreatic haemorrhage in animals treated with Xigris®. Pre-treatment with Xigris® was associated with a significant reduction in pancreatic injury. This effect was absent when Xigris® was administered after induction of acute pancreatitis. Xigris® did not lead to pancreatic haemorrhage in experimental acute pancreatitis. Administration of Xigris® prior to induction of acute pancreatitis was associated with amelioration of injury. This effect was not seen with administration of Xigris® after induction of acute pancreatitis.

Plasma levels of soluble CD30 in kidney graft recipients as predictors of acute allograft rejection.

PubMed

Ayed, K; Abdallah, T B; Bardi, R; Abderrahim, E; Kheder, A

2006-09-01

In renal transplant recipients elevated soluble serum CD30 levels are associated with increased rejection and graft loss. We sought to determine the sCD30 plasma levels before and after kidney transplantation and to assess whether sCD30 was a predictive factor of immunological risk. sCD30 plasma levels were determined by an enzyme-linked immunosorbent assay assay in 52 kidney graft recipients before as well as 7, 15, and 21 days after transplantation. Eighteen patients developed acute allograft rejection (group I) and 34 patients showed uneventful courses (group II). Before transplantation sCD30 plasma levels were elevated in both groups (mean: 162.6 +/- 89.5 U/mL). After transplantation, group I recipients with acute rejection showed higher relative levels of plasma sCD30 on days 7 and 15 (120.8 +/- 74.6 U/mL and 210.6 +/- 108.7 U/mL respectively) compared with group II patients without rejection (95 +/- 45 U/mL and 59.4 +/- 31.6 U/mL), a difference that was significant for group I (P = .0003) and not significant for group II (P = .09). On day 21, sCD30 decreased in the two groups but remained higher among group I patients (120.6 +/- 92.7 U/mL). HLA antibodies were positive in 18 patients (34.6%) with 9 (50%) experiencing at last one episode of acute rejection. Among 34 patients negative for anti-HLA antibodies, nine displayed acute rejection only (26.4%), a difference that was not significant (P > .05). If we consider 100 U/mL as the minimum predictive level for allograft rejection, our results suggested that levels of sCD30 should be taken into consideration with the presence of HLA-antibodies detectable before and after transplantation, especially in patients with more than three HLA mismatches [RR = 3.20 (0.94 < RR < 10.91)]. These data suggested that measurement of plasma sCD30 is a useful procedure for the recognition of rejection in its earliest stages.

Epstein-Barr virus in multiple sclerosis.

PubMed

Abdelrahman, Hisham S; Selim, Heba S; Hashish, Mona H; Sultan, Lobna I

2014-08-01

Multiple sclerosis (MS) is an inflammatory disorder of the central nervous system. Many diseases are associated with Epstein-Barr virus (EBV) infection, such as infectious mononucleosis and many types of malignancies, and it is thought to be related to some diseases of autoimmune origin, such as rheumatoid arthritis, systemic lupus erythematosis, and others. The present study aimed to assess EBV in patients with MS. This case-control study was conducted from October 2012 to September 2013 on 75 MS patients and non-MS controls. Both were tested quantitatively for immunoglobulin G (IgG) antibodies against Epstein-Barr nuclear antigen-1 (EBNA1) and viral capsid antigen (VCA) using the enzyme linked immunosorbent assay technique. Seventy MS patients (93.3%) were positive for EBNA1 IgG compared with 68 controls (90.7%). In MS patients, the mean EBNA1 IgG serum level was 310.91 (±131.05) U/ml; meanwhile, among controls the mean serum EBNA IgG level was 177.81 (±104.98) U/ml.All patients with MS were positive for VCA IgG, whereas only 60 (80.0%) controls were positive. In the MS group, the VCA IgG mean level was 302.19 (±152.11) U/ml compared with 167.94 (±111.79) U/ml in controls. The differences in the serum levels of both markers between the two groups were statistically significant (P<0.001). EBV proved to have a unique immunological pattern in MS patients when compared with non-MS controls. Further studies for more confirmation of the relation between EBV and MS on a large scale are recommended.

SAFOD Brittle Microstructure and Mechanics Knowledge Base (SAFOD BM2KB)

NASA Astrophysics Data System (ADS)

Babaie, H. A.; Hadizadeh, J.; di Toro, G.; Mair, K.; Kumar, A.

2008-12-01

We have developed a knowledge base to store and present the data collected by a group of investigators studying the microstructures and mechanics of brittle faulting using core samples from the SAFOD (San Andreas Fault Observatory at Depth) project. The investigations are carried out with a variety of analytical and experimental methods primarily to better understand the physics of strain localization in fault gouge. The knowledge base instantiates an specially-designed brittle rock deformation ontology developed at Georgia State University. The inference rules embedded in the semantic web languages, such as OWL, RDF, and RDFS, which are used in our ontology, allow the Pellet reasoner used in this application to derive additional truths about the ontology and knowledge of this domain. Access to the knowledge base is via a public website, which is designed to provide the knowledge acquired by all the investigators involved in the project. The stored data will be products of studies such as: experiments (e.g., high-velocity friction experiment), analyses (e.g., microstructural, chemical, mass transfer, mineralogical, surface, image, texture), microscopy (optical, HRSEM, FESEM, HRTEM]), tomography, porosity measurement, microprobe, and cathodoluminesence. Data about laboratories, experimental conditions, methods, assumptions, equipments, and mechanical properties and lithology of the studied samples will also be presented on the website per investigation. The ontology was modeled applying the UML (Unified Modeling Language) in Rational Rose, and implemented in OWL-DL (Ontology Web Language) using the Protégé ontology editor. The UML model was converted to OWL-DL by first mapping it to Ecore (.ecore) and Generator model (.genmodel) with the help of the EMF (Eclipse Modeling Framework) plugin in Eclipse. The Ecore model was then mapped to a .uml file, which later was converted into an .owl file and subsequently imported into the Protégé ontology editing environment. The web-interface was developed in java using eclipse as the IDE. The web interfaces to query and submit data were implemented applying JSP, servlets, javascript, and AJAX. The Jena API, a Java framework for building Semantic Web applications, was used to develop the web-interface. Jena provided a programmatic environment for RDF, RDFS, OWL, and SPARQL query engine. Building web applications with AJAX helps retrieving data from the server asynchronously in the background without interfering with the display and behavior of the existing page. The application was deployed on an apache tomcat server at GSU. The SAFOD BM2KB website provides user-friendly search, submit, feedback, and other services. The General Search option allows users to search the knowledge base by selecting the classes (e.g., Experiment, Surface Analysis), their respective attributes (e.g., apparatus, date performed), and the relationships to other classes (e.g., Sample, Laboratory). The Search by Sample option allows users to search the knowledge base based on sample number. The Search by Investigator lets users to search the knowledge base by choosing an investigator who is involved in this project. The website also allows users to submit new data. The Submit Data option opens a page where users can submit the SAFOD data to our knowledge base by selecting specific classes and attributes. The submitted data then become available for query as part of the knowledge base. The SAFOD BM2KB can be accessed from the main SAFOD website.

Object-oriented design tools for supramolecular devices and biomedical nanotechnology.

PubMed

Lee, Stephen C; Bhalerao, Khaustaub; Ferrari, Mauro

2004-05-01

Nanotechnology provides multifunctional agents for in vivo use that increasingly blur the distinction between pharmaceuticals and medical devices. Realization of such therapeutic nanodevices requires multidisciplinary effort that is difficult for individual device developers to sustain, and identification of appropriate collaborations outside ones own field can itself be challenging. Further, as in vivo nanodevices become increasingly complex, their design will increasingly demand systems level thinking. System engineering tools such as object-oriented analysis, object-oriented design (OOA/D) and unified modeling language (UML) are applicable to nanodevices built from biological components, help logically manage the knowledge needed to design them, and help identify useful collaborative relationships for device designers. We demonstrate the utility of these systems engineering tools by reverse engineering an existing molecular device (the bacmid molecular cloning system) using them, and illustrate how object-oriented approaches identify fungible components (objects) in nanodevices in a way that facilitates design of families of related devices, rather than single inventions. We also explore the utility of object-oriented approaches for design of another class of therapeutic nanodevices, vaccines. While they are useful for design of current nanodevices, the power of systems design tools for biomedical nanotechnology will become increasingly apparent as the complexity and sophistication of in vivo nanosystems increases. The nested, hierarchical nature of object-oriented approaches allows treatment of devices as objects in higher-order structures, and so will facilitate concatenation of multiple devices into higher-order, higher-function nanosystems.

Consistency of Rasch Model Parameter Estimation: A Simulation Study.

ERIC Educational Resources Information Center

van den Wollenberg, Arnold L.; And Others

1988-01-01

The unconditional--simultaneous--maximum likelihood (UML) estimation procedure for the one-parameter logistic model produces biased estimators. The UML method is inconsistent and is not a good alternative to conditional maximum likelihood method, at least with small numbers of items. The minimum Chi-square estimation procedure produces unbiased…

A Systems Analysis and Design Case Study for a Business Modeling Learning Experience for a Capstone CIS/IS Systems Development Class

ERIC Educational Resources Information Center

Russell, Jack; Russell, Barbara

2015-01-01

The goal is to provide a robust and challenging problem statement for a capstone, advanced systems analysis and design course for CIS/MIS/CS majors. In addition to the problem narrative, a representative solution for much of the business modeling deliverables is presented using the UML paradigm. A structured analysis deliverable will be the topic…

Information Retrieval Using UMLS-based Structured Queries

PubMed Central

Fagan, Lawrence M.; Berrios, Daniel C.; Chan, Albert; Cucina, Russell; Datta, Anupam; Shah, Maulik; Surendran, Sujith

2001-01-01

During the last three years, we have developed and described components of ELBook, a semantically based information-retrieval system [1-4]. Using these components, domain experts can specify a query model, indexers can use the query model to index documents, and end-users can search these documents for instances of indexed queries.

Arranging ISO 13606 archetypes into a knowledge base using UML connectors.

PubMed

Kopanitsa, Georgy

2014-01-01

To enable the efficient reuse of standard based medical data we propose to develop a higher-level information model that will complement the archetype model of ISO 13606. This model will make use of the relationships that are specified in UML to connect medical archetypes into a knowledge base within a repository. UML connectors were analysed for their ability to be applied in the implementation of a higher-level model that will establish relationships between archetypes. An information model was developed using XML Schema notation. The model allows linking different archetypes of one repository into a knowledge base. Presently it supports several relationships and will be advanced in future.

Graphical modeling and query language for hospitals.

PubMed

Barzdins, Janis; Barzdins, Juris; Rencis, Edgars; Sostaks, Agris

2013-01-01

So far there has been little evidence that implementation of the health information technologies (HIT) is leading to health care cost savings. One of the reasons for this lack of impact by the HIT likely lies in the complexity of the business process ownership in the hospitals. The goal of our research is to develop a business model-based method for hospital use which would allow doctors to retrieve directly the ad-hoc information from various hospital databases. We have developed a special domain-specific process modelling language called the MedMod. Formally, we define the MedMod language as a profile on UML Class diagrams, but we also demonstrate it on examples, where we explain the semantics of all its elements informally. Moreover, we have developed the Process Query Language (PQL) that is based on MedMod process definition language. The purpose of PQL is to allow a doctor querying (filtering) runtime data of hospital's processes described using MedMod. The MedMod language tries to overcome deficiencies in existing process modeling languages, allowing to specify the loosely-defined sequence of the steps to be performed in the clinical process. The main advantages of PQL are in two main areas - usability and efficiency. They are: 1) the view on data through "glasses" of familiar process, 2) the simple and easy-to-perceive means of setting filtering conditions require no more expertise than using spreadsheet applications, 3) the dynamic response to each step in construction of the complete query that shortens the learning curve greatly and reduces the error rate, and 4) the selected means of filtering and data retrieving allows to execute queries in O(n) time regarding the size of the dataset. We are about to continue developing this project with three further steps. First, we are planning to develop user-friendly graphical editors for the MedMod process modeling and query languages. The second step is to do evaluation of usability the proposed language and tool involving the physicians from several hospitals in Latvia and working with real data from these hospitals. Our third step is to develop an efficient implementation of the query language.

The Equivalence of Two Methods of Parameter Estimation for the Rasch Model.

ERIC Educational Resources Information Center

Blackwood, Larry G.; Bradley, Edwin L.

1989-01-01

Two methods of estimating parameters in the Rasch model are compared. The equivalence of likelihood estimations from the model of G. J. Mellenbergh and P. Vijn (1981) and from usual unconditional maximum likelihood (UML) estimation is demonstrated. Mellenbergh and Vijn's model is a convenient method of calculating UML estimates. (SLD)

Modified UMS, Modified SemRep and SemMedDB-UTH | Informatics Technology for Cancer Research (ITCR)

Cancer.gov

Modified UMLS, modified SemRep and SemMedDB-UTH – these are resources (UMLS, SemMedDB-UT) and tools (SemRep) created and maintained by National Library of Medicine that we have modified for personalized cancer therapy and returned to the NLM.

A Software Hub for High Assurance Model-Driven Development and Analysis

DTIC Science & Technology

2007-01-23

verification of UML models in TLPVS. In Thomas Baar, Alfred Strohmeier, Ana Moreira, and Stephen J. Mellor, editors, UML 2004 - The Unified Modeling...volume 3785 of Lecture Notes in Computer Science, pages 52–65, Manchester, UK, Nov 2005. Springer. [GH04] Günter Graw and Peter Herrmann. Transformation

Modeling Value Chain Analysis of Distance Education using UML

NASA Astrophysics Data System (ADS)

Acharya, Anal; Mukherjee, Soumen

2010-10-01

Distance education continues to grow as a methodology for the delivery of course content in higher education in India as well as abroad. To manage this growing demand and to provide certain flexibility, there must be certain strategic planning about the use of ICT tools. Value chain analysis is a framework for breaking down the sequence of business functions into a set of activities through which utility could be added to service. Thus it can help to determine the competitive advantage that is enjoyed by an institute. To implement these business functions certain visual representation is required. UML allows for this representation by using a set of structural and behavioral diagrams. In this paper, the first section defines a framework for value chain analysis and highlights its advantages. The second section gives a brief overview of related work in this field. The third section gives a brief discussion on distance education. The fourth section very briefly introduces UML. The fifth section models value chain of distance education using UML. Finally we discuss the limitations and the problems posed in this domain.

Celiac disease: Serologic prevalence in patients with irritable bowel syndrome.

PubMed

Mehdi, Zobeiri; Sakineh, Ebrahimi; Mohammad, Farahvash; Mansour, Rezaei; Alireza, Abdollahi

2012-09-01

The prevalence of irritable bowel syndrome (IBS) in the community is 10%-20% and have symptom based diagnostic criteria. Many symptoms of celiac disease (CD) with 1% prevalence in some communities can mimic IBS. Sensitive and specific serologic tests of CD can detect asymptomatic cases. The purpose of this study was to compare the level of anti-tissue-transglutaminase (tTG) IgA in IBS patients and controls group. This case-control study was performed at a University hospital in which 107 patients with IBS who met the Rome II criteria for their diagnosis were compared with 126 healthy age and sex-matched controls. Both groups were investigated for CD by analysis of their serum tTG IgA antibody with human recombinant antigen. Titers were positive containing over 10u/ml and borderline if they were between 4 and 10 u/ml. 86 percent of IBS patients were female. The mean antibody level was 0.837 u/ml in IBS group and 0.933 u/ml in control group without any significant difference. Results of this study may intensify disagreement on the situation of CD in IBS patients.

Alteration of white-rot basidiomycetes cellulase and xylanase activities in the submerged co-cultivation and optimization of enzyme production by Irpex lacteus and Schizophyllum commune.

PubMed

Metreveli, Eka; Kachlishvili, Eva; Singer, Steven W; Elisashvili, Vladimir

2017-10-01

Mono and dual cultures of four white-rot basidiomycete species were evaluated for cellulase and xylanase activity under submerged fermentation conditions. Co-cultivation of Pycnoporus coccineus or Trametes hirsuta with Schizophyllum commune displayed antagonistic interactions resulting in the decrease of endoglucanase and total cellulase activities. In contrast, increases in cellulase and xylanase activity were revealed through the compatible interactions of Irpex lacteus with S. commune. Co-cultivation conditions were optimized for maximum enzyme production by I. lacteus and S. commune, the best producers of cellulase/xylanase and β-glucosidase, respectively. An optimized medium for the target enzyme production by the mixed culture was established in a laboratory fermenter yielding 7U/mL total cellulase, 142U/mL endoglucanase, 104U/mL xylanase, and 5.2U/mL β-glucosidase. The dual culture approach resulted in an enzymatic mixture with 11% improved lignocellulose saccharification potential compared to enzymes from a monoculture of I. lacteus. Copyright © 2017 Elsevier Ltd. All rights reserved.

Co-production of tannase and pectinase by free and immobilized cells of the yeast Rhodotorula glutinis MP-10 isolated from tannin-rich persimmon (Diospyros kaki L.) fruits.

PubMed

Taskin, Mesut

2013-02-01

Hyper tannase and pectinase-producing yeast Rhodotorula glutinis MP-10 was isolated from persimmon (Diospyros kaki L.) fruits. The main pectinase activity of yeast was exo-polygalacturonase. No pectin methyl esterase and too low pectin lyase activities were detected for this yeast. The maximum exo-activities of tannase and polygalacturonase were determined as 15.2 and 26.9 U/mL for free cells and 19.8 and 28.6 U/mL for immobilized cells, respectively. Immobilized cells could be reused in 13 successive reaction cycles without any loss in the maximum tannase and polygalacturonase activities. Besides, too little decreases in activities of these enzymes were recorded between 14 and 18 cycles. At the end of 18 successive reaction cycles, total 503.1 U/mL of polygalacturonase and 349.6 U/mL of tannase could be produced using the same immobilized cells. This is the first report on the use of free and/or immobilized cells of a microorganism for the co-production of tannase and pectinase.

Evaluation of serum sCD30 in renal transplantation patients with and without acute rejection.

PubMed

Cervelli, C; Fontecchio, G; Scimitarra, M; Azzarone, R; Famulari, A; Pisani, F; Battistoni, C; Di Iulio, B; Fracassi, D; Scarnecchia, M A; Papola, F

2009-05-01

Despite new immunosuppressive approaches, acute rejection episodes (ARE) are still a major cause of early kidney dysfunction with a negative impact on long-term allograft survival. Noninvasive markers able to identify renal ARE earlier than creatinine measurement include sCD30. We sought to establish whether circulating levels of sCD30 in pretransplantation and posttransplantation periods were of clinical relevance to avoid graft damage. Quantitative detection of serum sCD30 was performed using an enzyme-linked immunosorbent assay. Our results demonstrated that the mean concentrations of sCD30 were significantly higher in the sera of renal transplant recipients with ARE (30.04 U/mL) and in uremic patients on the waiting list (37.7 U/mL) compared with healthy controls (HC; 9.44 U/mL), but not nonrejecting patients (12.01 U/mL). Statistical analysis revealed a strong association between high sCD30 levels in posttransplantation sera and ARE risk. This study suggested that sCD30 levels were a reliable predictor of ARE among deceased-donor kidney recipients.

Dynamic Gate Product and Artifact Generation from System Models

NASA Technical Reports Server (NTRS)

Jackson, Maddalena; Delp, Christopher; Bindschadler, Duane; Sarrel, Marc; Wollaeger, Ryan; Lam, Doris

2011-01-01

Model Based Systems Engineering (MBSE) is gaining acceptance as a way to formalize systems engineering practice through the use of models. The traditional method of producing and managing a plethora of disjointed documents and presentations ("Power-Point Engineering") has proven both costly and limiting as a means to manage the complex and sophisticated specifications of modern space systems. We have developed a tool and method to produce sophisticated artifacts as views and by-products of integrated models, allowing us to minimize the practice of "Power-Point Engineering" from model-based projects and demonstrate the ability of MBSE to work within and supersede traditional engineering practices. This paper describes how we have created and successfully used model-based document generation techniques to extract paper artifacts from complex SysML and UML models in support of successful project reviews. Use of formal SysML and UML models for architecture and system design enables production of review documents, textual artifacts, and analyses that are consistent with one-another and require virtually no labor-intensive maintenance across small-scale design changes and multiple authors. This effort thus enables approaches that focus more on rigorous engineering work and less on "PowerPoint engineering" and production of paper-based documents or their "office-productivity" file equivalents.

High pre-transplant soluble CD30 levels are predictive of the grade of rejection.

PubMed

Rajakariar, Ravindra; Jivanji, Naina; Varagunam, Mira; Rafiq, Mohammad; Gupta, Arun; Sheaff, Michael; Sinnott, Paul; Yaqoob, M M

2005-08-01

In renal transplantation, serum soluble CD30 (sCD30) levels in graft recipients are associated with increased rejection and graft loss. We investigated whether pre-transplant sCD30 concentrations are predictive of the grade of rejection. Pre-transplant sera of 51 patients with tubulointerstitial rejection (TIR), 16 patients with vascular rejection (VR) and an age-matched control group of 41 patients with no rejection (NR) were analyzed for sCD30. The transplant biopsies were immunostained for C4d. The median sCD30 level was significantly elevated in the group with VR (248 Units (U)/mL, range: 92-802) when compared with TIR (103 U/mL, range: 36-309, p<0.001) and NR (179 U/mL, range: 70-343, p<0.03). Moreover, patients with TIR had significantly lower sCD30 levels compared to NR. Based on C4d staining, a TH2 driven process, the median sCD30 levels were significantly raised in C4d+ patients compared with C4d- group (177 U/mL vs. 120 U/mL, p<0.05). sCD30 levels measured at time of transplantation correlate with the grade of rejection. High pre-transplant levels are associated with antibody-mediated rejection which carries a poorer prognosis. sCD30 could be another tool to assess immunological risk prior to transplantation and enable a patient centered approach to immunosuppression.

Scale-up of an alkaline protease from Bacillus pumilus MTCC 7514 utilizing fish meal as a sole source of nutrients.

PubMed

Gupta, Rishikesh Kumar; Prasad, Dinesh; Sathesh, Jaykumar; Naidu, Ramachandra Boopathy; Kamini, Numbi Ramudu; Palanivel, Saravanan; Gowthaman, Marichetti Kuppuswami

2012-09-01

Fish meal grades SL1 and SL2 from Sardine (Sardinella longiceps) and NJ from Pink Perch (Nemipterus japonicas) were evaluated as a sole source of carbon and nitrogen in the medium for alkaline protease production by Bacillus pumilus MTCC 7514. The analysis of the fish meal suggests that the carbon and nitrogen contents in fish meal are sufficient to justify its choice as replacement for other nutrients. Protease production increased significantly (4,914 U/ml) in medium containing only fish meal, compared with the basal medium (2,646 U/ml). However, the elimination of inorganic salts from media reduced the protease productivity. In addition, all the three grades of fish meal yielded almost the same amounts of protease when employed as the sole source of carbon and nitrogen. Nevertheless, the best results were observed in fish meal SL1 medium. Furthermore, protease production was enhanced to 6,966 U/ml and 7,047 U/ml on scaling up from flask (4,914 U/ml) to 3.7 and 20 L fermenters, respectively, using fish meal (10 g/l). Similarly, the corresponding improvement in productivities over flask (102.38 U/ml/h) was 193.5 and 195.75 U/ml/h in 3.7 and 20 L fermenters, respectively. The crude protease was found to have dehairing ability in leather processing, which is bound to have great environmental benefits.

Using knowledge for indexing health web resources in a quality-controlled gateway.

PubMed

Joubert, Michel; Darmoni, Stefan J; Avillach, Paul; Dahamna, Badisse; Fieschi, Marius

2008-01-01

The aim of this study is to provide to indexers MeSH terms to be considered as major ones in a list of terms automatically extracted from a document. We propose a method combining symbolic knowledge - the UMLS Metathesaurus and Semantic Network - and statistical knowledge drawn from co-occurrences of terms in the CISMeF database (a French-language quality-controlled health gateway) using data mining measures. The method was tested on CISMeF corpus of 293 resources. There was a proportion of 0.37+/-0.26 major terms in the processed records. The method produced lists of terms with a proportion of terms initially pointed out as major of 0.54+/-0.31. The method we propose reduces the number of terms, which seem not useful for content description of resources, such as "check tags", but retains the most descriptive ones. Discarding these terms is accounted for by: 1) the removal by using semantic knowledge of associations of concepts bearing no real medical significance, 2) the removal by using statistical knowledge of nonstatistically significant associations of terms. This method can assist effectively indexers in their daily work and will be soon applied in the CISMeF system.

Terminology tools: state of the art and practical lessons.

PubMed

Cimino, J J

2001-01-01

As controlled medical terminologies evolve from simple code-name-hierarchy arrangements, into rich, knowledge-based ontologies of medical concepts, increased demands are placed on both the developers and users of the terminologies. In response, researchers have begun developing tools to address their needs. The aims of this article are to review previous work done to develop these tools and then to describe work done at Columbia University and New York Presbyterian Hospital (NYPH). Researchers working with the Systematized Nomenclature of Medicine (SNOMED), the Unified Medical Language System (UMLS), and NYPH's Medical Entities Dictionary (MED) have created a wide variety of terminology browsers, editors and servers to facilitate creation, maintenance and use of these terminologies. Although much work has been done, no generally available tools have yet emerged. Consensus on requirement for tool functions, especially terminology servers is emerging. Tools at NYPH have been used successfully to support the integration of clinical applications and the merger of health care institutions. Significant advancement has occurred over the past fifteen years in the development of sophisticated controlled terminologies and the tools to support them. The tool set at NYPH provides a case study to demonstrate one feasible architecture.

[Analysis of health terminologies for use as ontologies in healthcare information systems].

PubMed

Romá-Ferri, Maria Teresa; Palomar, Manuel

2008-01-01

Ontologies are a resource that allow the concept of meaning to be represented informatically, thus avoiding the limitations imposed by standardized terms. The objective of this study was to establish the extent to which terminologies could be used for the design of ontologies, which could be serve as an aid to resolve problems such as semantic interoperability and knowledge reusability in healthcare information systems. To determine the extent to which terminologies could be used as ontologies, six of the most important terminologies in clinical, epidemiologic, documentation and administrative-economic contexts were analyzed. The following characteristics were verified: conceptual coverage, hierarchical structure, conceptual granularity of the categories, conceptual relations, and the language used for conceptual representation. MeSH, DeCS and UMLS ontologies were considered lightweight. The main differences among these ontologies concern conceptual specification, the types of relation and the restrictions among the associated concepts. SNOMED and GALEN ontologies have declaratory formalism, based on logical descriptions. These ontologies include explicit qualities and show greater restrictions among associated concepts and rule combinations and were consequently considered as heavyweight. Analysis of the declared representation of the terminologies shows the extent to which they could be reused as ontologies. Their degree of usability depends on whether the aim is for healthcare information systems to solve problems of semantic interoperability (lightweight ontologies) or to reuse the systems' knowledge as an aid to decision making (heavyweight ontologies) and for non-structured information retrieval, extraction, and classification.

Downregulation of cell survival signalling pathways and increased cell damage in hydrogen peroxide-treated human renal proximal tubular cells by alpha-erythropoietin.

PubMed

Andreucci, M; Fuiano, G; Presta, P; Lucisano, G; Leone, F; Fuiano, L; Bisesti, V; Esposito, P; Russo, D; Memoli, B; Faga, T; Michael, A

2009-08-01

Erythropoietin has been shown to have a protective effect in certain models of ischaemia-reperfusion, and in some cases the protection has been correlated with activation of signalling pathways known to play a role in cell survival and proliferation. We have studied whether erythropoietin would overcome direct toxic effects of hydrogen peroxide (H(2)O(2)) treatment to human renal proximal tubular (HK-2) cells. HK-2 cells were incubated with H(2)O(2) (2 mm) for 2 h with or without erythropoietin at concentrations of 100 and 400 U/ml, and cell viability/proliferation was assessed by chemical reduction of MTT. Changes in phosphorylation state of the kinases Akt, glycogen synthase kinase-3beta (GSK-3beta), mammalian target of rapamycin (mTOR) and extracellular signal-regulated kinase 1 and 2 (ERK1/ERK2) were also analysed. Cells incubated with H(2)O(2) alone showed a significant decrease in viability, which did not significantly change by addition of erythropoietin at concentration of 100 U/ml, but was further reduced when concentration of erythropoietin was increased to 400 U/ml. Phosphorylation state of the kinases Akt, GSK-3beta, mTOR and ERK1/ERK2 of H(2)O(2)-treated HK-2 cells was slightly altered in the presence of erythropoietin at concentration of 100 U/ml, but was significantly less in the presence of erythropoietin at a concentration of 400 U/ml. Phosphorylation of forkhead transcription factor FKHRL1 was diminished in cells incubated with H(2)O(2) and erythropoietin at a concentration of 400 U/ml. Erythropoietin, at high concentrations, may significantly increase cellular damage in HK-2 cells subjected to oxidative stress, which may be due in part to decrease in activation of important signalling pathways involved in cell survival and/or cell proliferation.

INSULIN GLARGINE 300 U/ML IS ASSOCIATED WITH LESS WEIGHT GAIN WHILE MAINTAINING GLYCEMIC CONTROL AND LOW RISK OF HYPOGLYCEMIA COMPARED WITH INSULIN GLARGINE 100 U/ML IN AN AGING POPULATION WITH TYPE 2 DIABETES.

PubMed

Munshi, Medha N; Gill, Jasvinder; Chao, Jason; Nikonova, Elena V; Patel, Meenakshi

2018-02-01

Assess efficacy, hypoglycemia, and weight gain in patients with type 2 diabetes (T2D) treated with insulin glargine 300 U/mL (Gla-300) or 100 U/mL (Gla-100) across different age groups. Pooled data were generated for patients randomized to Gla-300 or Gla-100 in the EDITION 2 (NCT01499095) and 3 (NCT01676220) studies. In 4 age groups (<55, ≥55 to <60, ≥60 to <65, ≥65 years), glycated hemoglobin A1C (A1C), percentage of patients reaching A1C <7.5% (58 mmol/mol), weight change, confirmed hypoglycemia (blood glucose ≤70 mg/dL), and/or severe hypoglycemia (events requiring third-party assistance) were analyzed with descriptive statistics and logistic, binomial, and analysis of covariance regression modeling. A1C reductions from baseline and proportions of patients at target were similar for Gla-300 and Gla-100 across all age groups at 6 and 12 months, but hypoglycemia incidence and event rate were lower with Gla-300 at 6 (both P<.001) and 12 months ( P<.001 and P = .005, respectively). Patients on Gla-300 gained less weight than those on Gla-100 at 6 ( P = .027) and 12 months ( P = .021). Changes in weight and daily weight-adjusted insulin dose decreased with increasing age at 6 ( P<.001 and P = .017, respectively) and 12 months ( P<.001 and P = .011, respectively). Older patients with T2D may benefit from treatment with Gla-300, which is associated with a lower hypoglycemia rate and less weight gain with similar efficacy compared with Gla-100. A1C = glycated hemoglobin A1C BMI = body mass index Gla-100 = insulin glargine 100 U/mL Gla-300 = insulin glargine 300 U/mL OAD = oral antidiabetes drug T2D = type 2 diabetes.

Soluble CD30 in patients with antibody-mediated rejection of the kidney allograft.

PubMed

Slavcev, Antonij; Honsova, Eva; Lodererova, Alena; Pavlova, Yelena; Sajdlova, Helena; Vitko, Stefan; Skibova, Jelena; Striz, Ilja; Viklicky, Ondrej

2007-07-01

The aim of our retrospective study was to evaluate the clinical significance of measurement of the soluble CD30 (sCD30) molecule for the prediction of antibody-mediated (humoral) rejection (HR). Sixty-two kidney transplant recipients (thirty-one C4d-positive and thirty-one C4d-negative patients) were included into the study. Soluble CD30 levels were evaluated before transplantation and during periods of graft function deterioration. The median concentrations of the sCD30 molecule were identical in C4d-positive and C4d-negative patients before and after transplantation (65.5 vs. 65.0 and 28.2 vs. 36.0 U/ml, respectively). C4d+ patients who developed DSA de novo had a tendency to have higher sCD30 levels before transplantation (80.7+/-53.6 U/ml, n=8) compared with C4d-negative patients (65.0+/-33.4 U/ml, n=15). Soluble CD30 levels were evaluated as positive and negative (>or=100 U/ml and <100 U/ml respectively) and the sensitivity, specificity and accuracy of sCD30 estimation with regard to finding C4d deposits in peritubular capillaries were determined. The sensitivity of sCD30+ testing was generally below 40%, while the specificity of the test, i.e. the likelihood that if sCD30 testing is negative, C4d deposits would be absent, was 82%. C4d+ patients who developed DSA de novo were evaluated separately; the specificity of sCD30 testing for the incidence of HR in this cohort was 86%. We could not confirm in our study that high sCD30 levels (>or=100 U/ml) might be predictive for the incidence of HR. Negative sCD30 values might be however helpful for identifying patients with a low risk for development of DSA and antibody-mediated rejection.

Evaluation of serum CA27.29, CA15-3 and CEA in patients with breast cancer.

PubMed

Hou, M F; Chen, Y L; Tseng, T F; Lin, C M; Chen, M S; Huang, C J; Huang, Y S; Hsieh, J S; Huang, T J; Jong, S B; Huang, Y F

1999-09-01

The Truquant BR radioimmunoassay (RIA) using monoclonal antibody BR 27.29 to recognize a peptide sequence on the MUC-1 gene product for quantification of the CA 27.29 antigen in serum was used in this report to evaluate in 145 patients with breast cancer and compared the other conventional serum markers such as CA15-3 and CEA. The upper limit of normal (25 u/ml) was determined from CA27.29 values 12.4 +/- 4.1 u/ml (mean +/- 3 S.D.) for 112 female subjects apparently free of disease. The CA15-3 levels above 25 u/ml and CEA levels above 5 ng/ml were considered positive values. Thirty-seven cases of 145 patients studied had elevated CA 27.29 levels (sensitivity: 25.5%), 35 of 145 had positive CA15-3 levels (sensitivity 24.1%) and 27 of 145 patients had positive CEA levels (sensitivity: 18.6%) (p < 0.05). One hundred and ten cases of the breast cancer patients (75.8%) did not have metastatic disease. In this group CA 27.29 sensitivity was 6.4%, while CA15-3 sensitivity was 5.5% and CEA sensitivity was 4.5% (p > 0.05). Mean values were 10.2 +/- 9.2 u/ml for CA 27.29, 14.1 +/- 5.6 u/ml for CA 15-3 and 1.7 +/- 1.5 ng/ml for CEA. Thirty-five patients (24.2%) had metastatic disease. In this group CA 27.29 sensitivity was 85.7%, CA15-3 sensitivity was 82.8% and CEA sensitivity was 62.8% (p < 0.05). Mean values for CA27.29 was 152.6 +/- 131.6 u/ml, CA15-3 was 123.1 +/- 107.6 u/ml and 21.8 +/- 36.9 ng/ml of CEA. With regard to the correlation of three tumor markers with clinical stages, patients had significantly higher levels of CA27.29 than CEA, but they were similar to CA 15-3 in metastatic breast cancer. These results suggest CA27.29 to be more sensitive and specific than CEA, but that it is similar to CA15-3 for metastatic breast cancer detection and monitoring.

Prognostic index for chronic- and smoldering-type adult T-cell leukemia-lymphoma.

PubMed

Katsuya, Hiroo; Shimokawa, Mototsugu; Ishitsuka, Kenji; Kawai, Kazuhiro; Amano, Masahiro; Utsunomiya, Atae; Hino, Ryosuke; Hanada, Shuichi; Jo, Tatsuro; Tsukasaki, Kunihiro; Moriuchi, Yukiyoshi; Sueoka, Eisaburo; Yoshida, Shinichiro; Suzushima, Hitoshi; Miyahara, Masaharu; Yamashita, Kiyoshi; Eto, Tetsuya; Suzumiya, Junji; Tamura, Kazuo

2017-07-06

Adult T-cell leukemia-lymphoma (ATL) has been divided into 4 clinical subtypes: acute, lymphoma, chronic, and smoldering. The aim of this study is to develop a novel prognostic index (PI) for chronic and smoldering ATL. We conducted a nationwide retrospective survey on ATL patients, and 248 fully eligible individuals were used in this analysis. In the univariate analysis, sex, performance status, log 10 (soluble interleukin-2 receptor [sIL-2R]), neutrophils count, and lymphadenopathy showed values of P < .05 in training samples. A multivariate analysis was performed on these factors, and only log 10 (sIL-2R) was identified as an independent prognostic factor in training samples. Using a regression coefficient of this variable, a prognostic model was formulated to identify different levels of risk: indolent ATL-PI (iATL-PI) = 1.51 × log 10 (sIL-2R [U/mL]). The values calculated by iATL-PI were divided into 3 groups using a quartile point. In the validation sample, median survival times (MSTs) were 1.6 years, 5.5 years, and not reached for patients in the high-, intermediate-, and low-risk groups, respectively ( P < .0001). To make the scoring system clinically practicable, we simplified iATL-PI according to trichotomizing sIL-2R at 1000 and 6000 U/mL, using a quartile point. Patients with more than 6000 U/mL sIL-2R were categorized into the high-risk group, less than and equal to 1000 U/mL into the low-risk group, and the others into the intermediate-risk group, and MSTs were 1.6 years, not reached, and 5.5 years, respectively ( P < .0001). iATL-PI has potential as a novel tool for a risk-adapted therapeutic approach. © 2017 by The American Society of Hematology.

Interleukin-2 Receptor and Angiotensin-Converting Enzyme as Markers for Ocular Sarcoidosis

PubMed Central

Gundlach, Enken; Hoffmann, Michael Marcus; Prasse, Antje; Heinzelmann, Sonja; Ness, Thomas

2016-01-01

Purpose To study the impact of soluble IL2 receptor (sIL2R), chest x-ray (CxR), and angiotensin-converting enzyme (ACE) as markers for sarcoidosis in uveitis patients. Design Retrospective study. Methods Serum concentrations of sIL2R and ACE were measured in patients with active uveitis. Those with elevated sIL2R and /or ACE values were examined for suspected systemic sarcoidosis. Main Outcome Measure Our main outcome parameters were the specificity and sensitivity of sIL2R, CxR and ACE in screening for ocular sarcoidosis. Results We measured 261 patients with uveitis for sarcoidosis using sIL2R and ACE between January 2008 and November 2011; sarcoidosis was been diagnosed using other tests (e.g. computer tomography, brochoalveolar lavage, biopsy) in 41 of 53 patients with elevated sIL2R values (>639 U/ml) and in one patient with normal sIL2R (582 U/ml). Their mean sIL2R value was 1310 U/ml, extending from 582 to 8659 U/ml. Only 9 patients, however, presented elevated ACE (>82 U/l). Their mean ACE value was 116.4 U/l, ranging from 84.1 to 175.5 U/l. IL2R specificity was 94% with 98% sensitivity. In contrast, ACE had a specificity of 99.5%, but a sensitivity of only 22%; the chest x-ray had a specificity of 100% with 50% sensitivity in detecting sarcoidosis. We observed the entire spectrum of uveitis: sixteen patients suffered from anterior, 8 from intermediate, 16 from posterior, and 2 from panuveitis. Conclusions An elevated level of soluble IL2R suggests sarcoidosis with uveitis more convincingly than ACE, making sIL2R a more effective marker parameter for sarcoidosis than ACE or chest x-ray in uveitis patients. PMID:26799486

Modeling Real-Time Applications with Reusable Design Patterns

NASA Astrophysics Data System (ADS)

Rekhis, Saoussen; Bouassida, Nadia; Bouaziz, Rafik

Real-Time (RT) applications, which manipulate important volumes of data, need to be managed with RT databases that deal with time-constrained data and time-constrained transactions. In spite of their numerous advantages, RT databases development remains a complex task, since developers must study many design issues related to the RT domain. In this paper, we tackle this problem by proposing RT design patterns that allow the modeling of structural and behavioral aspects of RT databases. We show how RT design patterns can provide design assistance through architecture reuse of reoccurring design problems. In addition, we present an UML profile that represents patterns and facilitates further their reuse. This profile proposes, on one hand, UML extensions allowing to model the variability of patterns in the RT context and, on another hand, extensions inspired from the MARTE (Modeling and Analysis of Real-Time Embedded systems) profile.

Development of a sandwich ELISA for the quantification of enterovirus 71.

PubMed

Ma, Shujun; Mao, Qunying; Liang, Zhenglun; Zhang, Cuijuan; Yang, Wenxing; Sun, Zhe; Zhang, Haijiang; Shen, Xinliang; Bi, Shengli; Sun, Le

2014-05-01

Since 2008, enterovirus 71 (EV71) has been responsible for high-mortality seasonal epidemics of hand, foot and mouth disease in China. Currently many groups in the world are in the process of developing EV71 vaccines to combat this deadly disease. We have developed three EV71-specific monoclonal antibodies, and in this study we report the establishment of a fast and cost-effective sandwich ELISA kit for measurement of virus concentration in EV71 vaccines using a pair of mouse anti-EV71 monoclonal antibodies. The system is specific for EV71 virus, with no cross-reactivity to coxsackievirus A16, H1N1, rabies, and hepatitis A. Using a reference EV71 vaccine standard, the sensitivity of the assay kit was determined to be 0.82 U/ml, with a linear range between 3.75 and 120 U/ml.

Sustained contraction and endothelial dysfunction induced by reactive oxygen species in porcine coronary artery.

PubMed

Ishihara, Yasuhiro; Sekine, Masaya; Hatano, Ai; Shimamoto, Norio

2008-09-01

A combination of purine and xanthine oxidase (XOD) dose-dependently elicited sustained contraction of porcine coronary arterial rings and resulted in increased concentrations of superoxide anions and hydrogen peroxide. These contractile responses appeared, with a delay, after the application of purine and XOD, used as a reactive oxygen species (ROS)-generating system. Coronary arteries precontracted with prostaglandin F(2alpha) failed to relax in response to substance P after exposing the arterial preparation to this ROS-generating system. The contractile response of the coronary artery to the ROS-generating system was almost completely inhibited by catalase (130 U/ml), and was partially inhibited by superoxide dismutase (60 U/ml), or mannitol (30 mM). A voltage-dependent L-type Ca(2+) channel antagonist, nicardipine, had no effect on contraction. Dysfunction of endothelial cells was completely prevented by catalase, but not by superoxide dismutase or mannitol. These results suggest that superoxide anions, hydrogen peroxide and hydroxyl radicals might be involved in eliciting sustained, delayed-onset coronary artery contraction, which is not related to L-type Ca(2+) channels. They also suggest that hydrogen peroxide might play a major role in endothelial dysfunction of the porcine coronary artery.

Automated UMLS-Based Comparison of Medical Forms

PubMed Central

Dugas, Martin; Fritz, Fleur; Krumm, Rainer; Breil, Bernhard

2013-01-01

Medical forms are very heterogeneous: on a European scale there are thousands of data items in several hundred different systems. To enable data exchange for clinical care and research purposes there is a need to develop interoperable documentation systems with harmonized forms for data capture. A prerequisite in this harmonization process is comparison of forms. So far – to our knowledge – an automated method for comparison of medical forms is not available. A form contains a list of data items with corresponding medical concepts. An automatic comparison needs data types, item names and especially item with these unique concept codes from medical terminologies. The scope of the proposed method is a comparison of these items by comparing their concept codes (coded in UMLS). Each data item is represented by item name, concept code and value domain. Two items are called identical, if item name, concept code and value domain are the same. Two items are called matching, if only concept code and value domain are the same. Two items are called similar, if their concept codes are the same, but the value domains are different. Based on these definitions an open-source implementation for automated comparison of medical forms in ODM format with UMLS-based semantic annotations was developed. It is available as package compareODM from http://cran.r-project.org. To evaluate this method, it was applied to a set of 7 real medical forms with 285 data items from a large public ODM repository with forms for different medical purposes (research, quality management, routine care). Comparison results were visualized with grid images and dendrograms. Automated comparison of semantically annotated medical forms is feasible. Dendrograms allow a view on clustered similar forms. The approach is scalable for a large set of real medical forms. PMID:23861827

Diagram, a Learning Environment for Initiation to Object-Oriented Modeling with UML Class Diagrams

ERIC Educational Resources Information Center

Py, Dominique; Auxepaules, Ludovic; Alonso, Mathilde

2013-01-01

This paper presents Diagram, a learning environment for object-oriented modelling (OOM) with UML class diagrams. Diagram an open environment, in which the teacher can add new exercises without constraints on the vocabulary or the size of the diagram. The interface includes methodological help, encourages self-correcting and self-monitoring, and…

Production of Cellulolytic and Hemicellulolytic Enzymes From Aureobasidium pulluans on Solid State Fermentation

NASA Astrophysics Data System (ADS)

Leite, Rodrigo Simões Ribeiro; Bocchini, Daniela Alonso; da Silva Martins, Eduardo; Silva, Dênis; Gomes, Eleni; da Silva, Roberto

This article investigates a strain of the yeast Aureobasidium pullulans for cellulase and hemicellulase production in solid state fermentation. Among the substrates analyzed, the wheat bran culture presented the highest enzymatic production (1.05 U/mL endoglucanase, 1.3 U/mL β-glucosidase, and 5.0 U/mL xylanase). Avicelase activity was not detected. The optimum pH and temperature for xylanase, endoglucanase and β-glucosidase were 5.0 and 50, 4.5 and 60, 4.0 and 75°C, respectively. These enzymes remained stable between a wide range of pH. The β-glucosidase was the most thermostable enzyme remaining 100% active when incubated at 75°C for 1 h.

Version Control in Project-Based Learning

ERIC Educational Resources Information Center

Milentijevic, Ivan; Ciric, Vladimir; Vojinovic, Oliver

2008-01-01

This paper deals with the development of a generalized model for version control systems application as a support in a range of project-based learning methods. The model is given as UML sequence diagram and described in detail. The proposed model encompasses a wide range of different project-based learning approaches by assigning a supervisory…

Design Of Computer Based Test Using The Unified Modeling Language

NASA Astrophysics Data System (ADS)

Tedyyana, Agus; Danuri; Lidyawati

2017-12-01

The Admission selection of Politeknik Negeri Bengkalis through interest and talent search (PMDK), Joint Selection of admission test for state Polytechnics (SB-UMPN) and Independent (UM-Polbeng) were conducted by using paper-based Test (PBT). Paper Based Test model has some weaknesses. They are wasting too much paper, the leaking of the questios to the public, and data manipulation of the test result. This reasearch was Aimed to create a Computer-based Test (CBT) models by using Unified Modeling Language (UML) the which consists of Use Case diagrams, Activity diagram and sequence diagrams. During the designing process of the application, it is important to pay attention on the process of giving the password for the test questions before they were shown through encryption and description process. RSA cryptography algorithm was used in this process. Then, the questions shown in the questions banks were randomized by using the Fisher-Yates Shuffle method. The network architecture used in Computer Based test application was a client-server network models and Local Area Network (LAN). The result of the design was the Computer Based Test application for admission to the selection of Politeknik Negeri Bengkalis.

Semantic web data warehousing for caGrid

PubMed Central

McCusker, James P; Phillips, Joshua A; Beltrán, Alejandra González; Finkelstein, Anthony; Krauthammer, Michael

2009-01-01

The National Cancer Institute (NCI) is developing caGrid as a means for sharing cancer-related data and services. As more data sets become available on caGrid, we need effective ways of accessing and integrating this information. Although the data models exposed on caGrid are semantically well annotated, it is currently up to the caGrid client to infer relationships between the different models and their classes. In this paper, we present a Semantic Web-based data warehouse (Corvus) for creating relationships among caGrid models. This is accomplished through the transformation of semantically-annotated caBIG® Unified Modeling Language (UML) information models into Web Ontology Language (OWL) ontologies that preserve those semantics. We demonstrate the validity of the approach by Semantic Extraction, Transformation and Loading (SETL) of data from two caGrid data sources, caTissue and caArray, as well as alignment and query of those sources in Corvus. We argue that semantic integration is necessary for integration of data from distributed web services and that Corvus is a useful way of accomplishing this. Our approach is generalizable and of broad utility to researchers facing similar integration challenges. PMID:19796399

A step forward in laccase exploitation: Recombinant production and evaluation of techno-economic feasibility of the process.

PubMed

Pezzella, Cinzia; Giacobelli, Valerio Guido; Lettera, Vincenzo; Olivieri, Giuseppe; Cicatiello, Paola; Sannia, Giovanni; Piscitelli, Alessandra

2017-10-10

Protein heterologous production offers viable opportunities to tailor laccase properties to specific industrial needs. The high redox potential laccase POXA1b from Pleurotus ostreatus was chosen as case study of marketable enzyme, due to its desirable properties in terms of activity/stability profile, and already assessed applicability. POXA1b was heterologously produced in Pichia pastoris by investigating the effect of inducible and constitutive expression systems on both the yield and the cost of its production. System performances were first assessed in shaken-flasks and then scaled-up in bioreactor. The production level obtained in the inducible system is 42U/mL, while the activity value achieved with the constitutive one is 60U/mL, the highest obtained in constitutive systems so far. The economic feasibility of recombinant laccase production was simulated, describing the case of an Italian small-medium enterprise. Two scenarios were evaluated: Scenario (I) production based on methanol inducible system; Scenario (II) production based on the constitutive system, fed with glycerol. At all the scales the glycerol-based fermentation is more economic than the methanol-based one. The price forecast for rPOXA1b production is 0.34€kU -1 for glycerol-based process, and is very competitive with the current price of commercial laccase. Copyright © 2017 Elsevier B.V. All rights reserved.

Enzymatic comparison and mortality of Beauveria bassiana against cabbage caterpillar Pieris brassicae LINN.

PubMed

Dhawan, Manish; Joshi, Neelam

Beauveria bassiana, an entomopathogenic fungus, is the alternative biocontrol agent exploited against major economic crop pests. Pieris brassicae L. is an emerging pest of the Brassicaceae family. Therefore, in the present study, fungal isolates of Beauveria bassiana, viz. MTCC 2028, MTCC 4495, MTCC 6291, and NBAII-11, were evaluated for their virulence against third instar larvae of P. brassicae. Among all these fungal isolates, maximum mortality (86.66%) was recorded in B. bassiana MTCC 4495 at higher concentration of spores (10 9 conidia/ml), and the minimum mortality (30.00%) was recorded in B. bassiana MTCC 6291 at a lower concentration (10 7 conidia/ml) after ten days of treatment. The extracellular cuticle-degrading enzyme activities of fungal isolates were measured. Variability was observed both in the pattern of enzyme secretion and the level of enzyme activities among various fungal isolates. B. bassiana MTCC 4495 recorded the maximum mean chitinase (0.51U/ml), protease (1.12U/ml), and lipase activities (1.36U/ml). The minimum mean chitinase and protease activities (0.37 and 0.91U/ml, respectively) were recorded in B. bassiana MTCC 6291. The minimum mean lipase activity (1.04U/ml) was recorded in B. bassiana NBAII-11. Our studies revealed B. bassiana MTCC 4495 as the most pathogenic isolate against P. brassicae, which also recorded maximum extracellular enzyme activities, suggesting the possible roles of extracellular enzymes in the pathogenicity of B. bassiana against P. brassicae. Copyright © 2017 Sociedade Brasileira de Microbiologia. Published by Elsevier Editora Ltda. All rights reserved.

Celiac disease: Serologic prevalence in patients with irritable bowel syndrome

PubMed Central

Mehdi, Zobeiri; Sakineh, Ebrahimi; Mohammad, Farahvash; Mansour, Rezaei; Alireza, Abdollahi

2012-01-01

Background: The prevalence of irritable bowel syndrome (IBS) in the community is 10%–20% and have symptom based diagnostic criteria. Many symptoms of celiac disease (CD) with 1% prevalence in some communities can mimic IBS. Sensitive and specific serologic tests of CD can detect asymptomatic cases. The purpose of this study was to compare the level of anti-tissue-transglutaminase (tTG) IgA in IBS patients and controls group. Materials and Methods: This case-control study was performed at a University hospital in which 107 patients with IBS who met the Rome II criteria for their diagnosis were compared with 126 healthy age and sex-matched controls. Both groups were investigated for CD by analysis of their serum tTG IgA antibody with human recombinant antigen. Titers were positive containing over 10u/ml and borderline if they were between 4 and 10 u/ml. Result: 86 percent of IBS patients were female. The mean antibody level was 0.837 u/ml in IBS group and 0.933 u/ml in control group without any significant difference. Discussion and Conclusion: Results of this study may intensify disagreement on the situation of CD in IBS patients. PMID:23826010

Resolving anaphoras for the extraction of drug-drug interactions in pharmacological documents

PubMed Central

2010-01-01

Background Drug-drug interactions are frequently reported in the increasing amount of biomedical literature. Information Extraction (IE) techniques have been devised as a useful instrument to manage this knowledge. Nevertheless, IE at the sentence level has a limited effect because of the frequent references to previous entities in the discourse, a phenomenon known as 'anaphora'. DrugNerAR, a drug anaphora resolution system is presented to address the problem of co-referring expressions in pharmacological literature. This development is part of a larger and innovative study about automatic drug-drug interaction extraction. Methods The system uses a set of linguistic rules drawn by Centering Theory over the analysis provided by a biomedical syntactic parser. Semantic information provided by the Unified Medical Language System (UMLS) is also integrated in order to improve the recognition and the resolution of nominal drug anaphors. Besides, a corpus has been developed in order to analyze the phenomena and evaluate the current approach. Each possible case of anaphoric expression was looked into to determine the most effective way of resolution. Results An F-score of 0.76 in anaphora resolution was achieved, outperforming significantly the baseline by almost 73%. This ad-hoc reference line was developed to check the results as there is no previous work on anaphora resolution in pharmalogical documents. The obtained results resemble those found in related-semantic domains. Conclusions The present approach shows very promising results in the challenge of accounting for anaphoric expressions in pharmacological texts. DrugNerAr obtains similar results to other approaches dealing with anaphora resolution in the biomedical domain, but, unlike these approaches, it focuses on documents reflecting drug interactions. The Centering Theory has proved being effective at the selection of antecedents in anaphora resolution. A key component in the success of this framework is the analysis provided by the MMTx program and the DrugNer system that allows to deal with the complexity of the pharmacological language. It is expected that the positive results of the resolver increases performance of our future drug-drug interaction extraction system. PMID:20406499

Knowledge translation: a case study on pneumonia research and clinical guidelines in a low- income country.

PubMed

Goyet, Sophie; Barennes, Hubert; Libourel, Therese; van Griensven, Johan; Frutos, Roger; Tarantola, Arnaud

2014-06-26

The process and effectiveness of knowledge translation (KT) interventions targeting policymakers are rarely reported. In Cambodia, a low-income country (LIC), an intervention aiming to provide evidence-based knowledge on pneumonia to health authorities was developed to help update pediatric and adult national clinical guidelines. Through a case study, we assessed the effectiveness of this KT intervention, with the goal of identifying the barriers to KT and suggest strategies to facilitate KT in similar settings. An extensive search for all relevant sources of data documenting the processes of updating adult and pediatric pneumonia guidelines was done. Documents included among others, reports, meeting minutes, and email correspondences. The study was conducted in successive phases: an appraisal of the content of both adult and pediatric pneumonia guidelines; an appraisal of the quality of guidelines by independent experts, using the AGREE-II instrument; a description and modeling of the KT process within the guidelines updating system, using the Unified Modeling Language (UML) tools 2.2; and the listing of the barriers and facilitators to KT we identified during the study. The first appraisal showed that the integration of the KT key messages in pediatric and adult guidelines varied with a better efficiency in the pediatric guidelines. The overall AGREE-II quality assessments scored 37% and 44% for adult and pediatric guidelines, respectively. Scores were lowest for the domains of 'rigor of development' and 'editorial independence.' The UML analysis highlighted that time frames and constraints of the involved stakeholders greatly differed and that there were several missed opportunities to translate on evidence into the adult pneumonia guideline. Seventeen facilitating factors and 18 potential barriers to KT were identified. Main barriers were related to the absence of a clear mandate from the Ministry of Health for the researchers and to a lack of synchronization between knowledge production and policy-making. Study findings suggest that stakeholders, both researchers and policy makers planning to update clinical guidelines in LIC may need methodological support to overcome the expected barriers.

Knowledge translation: a case study on pneumonia research and clinical guidelines in a low- income country

PubMed Central

2014-01-01

Background The process and effectiveness of knowledge translation (KT) interventions targeting policymakers are rarely reported. In Cambodia, a low-income country (LIC), an intervention aiming to provide evidence-based knowledge on pneumonia to health authorities was developed to help update pediatric and adult national clinical guidelines. Through a case study, we assessed the effectiveness of this KT intervention, with the goal of identifying the barriers to KT and suggest strategies to facilitate KT in similar settings. Methods An extensive search for all relevant sources of data documenting the processes of updating adult and pediatric pneumonia guidelines was done. Documents included among others, reports, meeting minutes, and email correspondences. The study was conducted in successive phases: an appraisal of the content of both adult and pediatric pneumonia guidelines; an appraisal of the quality of guidelines by independent experts, using the AGREE-II instrument; a description and modeling of the KT process within the guidelines updating system, using the Unified Modeling Language (UML) tools 2.2; and the listing of the barriers and facilitators to KT we identified during the study. Results The first appraisal showed that the integration of the KT key messages in pediatric and adult guidelines varied with a better efficiency in the pediatric guidelines. The overall AGREE-II quality assessments scored 37% and 44% for adult and pediatric guidelines, respectively. Scores were lowest for the domains of ‘rigor of development’ and ‘editorial independence.’ The UML analysis highlighted that time frames and constraints of the involved stakeholders greatly differed and that there were several missed opportunities to translate on evidence into the adult pneumonia guideline. Seventeen facilitating factors and 18 potential barriers to KT were identified. Main barriers were related to the absence of a clear mandate from the Ministry of Health for the researchers and to a lack of synchronization between knowledge production and policy-making. Conclusions Study findings suggest that stakeholders, both researchers and policy makers planning to update clinical guidelines in LIC may need methodological support to overcome the expected barriers. PMID:24969242

Modelling aspects regarding the control in 13C isotope separation column

NASA Astrophysics Data System (ADS)

Boca, M. L.

2016-08-01

Carbon represents the fourth most abundant chemical element in the world, having two stable and one radioactive isotope. The 13Carbon isotopes, with a natural abundance of 1.1%, plays an important role in numerous applications, such as the study of human metabolism changes, molecular structure studies, non-invasive respiratory tests, Alzheimer tests, air pollution and global warming effects on plants [9] A manufacturing control system manages the internal logistics in a production system and determines the routings of product instances, the assignment of workers and components, the starting of the processes on not-yet-finished product instances. Manufacturing control does not control the manufacturing processes themselves, but has to cope with the consequences of the processing results (e.g. the routing of products to a repair station). In this research it was fulfilled some UML (Unified Modelling Language) diagrams for modelling the C13 Isotope Separation column, implement in STARUML program. Being a critical process and needing a good control and supervising, the critical parameters in the column, temperature and pressure was control using some PLC (Programmable logic controller) and it was made some graphic analyze for this to observe some critical situation than can affect the separation process. The main parameters that need to be control are: -The liquid nitrogen (N2) level in the condenser. -The electrical power supplied to the boiler. -The vacuum pressure.

Design Considerations of a Virtual Laboratory for Advanced X-ray Sources

NASA Astrophysics Data System (ADS)

Luginsland, J. W.; Frese, M. H.; Frese, S. D.; Watrous, J. J.; Heileman, G. L.

2004-11-01

The field of scientific computation has greatly advanced in the last few years, resulting in the ability to perform complex computer simulations that can predict the performance of real-world experiments in a number of fields of study. Among the forces driving this new computational capability is the advent of parallel algorithms, allowing calculations in three-dimensional space with realistic time scales. Electromagnetic radiation sources driven by high-voltage, high-current electron beams offer an area to further push the state-of-the-art in high fidelity, first-principles simulation tools. The physics of these x-ray sources combine kinetic plasma physics (electron beams) with dense fluid-like plasma physics (anode plasmas) and x-ray generation (bremsstrahlung). There are a number of mature techniques and software packages for dealing with the individual aspects of these sources, such as Particle-In-Cell (PIC), Magneto-Hydrodynamics (MHD), and radiation transport codes. The current effort is focused on developing an object-oriented software environment using the Rational© Unified Process and the Unified Modeling Language (UML) to provide a framework where multiple 3D parallel physics packages, such as a PIC code (ICEPIC), a MHD code (MACH), and a x-ray transport code (ITS) can co-exist in a system-of-systems approach to modeling advanced x-ray sources. Initial software design and assessments of the various physics algorithms' fidelity will be presented.

Mission Simulation Toolkit

NASA Technical Reports Server (NTRS)

Pisaich, Gregory; Flueckiger, Lorenzo; Neukom, Christian; Wagner, Mike; Buchanan, Eric; Plice, Laura

2007-01-01

The Mission Simulation Toolkit (MST) is a flexible software system for autonomy research. It was developed as part of the Mission Simulation Facility (MSF) project that was started in 2001 to facilitate the development of autonomous planetary robotic missions. Autonomy is a key enabling factor for robotic exploration. There has been a large gap between autonomy software (at the research level), and software that is ready for insertion into near-term space missions. The MST bridges this gap by providing a simulation framework and a suite of tools for supporting research and maturation of autonomy. MST uses a distributed framework based on the High Level Architecture (HLA) standard. A key feature of the MST framework is the ability to plug in new models to replace existing ones with the same services. This enables significant simulation flexibility, particularly the mixing and control of fidelity level. In addition, the MST provides automatic code generation from robot interfaces defined with the Unified Modeling Language (UML), methods for maintaining synchronization across distributed simulation systems, XML-based robot description, and an environment server. Finally, the MSF supports a number of third-party products including dynamic models and terrain databases. Although the communication objects and some of the simulation components that are provided with this toolkit are specifically designed for terrestrial surface rovers, the MST can be applied to any other domain, such as aerial, aquatic, or space.

A Flexible Statechart-to-Model-Checker Translator

NASA Technical Reports Server (NTRS)

Rouquette, Nicolas; Dunphy, Julia; Feather, Martin S.

2000-01-01

Many current-day software design tools offer some variant of statechart notation for system specification. We, like others, have built an automatic translator from (a subset of) statecharts to a model checker, for use to validate behavioral requirements. Our translator is designed to be flexible. This allows us to quickly adjust the translator to variants of statechart semantics, including problem-specific notational conventions that designers employ. Our system demonstration will be of interest to the following two communities: (1) Potential end-users: Our demonstration will show translation from statecharts created in a commercial UML tool (Rational Rose) to Promela, the input language of Holzmann's model checker SPIN. The translation is accomplished automatically. To accommodate the major variants of statechart semantics, our tool offers user-selectable choices among semantic alternatives. Options for customized semantic variants are also made available. The net result is an easy-to-use tool that operates on a wide range of statechart diagrams to automate the pathway to model-checking input. (2) Other researchers: Our translator embodies, in one tool, ideas and approaches drawn from several sources. Solutions to the major challenges of statechart-to-model-checker translation (e.g., determining which transition(s) will fire, handling of concurrent activities) are retired in a uniform, fully mechanized, setting. The way in which the underlying architecture of the translator itself facilitates flexible and customizable translation will also be evident.

Association of Anti-glycan Antibodies and Inflammatory Bowel Disease Course.

PubMed

Paul, S; Boschetti, G; Rinaudo-Gaujous, M; Moreau, A; Del Tedesco, E; Bonneau, J; Presles, E; Mounsef, F; Clavel, L; Genin, C; Flourié, B; Phelip, J-M; Nancey, S; Roblin, X

2015-06-01

The usefulness of anti-glycan antibodies alone or combined with anti-Saccharomyces cerevisiae [ASCA] or perinuclear antineutrophil cytoplasmic [pANCA] antibodies for diagnosis of inflammatory bowel disease [IBD], differentiation between Crohn's disease [CD] and ulcerative colitis [UC], disease stratification including IBD phenotype, and also for determination of the course of the disease, remain unclear. A large panel of serological anti-glycan carbohydrate antibodies, including anti-mannobioside IgG antibodies [AMCA], anti-chitobioside IgA [ACCA], anti-laminaribioside IgG antibodies [ALCA], anti-laminarin [anti-L] and anti-chitine [anti-C] were measured in the serum from a cohort of 195 patients with IBD] [107 CD and 88 UC]. The respective accuracy of isolated or combined markers for diagnosis, disease differentiation, stratification disease phenotype, and severity of the disease course, defined by a wide panel of criteria obtained from the past medical history, was assessed. The positivity of at least one anti-glycan antibody was detected in a significant higher proportion of CD and UC compared with healthy controls [p < 0.0001 and p < 0.0007, respectively]. Whereas ASCA and ANCA antibody status had the highest efficacy to be associated with CD in comparison with UC (area under receiver operating characteristic curve [AUROC] = 0.70 for each], the adjunction of anti-laminarin antibody substantially improved the differentiation between CD and UC [AUROC = 0.77]. Titres of ACCA [> 51U/ml] and anti-laminarin [> 31U/ml] were significantly linked with a higher association with steroid dependency (odds ratio [OR] =2.0 [1.0-4.0], p = 0.03 and OR = 2.4 [1.1-5.2], p = 0.02, respectively]. We further defined the respective performance of anti-glycan antibodies to discriminate between patients with severe or not severe CD and UC course and determined the associated optimal cut-off values: severe CD course was significantly more likely in case of AMCA > 77U/ml [OR = 4.3; p = 0.002], ASCA > 63U/ml [OR = 3.5; p < 0.009] and at a lesser degree ACCA > 50U/ml [OR = 2.8; p < 0.02] and severe UC course was significantly associated with AMCA > 52U/ml [OR = 3.4; p = 0.04] and ACCA > 25U/ml [OR = 3.0; p < 0.04]. Anti-glycan antibodies are valuable serological markers, especially AMCA antibodies that may help clinicians to promptly classify patients into high risk for severe disease. Copyright © 2015 European Crohn’s and Colitis Organisation (ECCO). Published by Oxford University Press. All rights reserved. For permissions, please email: journals.permissions@oup.com.

Building a reference functional model for EHR systems.

PubMed

Sumita, Yuki; Takata, Mami; Ishitsuka, Keiju; Tominaga, Yasuyuki; Ohe, Kazuhiko

2007-09-01

Our aim was to develop a reference functional model for electric health record systems (RFM). Such a RFM is built from functions using functional descriptive elements (FDEs) and represents the static relationships between them. This paper presents a new format for describing electric health record (EHR) system functions. Questionnaire and field interview survey was conducted in five hospitals in Japan and one in the USA, to collect data on EHR system functions. Based on survey results, a reference functional list (RFL) was created, in which each EHR system function was listed and divided into 13 FDE types. By analyzing the RFL, we built the meta-functional model and the functional model using UML class diagrams. The former defines language for expressing the functional model, while the latter represents functions, FDEs and their static relationships. A total of 385 functions were represented in the RFL. Six patterns were found for the relationships between functions. The meta-functional model was created as a new format for describing functions. Examples of the functional model, which included the six patterns in the relationships between functions and 11 verbs, were created. We present the meta-functional model, which is a new description format for the functional structure and relationships. Although a more detailed description is required to apply the RFM to the semiautomatic generation of functional specification documents, our RFM can visualize functional structures and functional relationships, classify functions using multiple axes and identify the similarities and differences between functions. The RFM will promote not only the standardization of EHR systems, but also communications between system developers and healthcare providers in the EHR system-design processes. 2006 Elsevier Ireland Ltd

The Best of all Possible Worlds: Applying the Model Driven Architecture Approach to a JC3IEDM OWL Ontology Modeled in UML

DTIC Science & Technology

2014-04-25

EA’s Java application programming interface (API), the team built a tool called OWL2EA that can ingest an OWL file and generate the corresponding UML...ObjectItemStructure specification shown in Figure 10. Running this script in the relational database server MySQL creates the physical schema that

Vertical Mixing in the Dead Sea

NASA Astrophysics Data System (ADS)

Gertman, Isaac; Ozer, Tal; Katsenelson, Boris; Lensky, Nadav

2015-04-01

For hundreds of years, the Dead Sea was characterized by a stable haline stratification, supported by runoff. The penetration of the winter convection was limited to an upper mixed layer (UML) of about 30-50 m. Below the UML, a stable halocline prevented the mixing. As a result of the runoff reduction, the UML salinity increased and the gravitational stability diminished. During the winter of 1978-1979, the sea water overturned, ending the long-term stable hydrological regime. Since 1979, the haline stratification structure reoccurred twice after extremely rainy winters, in 1980-82 and 1992-1995. In other years, the sea was entirely mixed by winter thermal convection ( which occurs from November to March ) and had a seasonal pycnocline beneath the UML during summer. Profiles of temperature and quasi-salinity (density anomaly from 1000 kg/m3 for the chosen reference temperature of 32° C) during the last 19 years, show the formation of summer ``overturning halocline'' beneath the UML, and the thermocline that supports the stable stratification. Another warm and saline layer is formed also during the summer period near the bottom. This layer spreads from the southern part of the sea, where end-brine is discharged to the sea from the Israeli and Jordanian salt plants' evaporation ponds. The end-brine has extremely high salinity (˜ 350 g/kg) and, in spite of the high temperatures ( ˜ 45° C), high density (1350 kg/m^3), it therefore spreads as a gravitational current in the Dead Sea deep basin. Estimation of the density ratio (Rρ) for the Dead Sea water (where measurements of water salinity is quite difficult) was done using quasi-salinity (σ32) and potential temperature (θ): Rρ= [α(partialθ/partial z)]/[β(partial σ32/partial z)], where α and β are temperature expansion and quasi-salinity contraction coefficients respectively. The values of α and β for the Dead Sea water were defined from water samples collected during 2008. The Rρ values confirm that the summer Dead Sea thermohaline structure is appropriate for double diffusion mixing. A salt fingers regime beneath the UML (1.3< Rρ

Implementation of UML Schema to RDBM

NASA Astrophysics Data System (ADS)

Nagni, M.; Ventouras, S.; Parton, G.

2012-04-01

Multiple disciplines - especially those within the earth and physical sciences, and increasingly those within social science and medical fields - require Geographic Information (GI) i.e. information concerning phenomena implicitly or explicitly associated with a location relative to the Earth [1]. Therefore geographic datasets are increasingly being shared, exchanged and frequently used for purposes other than those for which they were originally intended. The ISO Technical Committee 211 (ISO/TC 211) together with Open Geospatial Consortium (OGC) provide a series of standards and guidelines for developing application schemas which should: a) capture relevant conceptual aspects of the data involved; and b) be sufficient to satisfy previously defined use-cases of a specific or cross-domain concerns. In addition, the Hollow World technology offers an accessible and industry-standardised methodology for creating and editing Application Schema UML models which conform to international standards for interoperable GI [2]. We present a technology which seamlessly transforms an Application Schema UML model to a relational database model (RDBM). This technology, using the same UML information model, complements the XML transformation of an information model produced by the FullMoon tool [2]. In preparation for the generation of a RDBM the UML model is first mapped to a collection of OO classes and relationships. Any external dependencies that exist are then resolved through the same mechanism. However, a RDBM does not support a hierarchical (relational) data structure - a function that may be required by UML models. Previous approaches have addressed this problem through use of nested sets or an adjacent list to represent such structure. Our unique strategy addresses the hierarchical data structure issue, whether singular or multiple inheritance, by hiding a delegation pattern within an OO class. This permits the object-relational mapping (ORM) software used to generate the RDBM to easily map the class into the RDBM. In other words the particular structure of the resulting OO class may expose a "composition-like aspect" to the ORM whilst maintaining an "inherited-like aspect" for use within an OO program. This methodology has been used to implement a software application to manages the new CEDA metadata model which is based on MOLES 3.4, Python, Django and SQLAlchemy.

Serum Paraoxonase Activity and Malondialdehyde Serum Concentrations Remain Unaffected in Response to Hydroxyurea Therapy in β-Thalassemia Patients.

PubMed

Zohaib, Muhammad; Ansari, Saqib H; Hashim, Zehra; Shamsi, Tahir S; Zarina, Shamshad

2016-07-01

β-Thalassemia is the most common hereditary disorder characterized by reduced production of β-globin chains of hemoglobin A (HbA). In recent years, hydroxyurea (HU) has shown promising therapeutic benefits in patients with β-thalassemia by fetal hemoglobin augmentation. We have analyzed effects of hydroxyurea treatment on oxidative stress in β-thalassemia patients by assessing activities of paraoxonase (PON) and arylesterase along with malondialdehyde (MDA) and total reactive oxygen species (ROS) concentrations. Blood samples from 159 individuals including 56 HU-treated and 58 untreated β-thalassemia patients and 45 healthy controls were analyzed. PON activity was found to be highest in healthy individuals (177.76 ± 4.44 U/mL) as compared to treated (52.67 ± 3.65 U/mL) and untreated (55.11 ± 3.26 U/mL) patients. A similar trend was observed in the case of arylesterase activity in normal, β-thalassemia-treated, and untreated (210.0 ± 11.25 U/mL, 163.03 ± 9.04 U/mL, 139.77 ± 10.10 U/mL) subjects. Serum MDA concentrations (2.59 ± 0.09 nmol/mL, 2.45 ± 0.08 nmol/mL, and 1.15 ± 0.05 nmol/mL) and total ROS concentrations (3.73 ± 0.20 nmol/mL, 3.54 ± 0.23 nmol/mL, and 2.45 ± 0.14 nmol/mL) were significantly elevated in both groups (untreated and treated) as compared to healthy individuals (P < .01). Oxidative stress was found to be markedly elevated in β-thalassemia patients as compared to healthy controls. Insignificant differences were, however, observed in mean concentrations of PON1 paraoxonase and arylesterase activities, serum MDA concentration and total ROS concentrations between HU-treated and untreated patients. We propose that HU therapy alone seems to be ineffective in managing oxidative stress and is likely to offer a better clinical outcome when supplemented with efficient iron chelation therapy and antioxidants. © 2015, The American College of Clinical Pharmacology.

Immunological monitoring after organ transplantation: potential role of soluble CD30 blood level measurement.

PubMed

Truong, Dinh Quang; Darwish, Ahmed A; Gras, Jérémie; Wieërs, Grégoire; Cornet, Anne; Robert, Annie; Mourad, Michel; Malaise, Jacques; de Ville de Goyet, Jean; Reding, Raymond; Latinne, Dominique

2007-06-01

Analysing the relevance of soluble CD30 (sCD30) in the bloodstream before and after transplantation may be important for the monitoring of transplant recipients. In this study, 27 patients (15 pediatric liver and 12 adult kidney graft recipients) were investigated. In the liver graft group, the patients who developed acute rejection during the first month (n=9) had a slightly higher sCD30 value on pre-transplantation baseline (day 0) and post-transplantation day 7, when compared to patients with normal graft function (n=6) (day 0: 102(1.6) U/ml versus 118(1.5) U/ml, p=0.52) and (day 7: 69(1.5) U/ml versus 83(1.6) U/ml, p=0.47). Increased serum sCD30 was shown to correlate with increased interleukin-10 circulating levels between day 0 and day 7 (r=0.53; p=0.04), whereas, no correlation could be evidenced between interferon-gamma (IFN-gamma) and sCD30 (r=0.02; p=0.47). Similarly, in the kidney transplantation group, no significant difference was found in sCD30 levels at day 0 in both groups with graft rejection or normal graft function (n=6) (85(1.3) U/ml versus 77(1.6) U/ml, p=0.66), but sCD30 decreased significantly at day 7 post-transplantation from baseline value in the rejection group (n=6) (77(1.6) versus 35(1.4); p=0.02). We conclude that increased serum sCD30 was correlated with increased IL-10 (interleukin-10) circulating levels, but not with IFN-gamma levels in the post-transplantation period. Neither pre-transplantation sCD30 nor sCD30 at day 7 post-transplantation could be correlated with acute rejection in liver graft recipient. The monitoring of sCD30 might constitute a tool to assess the risk of acute rejection in renal transplant but did not appear as a valuable mean for early immunological monitoring in the small group of liver allograft recipients patients analysed in this study.

A temperature-controlled cell for X-ray study of liquid systems using a commercial DRON-UM1 diffractometer

DOE Office of Scientific and Technical Information (OSTI.GOV)

Petrun`kin, S.P.; Garavina, E.V.; Trostin, V.N.

1995-02-01

A container (cell) and a temperature-control system have been designed enabling one to carry out x-ray diffraction study of liquid samples both at a fixed temperature and within a certain temperature range using a commercial DRON-UMl x-ray diffractometer. Special features of the cell and the materials used for it allow one to study both chemically inert and corrosive liquids.

Prognostic significance of preimmunotherapy serum CA27.29 (MUC-1) mucin level after active specific immunotherapy of metastatic adenocarcinoma patients.

PubMed

MacLean, G D; Reddish, M A; Longenecker, B M

1997-01-01

The TRUQUANT BR radioimmunoassay, which uses monoclonal antibody B27.29 to quantitate CA27.29 mucin antigen (MUC-1 gene product) in serum, has recently received Food and Drug Administration approval for predicting recurrent breast cancer in patients with stage II and III disease. The purpose of this study was to determine whether the new radioimmunoassay for serum MUC-1 has prognostic significance for patients with metastatic adenocarcinoma receiving active specific immunotherapy (ASI). Using 40 U/ml as the upper limit of "normal," patients with metastatic breast and ovarian cancer with a preimmunotherapy serum CA27.29 mucin > 40 U/ml (CA27.29 Hi patients) had a poorer survival than CA27.29 Lo patients (< or = 40 U/ml) after ASI. There was no significant correlation between preimmunotherapy CA27.29 serum levels and measurable tumor burden. The preimmunotherapy CA27.29 serum level was a predictor of poor survival of metastatic colorectal and pancreatic cancer patients independent of other prognostic factors. There seemed to be two populations of pancreatic cancer patients, separated at 60 U/ml serum CA27.29 (CA27.29 Hi versus Lo patients). A CA27.29 serum level of 22 U/ml separated patients with CA27.29 Hi vs. Lo colorectal cancer. Patients with CA27.29 Lo colorectal and pancreatic cancer survived longer after ASI compared with patients with CA27.29 Hi colorectal and pancreatic cancer, respectively. We suggest that various CA27.29 serum levels define poor prognosis patients (CA27.29 Hi secretors) versus good prognosis patients (CA27.29 Lo secretors) for different cancer types.

Black-Box System Testing of Real-Time Embedded Systems Using Random and Search-Based Testing

NASA Astrophysics Data System (ADS)

Arcuri, Andrea; Iqbal, Muhammad Zohaib; Briand, Lionel

Testing real-time embedded systems (RTES) is in many ways challenging. Thousands of test cases can be potentially executed on an industrial RTES. Given the magnitude of testing at the system level, only a fully automated approach can really scale up to test industrial RTES. In this paper we take a black-box approach and model the RTES environment using the UML/MARTE international standard. Our main motivation is to provide a more practical approach to the model-based testing of RTES by allowing system testers, who are often not familiar with the system design but know the application domain well-enough, to model the environment to enable test automation. Environment models can support the automation of three tasks: the code generation of an environment simulator, the selection of test cases, and the evaluation of their expected results (oracles). In this paper, we focus on the second task (test case selection) and investigate three test automation strategies using inputs from UML/MARTE environment models: Random Testing (baseline), Adaptive Random Testing, and Search-Based Testing (using Genetic Algorithms). Based on one industrial case study and three artificial systems, we show how, in general, no technique is better than the others. Which test selection technique to use is determined by the failure rate (testing stage) and the execution time of test cases. Finally, we propose a practical process to combine the use of all three test strategies.

Production, purification and application of extracellular chitinase from Cellulosimicrobium cellulans 191

PubMed Central

Fleuri, Luciana F.; Kawaguti, Haroldo Y.; Sato, Hélia H.

2009-01-01

This study concerned the production, purification and application of extracellular chitinase from Cellulosimicrobium cellulans strain 191. In shaken flasks the maximum yield of chitinase was 6.9 U/mL after 72 h of cultivation at 25°C and 200 rpm. In a 5 L fermenter with 1.5 vvm aeration, the highest yield obtained was 4.19 U/mL after 168 h of fermentation at 25°C and 200 rpm, and using 3 vvm, it was 4.38 U/mL after 144 h of fermentation. The chitinase (61 KDa) was purified about 6.65 times by Sepharose CL 4B 200 gel filtration with a yield of 46.61%. The purified enzyme was able to lyse the cell walls of some fungi and to form protoplasts. PMID:24031407

Allergy and parasites: the measurement of total and specific IgE levels in urban and rural communities in Rhodesia.

PubMed

Merrett, T G; Merrett, J; Cookson, J B

1976-03-01

Eighty adult asthmatics living in an African city had a significantly higher serum IgE level (799 u/ml) than the control group (350 u/ml). A high proportion (78.7%) of the asthmatics had demonstrable circulating mite-specific IgE antibodies. The rural population of a filariasis endemic region was investigated and although no allergic subjects were identified, the group had a significantly higher IgE level (1613 u/ml) than the asthmatics and also showed a relatively high incidence of grass pollen-specific IgE antibodies (35%). The discrepancy between clinical history and laboratory results supports the mast cell saturation hypothesis and suggests: (a) an explanation for the susceptibility to allergy of African and Asian immigrants to Great Britain, and (b) a practical approach for preventing allergic reactions in vivo.

Polygalacturonase production by calcium alginate immobilized Enterobacter aerogenes NBO2 cells.

PubMed

Darah, I; Nisha, M; Lim, Sheh-Hong

2015-03-01

Bacterial cells of Enterobacter aerogenes NBO2 were entrapped in calcium alginate beads in order to enhance polygalacturonase production compared to free cells. The optimized condition of 5 % (w/v) sodium alginate concentration, agitation speed of 250 rpm, and 15 beads of calcium alginate with inoculum size of 4 % (v/v; 5.4 × 10(7) cells/ml) produced 23.48 U/mL of polygalacturonase compared to free cells of 18.54 U/ml. There was about 26.6 % increment in polygalaturonase production. However, in this study, there was 296.6 % of increment in polygalacturonase production after improvement parameters compared to before improvement parameters of calcium alginate bead immobilization cells (5.92 U/ml). This research has indicated that optimized physical parameters of calcium alginate bead immobilization cells have significantly enhanced the production of polygalacturonase.

Path generation algorithm for UML graphic modeling of aerospace test software

NASA Astrophysics Data System (ADS)

Qu, MingCheng; Wu, XiangHu; Tao, YongChao; Chen, Chao

2018-03-01

Aerospace traditional software testing engineers are based on their own work experience and communication with software development personnel to complete the description of the test software, manual writing test cases, time-consuming, inefficient, loopholes and more. Using the high reliability MBT tools developed by our company, the one-time modeling can automatically generate test case documents, which is efficient and accurate. UML model to describe the process accurately express the need to rely on the path is reached, the existing path generation algorithm are too simple, cannot be combined into a path and branch path with loop, or too cumbersome, too complicated arrangement generates a path is meaningless, for aerospace software testing is superfluous, I rely on our experience of ten load space, tailor developed a description of aerospace software UML graphics path generation algorithm.

Interleukin-2-dependent long-term cultures of low-density lymphocytes allow the proliferation of lymphokine-activated killer cells with natural killer, Ti gamma/delta or TNK phenotype.

PubMed

Testa, U; Care, A; Montesoro, E; Fossati, C; Giannella, G; Masciulli, R; Fagioli, M; Bulgarini, D; Habetswallner, D; Isacchi, G

1990-01-01

We have developed a culture system for "long-term" growth of human lymphokine-activated killer (LAK) cells exhibiting an elevated, wide-spectrum antitumor cytotoxicity. The system allows the exponential growth of monocyte-depleted low-density lymphocytes in the presence of human serum and recombinant human interleukin-2 (10(3) U/ml), alone or in combination with interleukin-1 alpha or beta (both at 10 U/ml). Eighteen cultures were established from 18 normal adult donors. The membrane phenotypes of the final LAK cell population, assessed by a panel of monoclonal antibodies (mAb), consist of three main types: (a) NKH-1+, Ti alpha/beta-, Ti gamma/delta-, and CD3- lymphocytes; (b) NKH-1+, Ti alpha/beta-, Ti gamma/delta+, and CD3+ lymphocytes and (c) NKH-1+, Ti alpha/beta+, Ti gamma/delta- and CD3+ lymphocytes. Northern blot analysis showed that all these cell populations express relatively high levels of perforin RNA, particularly cells exhibiting the first phenotype. This culture system may provide a tool for cellular and molecular studies on the mechanisms of antitumor cytotoxicity, as well as the basis for new adoptive immunotherapy protocols in advanced center.

Automatically pairing measured findings across narrative abdomen CT reports.

PubMed

Sevenster, Merlijn; Bozeman, Jeffrey; Cowhy, Andrea; Trost, William

2013-01-01

Radiological measurements are one of the key variables in widely adopted guidelines (WHO, RECIST) that standardize and objectivize response assessment in oncology care. Measurements are typically described in free-text, narrative radiology reports. We present a natural language processing pipeline that extracts measurements from radiology reports and pairs them with extracted measurements from prior reports of the same clinical finding, e.g., lymph node or mass. A ground truth was created by manually pairing measurements in the abdomen CT reports of 50 patients. A Random Forest classifier trained on 15 features achieved superior results in an end-to-end evaluation of the pipeline on the extraction and pairing task: precision 0.910, recall 0.878, F-measure 0.894, AUC 0.988. Representing the narrative content in terms of UMLS concepts did not improve results. Applications of the proposed technology include data mining, advanced search and workflow support for healthcare professionals managing radiological measurements.

Requirements engineering for cross-sectional information chain models

PubMed Central

Hübner, U; Cruel, E; Gök, M; Garthaus, M; Zimansky, M; Remmers, H; Rienhoff, O

2012-01-01

Despite the wealth of literature on requirements engineering, little is known about engineering very generic, innovative and emerging requirements, such as those for cross-sectional information chains. The IKM health project aims at building information chain reference models for the care of patients with chronic wounds, cancer-related pain and back pain. Our question therefore was how to appropriately capture information and process requirements that are both generally applicable and practically useful. To this end, we started with recommendations from clinical guidelines and put them up for discussion in Delphi surveys and expert interviews. Despite the heterogeneity we encountered in all three methods, it was possible to obtain requirements suitable for building reference models. We evaluated three modelling languages and then chose to write the models in UML (class and activity diagrams). On the basis of the current project results, the pros and cons of our approach are discussed. PMID:24199080

Web-based UMLS concept retrieval by automatic text scanning: a comparison of two methods.

PubMed

Brandt, C; Nadkarni, P

2001-01-01

The Web is increasingly the medium of choice for multi-user application program delivery. Yet selection of an appropriate programming environment for rapid prototyping, code portability, and maintainability remain issues. We summarize our experience on the conversion of a LISP Web application, Search/SR to a new, functionally identical application, Search/SR-ASP using a relational database and active server pages (ASP) technology. Our results indicate that provision of easy access to database engines and external objects is almost essential for a development environment to be considered viable for rapid and robust application delivery. While LISP itself is a robust language, its use in Web applications may be hard to justify given that current vendor implementations do not provide such functionality. Alternative, currently available scripting environments for Web development appear to have most of LISP's advantages and few of its disadvantages.

Conducting requirements analyses for research using routinely collected health data: a model driven approach.

PubMed

de Lusignan, Simon; Cashman, Josephine; Poh, Norman; Michalakidis, Georgios; Mason, Aaron; Desombre, Terry; Krause, Paul

2012-01-01

Medical research increasingly requires the linkage of data from different sources. Conducting a requirements analysis for a new application is an established part of software engineering, but rarely reported in the biomedical literature; and no generic approaches have been published as to how to link heterogeneous health data. Literature review, followed by a consensus process to define how requirements for research, using, multiple data sources might be modeled. We have developed a requirements analysis: i-ScheDULEs - The first components of the modeling process are indexing and create a rich picture of the research study. Secondly, we developed a series of reference models of progressive complexity: Data flow diagrams (DFD) to define data requirements; unified modeling language (UML) use case diagrams to capture study specific and governance requirements; and finally, business process models, using business process modeling notation (BPMN). These requirements and their associated models should become part of research study protocols.

The Neighborhood Auditing Tool: A Hybrid Interface for Auditing the UMLS

PubMed Central

Morrey, C. Paul; Geller, James; Halper, Michael; Perl, Yehoshua

2009-01-01

The UMLS’s integration of more than 100 source vocabularies, not necessarily consistent with one another, causes some inconsistencies. The purpose of auditing the UMLS is to detect such inconsistencies and to suggest how to resolve them while observing the requirement of fully representing the content of each source in the UMLS. A software tool, called the Neighborhood Auditing Tool (NAT), that facilitates UMLS auditing is presented. The NAT supports “neighborhood-based” auditing, where, at any given time, an auditor concentrates on a single focus concept and one of a variety of neighborhoods of its closely related concepts. Typical diagrammatic displays of concept networks have a number of shortcomings, so the NAT utilizes a hybrid diagram/text interface that features stylized neighborhood views which retain some of the best features of both the diagrammatic layouts and text windows while avoiding the shortcomings. The NAT allows an auditor to display knowledge from both the Metathesaurus (concept) level and the Semantic Network (semantic type) level. Various additional features of the NAT that support the auditing process are described. The usefulness of the NAT is demonstrated through a group of case studies. Its impact is tested with a study involving a select group of auditors. PMID:19475725

Michaelis kinetic analysis of extracellular cellulase and amylase excreted by Lactobacillus plantarum during cassava fermentation

NASA Astrophysics Data System (ADS)

Frediansyah, Andri; Kurniadi, Muhamad

2017-01-01

Our previous study reveal that single culture of Lactobacillus plantarum has ability to ferment cassava tuber in relation to produce modified cassava flour (mocaf). It was used to accelerate a fermentation process. L. plantarum grow well and produce some extracellular enzymes i.e. cellulase to change the structure and breakdown the cell wall of cassava tuber. Then, the starchy materials will be hydrolyzed by i.e. amylase into simple sugar and convert to organic acid. All of these process will give new characteristic of cassava i.e. lower fiber content, good flavor, taste, aroma and texture and the amount of cyanide acid is lower. Therefore this present study was to analyze Michaelis kinetics of extracellular carboxymethyl cellulase and amylase production by L. plantarum during cassava fermentation. The maximum carboxymethyl cellulase and amylase activity of 8.60 U/ml and 14.07 U/ml, respectively, were obtained from filtrate which has been incubated at 37°C for 18 h under stationary conditions. The Vmax and Km of CMCase were 0.8506 × 10-3 U/ml and 0.9594 × 10-3 g/mL, respectively. For amylase were 9.291 × 10-3 U/ml and 0.9163 × 10-3 g/ml, respectively.

Effect of immobile isolated enzymes from rumen liquid by using alginate matrices on the bay leaf extraction

NASA Astrophysics Data System (ADS)

Paramita, Vita; Yulianto, Mohammad Endy; Yohana, Eflita; Arifan, Fahmi; Hanifah, Amjad, Muhammad Taqiyuddin

2015-12-01

This research aims to develop the enzymatically of bay leaves phytochemical extraction process. The novelty and the main innovations of this research is the development of extraction process by using enzymatic extractor and isolate the enzymes from rumen liquid to shift the equilibrium phase, increase the extraction rate and increase the extraction yield. The activity of rumen liquid enzyme was represented by the activity of cellulase and protease. The analyze of total flavonoid content was performed by using UV-Vis Spectrofometry. The activity of immobilized enzyme of cellulase (0.08±0.00 U/ml) was lower than the un-immobilized one (0.23±0.00 U/ml). However, there was no difference activity of the immobilized (0.75±0.00 U/ml) and un-immobilized (0.76±0.01 U/ml) of protease. The model of mass transfer of un-immobilized enzyme can be fitted on the experimental data, however the model of mass transfer of immobilized enzyme did not match with the experimental data. The mass transfer coefficient of enzymatic extraction flavonoids bay leaf without immobilization was 0.17167 s-1 which greater than the reported value of obtained KLa from extraction by using electric heating.

ARIANE: integration of information databases within a hospital intranet.

PubMed

Joubert, M; Aymard, S; Fieschi, D; Volot, F; Staccini, P; Robert, J J; Fieschi, M

1998-05-01

Large information systems handle massive volume of data stored in heterogeneous sources. Each server has its own model of representation of concepts with regard to its aims. One of the main problems end-users encounter when accessing different servers is to match their own viewpoint on biomedical concepts with the various representations that are made in the databases servers. The aim of the project ARIANE is to provide end-users with easy-to-use and natural means to access and query heterogeneous information databases. The objectives of this research work consist in building a conceptual interface by means of the Internet technology inside an enterprise Intranet and to propose a method to realize it. This method is based on the knowledge sources provided by the Unified Medical Language System (UMLS) project of the US National Library of Medicine. Experiments concern queries to three different information servers: PubMed, a Medline server of the NLM; Thériaque, a French database on drugs implemented in the Hospital Intranet; and a Web site dedicated to Internet resources in gastroenterology and nutrition, located at the Faculty of Medicine of Nice (France). Accessing to each of these servers is different according to the kind of information delivered and according to the technology used to query it. Dealing with health care professional workstation, the authors introduced in the ARIANE project quality criteria in order to attempt a homogeneous and efficient way to build a query system able to be integrated in existing information systems and to integrate existing and new information sources.

A Web Terminology Server Using UMLS for the Description of Medical Procedures

PubMed Central

Burgun, Anita; Denier, Patrick; Bodenreider, Olivier; Botti, Geneviève; Delamarre, Denis; Pouliquen, Bruno; Oberlin, Philippe; Lévéque, Jean M.; Lukacs, Bertrand; Kohler, François; Fieschi, Marius; Le Beux, Pierre

1997-01-01

Abstract The Model for Assistance in the Orientation of a User within Coding Systems (MAOUSSC) project has been designed to provide a representation for medical and surgical procedures that allows several applications to be developed from several viewpoints. It is based on a conceptual model, a controlled set of terms, and Web server development. The design includes the UMLS knowledge sources associated with additional knowledge about medico-surgical procedures. The model was implemented using a relational database. The authors developed a complete interface for the Web presentation, with the intermediary layer being written in PERL. The server has been used for the representation of medico-surgical procedures that occur in the discharge summaries of the national survey of hospital activities that is performed by the French Health Statistics Agency in order to produce inpatient profiles. The authors describe the current status of the MAOUSSC server and discuss their interest in using such a server to assist in the coordination of terminology tasks and in the sharing of controlled terminologies. PMID:9292841

Deriving a probabilistic syntacto-semantic grammar for biomedicine based on domain-specific terminologies

PubMed Central

Fan, Jung-Wei; Friedman, Carol

2011-01-01

Biomedical natural language processing (BioNLP) is a useful technique that unlocks valuable information stored in textual data for practice and/or research. Syntactic parsing is a critical component of BioNLP applications that rely on correctly determining the sentence and phrase structure of free text. In addition to dealing with the vast amount of domain-specific terms, a robust biomedical parser needs to model the semantic grammar to obtain viable syntactic structures. With either a rule-based or corpus-based approach, the grammar engineering process requires substantial time and knowledge from experts, and does not always yield a semantically transferable grammar. To reduce the human effort and to promote semantic transferability, we propose an automated method for deriving a probabilistic grammar based on a training corpus consisting of concept strings and semantic classes from the Unified Medical Language System (UMLS), a comprehensive terminology resource widely used by the community. The grammar is designed to specify noun phrases only due to the nominal nature of the majority of biomedical terminological concepts. Evaluated on manually parsed clinical notes, the derived grammar achieved a recall of 0.644, precision of 0.737, and average cross-bracketing of 0.61, which demonstrated better performance than a control grammar with the semantic information removed. Error analysis revealed shortcomings that could be addressed to improve performance. The results indicated the feasibility of an approach which automatically incorporates terminology semantics in the building of an operational grammar. Although the current performance of the unsupervised solution does not adequately replace manual engineering, we believe once the performance issues are addressed, it could serve as an aide in a semi-supervised solution. PMID:21549857

Global information infrastructure.

PubMed

Lindberg, D A

1994-01-01

The High Performance Computing and Communications Program (HPCC) is a multiagency federal initiative under the leadership of the White House Office of Science and Technology Policy, established by the High Performance Computing Act of 1991. It has been assigned a critical role in supporting the international collaboration essential to science and to health care. Goals of the HPCC are to extend USA leadership in high performance computing and networking technologies; to improve technology transfer for economic competitiveness, education, and national security; and to provide a key part of the foundation for the National Information Infrastructure. The first component of the National Institutes of Health to participate in the HPCC, the National Library of Medicine (NLM), recently issued a solicitation for proposals to address a range of issues, from privacy to 'testbed' networks, 'virtual reality,' and more. These efforts will build upon the NLM's extensive outreach program and other initiatives, including the Unified Medical Language System (UMLS), MEDLARS, and Grateful Med. New Internet search tools are emerging, such as Gopher and 'Knowbots'. Medicine will succeed in developing future intelligent agents to assist in utilizing computer networks. Our ability to serve patients is so often restricted by lack of information and knowledge at the time and place of medical decision-making. The new technologies, properly employed, will also greatly enhance our ability to serve the patient.

What Four Million Mappings Can Tell You about Two Hundred Ontologies

NASA Astrophysics Data System (ADS)

Ghazvinian, Amir; Noy, Natalya F.; Jonquet, Clement; Shah, Nigam; Musen, Mark A.

The field of biomedicine has embraced the Semantic Web probably more than any other field. As a result, there is a large number of biomedical ontologies covering overlapping areas of the field. We have developed BioPortal—an open community-based repository of biomedical ontologies. We analyzed ontologies and terminologies in BioPortal and the Unified Medical Language System (UMLS), creating more than 4 million mappings between concepts in these ontologies and terminologies based on the lexical similarity of concept names and synonyms. We then analyzed the mappings and what they tell us about the ontologies themselves, the structure of the ontology repository, and the ways in which the mappings can help in the process of ontology design and evaluation. For example, we can use the mappings to guide users who are new to a field to the most pertinent ontologies in that field, to identify areas of the domain that are not covered sufficiently by the ontologies in the repository, and to identify which ontologies will serve well as background knowledge in domain-specific tools. While we used a specific (but large) ontology repository for the study, we believe that the lessons we learned about the value of a large-scale set of mappings to ontology users and developers are general and apply in many other domains.

The relation between cerebral serotonin levels and conditioned behaviour in the rat following the administration of LSD-25 and UML.

PubMed

Torre, M; Torre, E; Bogetto, F

1975-01-01

Successive daily injections of LSD-25 and UML (1-methyl-d-lysergic acid butanolamide) caused progressive depression of brain 5-HT levels in the rat. On the fourth day, the decrease was significant with respect to the highly significant fall observed after a single administration, whereas it had been shown earlier that conditioned behaviour is no longer affected by LSD-25 after 3 days and that simultaneous administration of a single dose of LSD-25 and UML is equally ineffective in this respect. Its depression of 5-HT levels, however, has now been shown to be equal to that of LSD-25 alone at doses that influence conditioned behaviour. The findings indicate that changes in such behaviour are not dependent on brain 5-HT levels and that no link exists between such levels and the psychotomimetic effect of LSD-25 in man.

Protoplast fusion enhances lignocellulolytic enzyme activities in Trichoderma reesei.

PubMed

Cui, Yu-xiao; Liu, Jia-jing; Liu, Yan; Cheng, Qi-yue; Yu, Qun; Chen, Xin; Ren, Xiao-dong

2014-12-01

Protoplast fusion was used to obtain a higher production of lignocellulolytic enzymes with protoplast fusion in Trichoderma reesei. The fusant strain T. reesei JL6 was obtained from protoplast fusion from T. reesei strains QM9414, MCG77, and Rut C-30. Filter paper activity of T. reesei JL6 increased by 18% compared with that of Rut C-30. β-Glucosidase, hemicellulase and pectinase activities of T. reesei JL6 were also higher. The former activity was 0.39 Uml(-1), while those of QM9414, MCG77, and Rut C-30 were 0.13, 0.11, and 0.16 Uml(-1), respectively. Pectinase and hemicellulase activities of JL6 were 5.4 and 15.6 Uml(-1), respectively, which were slightly higher than those of the parents. The effects of corn stover and wheat bran carbon sources on the cellulase production and growth curve of T. reesei JL6 were also investigated.

Leveraging terminological resources for mapping between rare disease information sources.

PubMed

Rance, Bastien; Snyder, Michelle; Lewis, Janine; Bodenreider, Olivier

2013-01-01

Rare disease information sources are incompletely and inconsistently cross-referenced to one another, making it difficult for information seekers to navigate across them. The development of such cross-references established manually by experts is generally labor intensive and costly. To develop an automatic mapping between two of the major rare diseases information sources, GARD and Orphanet, by leveraging terminological resources, especially the UMLS. We map the rare disease terms from Orphanet and ORDR to the UMLS. We use the UMLS as a pivot to bridge between the rare disease terminologies. We compare our results to a mapping obtained through manually established cross-references to OMIM. Our mapping has a precision of 94%, a recall of 63% and an F1-score of 76%. Our automatic mapping should help facilitate the development of more complete and consistent cross-references between GARD and Orphanet, and is applicable to other rare disease information sources as well.

Structural Group-based Auditing of Missing Hierarchical Relationships in UMLS

PubMed Central

Chen, Yan; Gu, Huanying(Helen); Perl, Yehoshua; Geller, James

2009-01-01

The Metathesaurus of the UMLS was created by integrating various source terminologies. The inter-concept relationships were either integrated into the UMLS from the source terminologies or specially generated. Due to the extensive size and inherent complexity of the Metathesaurus, the accidental omission of some hierarchical relationships was inevitable. We present a recursive procedure which allows a human expert, with the support of an algorithm, to locate missing hierarchical relationships. The procedure starts with a group of concepts with exactly the same (correct) semantic type assignments. It then partitions the concepts, based on child-of hierarchical relationships, into smaller, singly rooted, hierarchically connected subgroups. The auditor only needs to focus on the subgroups with very few concepts and their concepts with semantic type reassignments. The procedure was evaluated by comparing it with a comprehensive manual audit and it exhibits a perfect error recall. PMID:18824248

Levels of soluble CD30 in cord blood and peripheral blood during childhood are not correlated with the development of atopic disease or a family history of atopy.

PubMed

Holmlund, U; Bengtsson, A; Nilsson, C; Kusoffsky, E; Lilja, G; Scheynius, A; Sverremark-Ekström, E

2003-11-01

The CD30 molecule has been linked to Th2 responses. Furthermore, elevated levels of the soluble form of CD30 (sCD30) in blood as well as of the expression of CD30 on the plasma membrane of T cells are associated with atopic disease. To assess the potential usefulness of sCD30 levels as a prognostic indicator of and/or diagnostic marker for the development of atopic disease in children. sCD30 levels in cord blood and peripheral blood from 36 2-year-old (10 atopic and 26 non-atopic) and 74 7-year-old (35 atopic and 39 non-atopic) children were determined employing an ELISA procedure. Atopy was diagnosed on the basis of clinical evaluation in combination with a positive skin prick test. No significant correlation between sCD30 levels in cord blood and the development of atopic disease at 2 or 7 years of age was observed. At 7 years of age, the circulating sCD30 levels in children with atopic disease (median 41 U/mL, range 6-503 U/mL) did not differ from the corresponding values for non-atopic subjects (median 41 U/mL, range 8-402 U/mL). The same was true for children at 2 years of age. Furthermore, the sCD30 levels of children who had developed atopic eczema/dermatitis syndrome by the age of 7 years (median 49 U/mL, range 14-503 U/mL) were not significantly elevated in comparison with those of the non-atopic children. Finally, neither sCD30 levels in cord blood nor peripheral blood at 2 or 7 years of age could be linked to a family history of atopy. These findings indicate that the sCD30 concentration in cord blood is not a reliable prognostic indicator of, nor a useful diagnostic marker for, atopic disease in children up to 7 years of age. If such correlations do exist, they might be masked by age-dependent variations in the circulating levels of sCD30, which may reflect individual differences in the maturation of children's immunological responses.

Gauge equivalence of two different IAnsaaumlItze Rfor non-Abelian charged vortices

DOE Office of Scientific and Technical Information (OSTI.GOV)

Paul, S.K.

1987-05-15

Recently the existence of non-Abelian charged vortices has been established by taking two different Ansa$uml: tze in SU(2) gauge theories. We point out that these two Ansa$uml: tze are in two topologically equivalent prescriptions. We show that they are gauge equivalent only at infinity. We also show that this gauge equivalence is not possible for Z/sub N/ vortices in SU(N) gauge theories for Ngreater than or equal to3.

Defining a Technical Basis for Comparing and Contrasting Emerging Dynamic Discovery Protocols

DTIC Science & Technology

2001-05-02

UPnP, SLP, Bluetooth , and HAVi • Projected specific UML models for Jini, UPnP, and SLP • Completed a Rapide Model of Jini structure, function, and...narrow application focus but targeting a different application domain. (e.g., HAVi, Salutation Consortium, and Bluetooth Service Discovery) • Sun has...Our General Approach? 1/31/2002 7 Particulars of Our Approach Define a Generic UML Model that Encompasses Jini, UPnP, SLP, HAVi, and Bluetooth

Production of a biodegradable plastic-degrading enzyme from cheese whey by the phyllosphere yeast Pseudozyma antarctica GB-4(1)W.

PubMed

Watanabe, Takashi; Shinozaki, Yukiko; Suzuki, Ken; Koitabashi, Motoo; Yoshida, Shigenobu; Sameshima-Yamashita, Yuka; Kuze Kitamoto, Hiroko

2014-08-01

Cheese whey is a by-product of cheese production and has high concentrations of lactose (about 5%) and other nutrients. Pseudozyma antarctica produces a unique cutinase-like enzyme, named PaE, that efficiently degrades biodegradable plastics. A previous study showed that a combination of 1% oil and 0.5% lactose increased cutinase-like enzyme production by another species of yeast. In this study, to produce PaE from cheese whey, we investigated the effects of soybean oil on PaE production (expressed as biodegradable plastic-degrading activity) by P. antarctica growing on lactose or cheese whey. In flask cultures, the final PaE activity was only 0.03 U/ml when soybean oil was used as the sole carbon source, but increased to 1.79 U/ml when a limited amount of soybean oil (under 0.5%) was combined with a relatively high concentration of lactose (6%). Using a 5-L jar fermentor with lactose fed-batch cultivation and periodic soybean oil addition, about 14.6 U/ml of PaE was obtained after 5 days of cultivation. When the lactose was replaced with cheese whey, PaE production was 10.8 U/ml after 3 days of cultivation. Copyright © 2014 The Society for Biotechnology, Japan. Published by Elsevier B.V. All rights reserved.

Prognostic value of preoperative serum CA 242 in Esophageal squamous cell carcinoma cases.

PubMed

Feng, Ji-Feng; Huang, Ying; Chen, Qi-Xun

2013-01-01

Carbohydrate antigen (CA) 242 is inversely related to prognosis in many cancers. However, few data regarding CA 242 in esophageal cancer (EC) are available. The aim of this study was to determine the prognostic value of CA 242 and propose an optimum cut-off point in predicting survival difference in patients with esophageal squamous cell carcinoma (ESCC). A retrospective analysis was conducted of 192 cases. A receiver operating characteristic (ROC) curve for survival prediction was plotted to verify the optimum cuf- off point. Univariate and multivariate analyses were performed to evaluate prognostic parameters for survival. The positive rate for CA 242 was 7.3% (14/192). The ROC curve for survival prediction gave an optimum cut-off of 2.15 (U/ml). Patients with CA 242 ≤ 2.15 U/ml had significantly better 5-year survival than patients with CA 242 >2.15 U/ml (45.4% versus 22.6%; P=0.003). Multivariate analysis showed that differentiation (P=0.033), CA 242 (P=0.017), T grade (P=0.004) and N staging (P<0.001) were independent prognostic factors. Preoperative CA 242 is a predictive factor for long-term survival in ESCC, especially in nodal-negative patients. We conclude that 2.15 U/ml may be the optimum cuf-off point for CA 242 in predicting survival in ESCC.

Different approaches for identifying important concepts in probabilistic biomedical text summarization.

PubMed

Moradi, Milad; Ghadiri, Nasser

2018-01-01

Automatic text summarization tools help users in the biomedical domain to acquire their intended information from various textual resources more efficiently. Some of biomedical text summarization systems put the basis of their sentence selection approach on the frequency of concepts extracted from the input text. However, it seems that exploring other measures rather than the raw frequency for identifying valuable contents within an input document, or considering correlations existing between concepts, may be more useful for this type of summarization. In this paper, we describe a Bayesian summarization method for biomedical text documents. The Bayesian summarizer initially maps the input text to the Unified Medical Language System (UMLS) concepts; then it selects the important ones to be used as classification features. We introduce six different feature selection approaches to identify the most important concepts of the text and select the most informative contents according to the distribution of these concepts. We show that with the use of an appropriate feature selection approach, the Bayesian summarizer can improve the performance of biomedical summarization. Using the Recall-Oriented Understudy for Gisting Evaluation (ROUGE) toolkit, we perform extensive evaluations on a corpus of scientific papers in the biomedical domain. The results show that when the Bayesian summarizer utilizes the feature selection methods that do not use the raw frequency, it can outperform the biomedical summarizers that rely on the frequency of concepts, domain-independent and baseline methods. Copyright © 2017 Elsevier B.V. All rights reserved.

Post-transplant monitoring of soluble CD30 level as predictor of graft outcome: a single center experience from China.

PubMed

Wang, Dong; Wu, Weizhen; Yang, Shunliang; Wang, Qinghua; Tan, Jianming

2012-12-01

There are no reliable parameters for post-transplantation immunological monitoring, which might enable recipient-tailored immunosuppressive therapy. 250 renal graft recipients were enrolled and detected for sCD30 level pre-transplantation, and on days 5 and 14, and on months 1, 3, 6, 12, 24, 36, 48 and 60 post-transplantation. Analysis was performed on correlation between sCD30 level and acute rejection, lung infection, or graft loss respectively. sCD30 levels descended to a nadir with a mean of 10.2 ± 3.8 U/mL on day 30 post-transplantation, then rose gradually, and approached 21.8 ± 10.1 U/mL on month 3, 34.2 ± 16.5 U/mL on month 6, and 42.9 ± 29.5 U/mL on month 12, then presented a stable level. Recipients with AR had significantly higher sCD30 levels than those without AR on days 5 and 14 post-transplantation. Recipients with pneumonia had significantly lower sCD30 levels within 3 months post-transplantation than those without pneumonia. Significantly higher sCD30 levels were recorded in recipients who suffered graft loss than those with normal graft function on days 5 and 14, and on months 6, 12, and 24. High sCD30 level (≥ 48.3 U/mL) at month 12 post-transplantation has an obvious detrimental effect on renal graft survival (p=0.000, HR=9.075). Serum sCD30 level might reflect immune state of renal graft recipients. Post-transplantation sequential monitoring of sCD30 level is necessary, which might not only identify recipients at the risk of acute rejection and graft loss, but also chosen as an independent predictor of pneumonia in renal transplant recipients. Copyright © 2012 Elsevier B.V. All rights reserved.

High soluble CD30 levels and associated anti-HLA antibodies in patients with failed renal allografts.

PubMed

Karahan, Gonca E; Caliskan, Yasar; Ozdilli, Kursat; Kekik, Cigdem; Bakkaloglu, Huseyin; Caliskan, Bahar; Turkmen, Aydin; Sever, Mehmet S; Oguz, Fatma S

2017-01-13

Serum soluble CD30 (sCD30), a 120-kD glycoprotein that belongs to the tumor necrosis factor receptor family, has been suggested as a marker of rejection in kidney transplant patients. The aim of this study was to evaluate the relationship between sCD30 levels and anti-HLA antibodies, and to compare sCD30 levels in patients undergoing hemodialysis (HD) with and without failed renal allografts and transplant recipients with functioning grafts. 100 patients undergoing HD with failed grafts (group 1), 100 patients undergoing HD who had never undergone transplantation (group 2), and 100 kidney transplant recipients (group 3) were included in this study. Associations of serum sCD30 levels and anti-HLA antibody status were analyzed in these groups. The sCD30 levels of group 1 and group 2 (154 ± 71 U/mL and 103 ± 55 U/mL, respectively) were significantly higher than those of the transplant recipients (group 3) (39 ± 21 U/mL) (p<0.001 and p<0.001). The serum sCD30 levels in group 1 (154 ± 71 U/mL) were also significantly higher than group 2 (103 ± 55 U/mL) (p<0.001). Anti-HLA antibodies were detected in 81 (81%) and 5 (5%) of patients in groups 1 and 2, respectively (p<0.001). When multiple regression analysis was performed to predict sCD30 levels, the independent variables in group 1 were the presence of class I anti-HLA antibodies (β = 0.295; p = 0.003) and age (β = -0.272; p = 0.005), and serum creatinine (β = 0.218; p = 0.027) and presence of class II anti-HLA antibodies (standardized β = 0.194; p = 0.046) in group 3. Higher sCD30 levels and anti-HLA antibodies in patients undergoing HD with failed renal allografts may be related to higher inflammatory status in these patients.

Increased serum advanced glycation end-products is a distinct finding in lean women with polycystic ovary syndrome (PCOS).

PubMed

Diamanti-Kandarakis, Evanthia; Katsikis, Ilias; Piperi, Christina; Kandaraki, Eleni; Piouka, Athanasia; Papavassiliou, Athanasios G; Panidis, Dimitrios

2008-10-01

Nonenzymatic advanced glycation and oxidation end-products, advanced glycation end-products (AGEs), impart a potent impact on vessels and other tissues in diabetic state and in euglycaemic conditions with increased oxidative stress. Insulin resistant (IR) polycystic ovary syndrome (PCOS) women, have elevated serum AGEs, increased receptor (RAGE) expression, and increased deposition with differential localization in the polycystic ovarian tissue (theca and granulosa) compared to normal. To determine whether the raised AGE levels in noninsulin resistant women with PCOS is a distinct finding compared with those presenting the isolated components of the syndrome and among PCOS subphenotypes. Noninsulin resistant women were selected in order to show that serum AGEs are elevated in PCOS independently of the presence of IR. Clinical trial. One hundred and ninety-three age- and BMI-matched young lean noninsulin resistant women were studied. Among them, 100 women were diagnosed with PCOS according to Rotterdam criteria, and divided to subphenotypes (hyperandrogenaemia with or without PCO morphology and with or without anovulation). Sixty-eight women with the isolated components of the PCOS phenotype were also studied along with 25 healthy women. Serum AGE levels, metabolic, hormonal profiles and intravaginal ultrasound were determined in all subjects. The studied population did not differ in BMI, fasting insulin concentration, waist : hip and glucose : insulin ratios. PCOS women exhibited statistically higher AGEs levels (7.96 +/- 1.87 U/ml, P < 0.001) compared with those with isolated hyperandrogenaemia (5.61 +/- 0.61 U/ml), anovulation (5.53 +/- 1.06 U/ml), US-PCO morphology (5.26 +/- 0.25 U/ml) and controls (5.86 +/- 0.89 U/ml). In PCOS, serum AGEs are distinctly elevated compared with women having the isolated characteristics of the syndrome. No difference was observed between PCOS subphenotypes. As chronic inflammation and increased oxidant stress have been incriminated in the pathophysiology of PCOS, the role of AGEs as inflammatory and oxidant mediators, may be linked with the metabolic and reproductive abnormalities of the syndrome.

Knowledge requirements for automated inference of medical textbook markup.

PubMed Central

Berrios, D. C.; Kehler, A.; Fagan, L. M.

1999-01-01

Indexing medical text in journals or textbooks requires a tremendous amount of resources. We tested two algorithms for automatically indexing nouns, noun-modifiers, and noun phrases, and inferring selected binary relations between UMLS concepts in a textbook of infectious disease. Sixty-six percent of nouns and noun-modifiers and 81% of noun phrases were correctly matched to UMLS concepts. Semantic relations were identified with 100% specificity and 94% sensitivity. For some medical sub-domains, these algorithms could permit expeditious generation of more complex indexing. PMID:10566445

Investigating the Role of Cyclin D1 in the Promotion of Genomic Instability and Breast Cancer

DTIC Science & Technology

2011-09-01

Tween-20, and protease/phosphatase inhibitors (1mM PMSF, 20U/mL aprotinin, 5mg/mL 12 leupeptin, 1mM DTT, 0.4mM NaF, and 10mM β- glycerophosphate ). Whole...inhibitors (1 mM PMSF, 20 U/ml aprotinin, 5 mg/ml leupeptin, 1 mM DTT, 0.4 mM NaF, and 10 mM b- glycerophosphate ), and protein concentration of samples was

Optimization of strand displacement amplification-sensitized G-quadruplex DNAzyme-based sensing system and its application in activity detection of uracil-DNA glycosylase.

PubMed

Du, Yi-Chen; Jiang, Hong-Xin; Huo, Yan-Fang; Han, Gui-Mei; Kong, De-Ming

2016-03-15

As an isothermal nucleic acid amplification technique, strand displacement amplification (SDA) reaction has been introduced in G-quadruplex DNAzyme-based sensing system to improve the sensing performance. To further provide useful information for the design of SDA-amplified G-quadruplex DNAzyme-based sensors, the effects of nicking site number in SDA template DNA were investigated. With the increase of the nicking site number from 1 to 2, enrichment of G-quadruplex DNAzyme by SDA is changed from a linear amplification to an exponential amplification, thus greatly increasing the amplification efficiency and subsequently improving the sensing performance of corresponding sensing system. The nicking site number cannot be further increased because more nicking sites might result in high background signals. However, we demonstrated that G-quadruplex DNAzyme enrichment efficiency could be further improved by introducing a cross-triggered SDA strategy, in which two templates each has two nicking sites are used. To validate the proposed cross-triggered SDA strategy, we used it to develop a sensing platform for the detection of uracil-DNA glycosylase (UDG) activity. The sensor enables sensitive detection of UDG activity in the range of 1 × 10(-4)-1 U/mL with a detection limit of 1 × 10(-4)U/mL. Copyright © 2015 Elsevier B.V. All rights reserved.

FuGEFlow: data model and markup language for flow cytometry.

PubMed

Qian, Yu; Tchuvatkina, Olga; Spidlen, Josef; Wilkinson, Peter; Gasparetto, Maura; Jones, Andrew R; Manion, Frank J; Scheuermann, Richard H; Sekaly, Rafick-Pierre; Brinkman, Ryan R

2009-06-16

Flow cytometry technology is widely used in both health care and research. The rapid expansion of flow cytometry applications has outpaced the development of data storage and analysis tools. Collaborative efforts being taken to eliminate this gap include building common vocabularies and ontologies, designing generic data models, and defining data exchange formats. The Minimum Information about a Flow Cytometry Experiment (MIFlowCyt) standard was recently adopted by the International Society for Advancement of Cytometry. This standard guides researchers on the information that should be included in peer reviewed publications, but it is insufficient for data exchange and integration between computational systems. The Functional Genomics Experiment (FuGE) formalizes common aspects of comprehensive and high throughput experiments across different biological technologies. We have extended FuGE object model to accommodate flow cytometry data and metadata. We used the MagicDraw modelling tool to design a UML model (Flow-OM) according to the FuGE extension guidelines and the AndroMDA toolkit to transform the model to a markup language (Flow-ML). We mapped each MIFlowCyt term to either an existing FuGE class or to a new FuGEFlow class. The development environment was validated by comparing the official FuGE XSD to the schema we generated from the FuGE object model using our configuration. After the Flow-OM model was completed, the final version of the Flow-ML was generated and validated against an example MIFlowCyt compliant experiment description. The extension of FuGE for flow cytometry has resulted in a generic FuGE-compliant data model (FuGEFlow), which accommodates and links together all information required by MIFlowCyt. The FuGEFlow model can be used to build software and databases using FuGE software toolkits to facilitate automated exchange and manipulation of potentially large flow cytometry experimental data sets. Additional project documentation, including reusable design patterns and a guide for setting up a development environment, was contributed back to the FuGE project. We have shown that an extension of FuGE can be used to transform minimum information requirements in natural language to markup language in XML. Extending FuGE required significant effort, but in our experiences the benefits outweighed the costs. The FuGEFlow is expected to play a central role in describing flow cytometry experiments and ultimately facilitating data exchange including public flow cytometry repositories currently under development.

Numerical simulation of inter-annual variations in the properties of the upper mixed layer in the Black Sea over the last 34 years

NASA Astrophysics Data System (ADS)

Shapiro, Georgy I.; Wobus, Fred; Zatsepin, Andrei G.; Akivis, Tatiana M.; Zanacchi, Marcus; Stanichny, Sergey

2014-05-01

The Black Sea is a nearly land-locked basin where a combination of salt and heat budgets results in a unique thermohaline water mass structure. An important feature of the Black Sea is that oxygen is dissolved and rich sea life made possible only in the upper water levels. This is due to a strong pycnocline which cannot be mixed even by strong winds or winter convection (Shapiro, 2008). The upper mixed layer (UML) with a nearly uniform temperature profile and a very sharp seasonal thermocline at its lower boundary develops during the summer season (Sur & Ilyin, 1997). The deepening of the UML has an important effect on the supply of nutrients into the euphotic upper layer from the underlying nutrient-rich water mass. The temperature of the UML at any given location is dependent on the surface heat flux, horizontal advection of heat, the depth and the rate of deepening of the UML. In this study we use a 3D ocean circulation model, NEMO-SHELF (O'Dea et al, 2012) to simulate the parameters of the UML in the Black Sea over the last 34 years. The model has horizontal resolution of 1/12×1/16 degrees and 33 layers in the vertical. The vertical discretization uses a hybrid enveloped s-z grid developed in Shapiro et al. (2012). The model is spun up from climatology (Suvorov et al., 2004); it is forced by the Drakkar Forcing Set v5.2 (Brodeau et al., 2010, Meinvielle et al., 2013) and river discharges from 8 major rivers are included. For each year the model is run from 1st January and the data for the period April to October are used for analysis. The sea surface temperature produced by the model is compared with satellite data ( Modis-Aqua, 2013) to show a good agreement. The model simulations are validated against in-situ observations (BSERP-3, 2004; Piotukh et al., 2011). The analysis is performed for the deep basin where the depth of the sea is greater than 1000m. It clearly shows the inter-annual variations of both the SST and the depth of UML. The depth of UML is calculated using the method by Thomson (1976). It is highly dependent on the meteorological forcing, in particular the wind speed. The correlation between the variations of parameters of UML, the weather patterns, buoyancy fluxes and the kinetic energy of the UML circulation is analysed. This study was supported by EU FP7 PERSEUS and EU FP7 MyOcean2 projects. References BSERP-3. Black Sea Ecosystem Recovery Project. BSERP-3 cruise, May 2004. http://www.research.plymouth.ac.uk/shelf/projects/Black_sea/C_S_BSERP3_final.pdf, 2004. Brodeau, L., B. Barnier, A-M. Treguier, T. Penduff, S. Gulev : An ERA40-based atmospheric forcing for global ocean circulation models, Ocean Modelling, 31, (3-4), 88-104, 2010, http://dx.doi.org/10.1016/j.ocemod.2009.10.005 Meinvielle, M., Brankart, J.-M., Brasseur, P., Barnier, B., Dussin, R., and Verron, J.: Optimal adjustment of the atmospheric forcing parameters of ocean models using sea surface temperature data assimilation, Ocean Sci., 9, 867-883, doi:10.5194/os-9-867-2013, 2013. MODIS-AQUA. http://aqua.nasa.gov/science/images_data.php, 2013. O'Dea, E. J., While, J., Furner, R., Arnold, A., Hyder, P., Storkey, D., Edwards, K.P., Siddorn, J.R., Martin, M.J., Liu, H., Holt, J.T.: An operational ocean forecast system incorporating SST data assimilation for the tidally driven European North-West European shelf. Journal of Operational Oceanography, 5, 3-17, 2012. Piotukh V.B., Zatsepin A.G., Kazmin A.S., Yakubenko V.G.: Impact of the winter cooling on the variability of the thermohaline characteristics of the active layer in the Black Sea. Oceanology, 41, 2, 221-230, 2011 Shapiro, G.I.: Black Sea Circulation. In: Encyclopedia of Ocean Sciences (Second Edition). Eds: J. H. Steele, K. K. Turekian, and S. A. Thorpe. ISBN: 978-0-12-374473-9, P.3519-3532, 2008. Sur, H. I., and Y. P. Ilyin: Evolution of satellite derived mesoscale thermal patterns in the Black Sea, Prog. Oceanogr., 39, 109-151, 1997 Suvorov, A.M., Eremeev, V.N., Belokopytov, V.N., Khaliulin, A.H., Godin, E.A., Ingerov, A.V., Palmer, D.R. and Levitus, S.: Digital Atlas: Physical Oceanography of the Black Sea. (CD-ROM), Environmental Services Data and Information Management Program, Marine Hydrophysical Institute of the National Academy of Sciences of Ukraine, 2004. Thompson, R. O. R. Y.: Climatological numerical models of the surface mixed layer of the ocean, J. Phys. Oceanogr., 6, 496-603, 1976

Alternative method for quantification of alfa-amylase activity.

PubMed

Farias, D F; Carvalho, A F U; Oliveira, C C; Sousa, N M; Rocha-Bezerrra, L C B; Ferreira, P M P; Lima, G P G; Hissa, D C

2010-05-01

A modification of the sensitive agar diffusion method was developed for macro-scale determination of alfa-amylase. The proposed modifications lower costs with the utilisation of starch as substrate and agar as supporting medium. Thus, a standard curve was built using alfa-amylase solution from Aspergillus oryzae, with concentrations ranging from 2.4 to 7,500 U.mL-1. Clear radial diffusion zones were measured after 4 hours of incubation at 20 A degrees C. A linear relationship between the logarithm of enzyme activities and the area of clear zones was obtained. The method was validated by testing alpha-amylase from barley at the concentrations of 2.4; 60; 300 and 1,500 U.mL-1. The proposed method turned out to be simpler, faster, less expensive and able to determine on a macro-scale alpha-amylase over a wide range (2.4 to 7,500 U.mL-1) in scientific investigation as well as in teaching laboratory activities.

Investigation of Marine-Derived Fungal Diversity and Their Exploitable Biological Activities

PubMed Central

Hong, Joo-Hyun; Jang, Seokyoon; Heo, Young Mok; Min, Mihee; Lee, Hwanhwi; Lee, Young Min; Lee, Hanbyul; Kim, Jae-Jin

2015-01-01

Marine fungi are potential producers of bioactive compounds that may have pharmacological and medicinal applications. Fungi were cultured from marine brown algae and identified using multiple target genes to confirm phylogenetic placement. These target genes included the internal transcribed spacer (ITS), the nuclear large subunit (LSU), and the β-tubulin region. Various biological activities of marine-derived fungi were evaluated, including their antifungal, antioxidant and cellulolytic enzyme activities. As a result, a total of 50 fungi was isolated from the brown algae Sargassum sp. Among the 50 isolated fungi, Corollospora angusta was the dominant species in this study. The genus Arthrinium showed a relatively strong antifungal activity to all of the target plant pathogenic fungi. In particular, Arthrinium saccharicola KUC21221 showed high radical scavenging activity and the highest activities in terms of filter paper units (0.39 U/mL), endoglucanase activity (0.38 U/mL), and β-glucosidase activity (1.04 U/mL). PMID:26133554

Leveraging Terminological Resources for Mapping between Rare Disease Information Sources

PubMed Central

Rance, Bastien; Snyder, Michelle; Lewis, Janine; Bodenreider, Olivier

2015-01-01

Background Rare disease information sources are incompletely and inconsistently cross-referenced to one another, making it difficult for information seekers to navigate across them. The development of such cross-references established manually by experts is generally labor intensive and costly. Objectives To develop an automatic mapping between two of the major rare diseases information sources, GARD and Orphanet, by leveraging terminological resources, especially the UMLS. Methods We map the rare disease terms from Orphanet and ORDR to the UMLS. We use the UMLS as a pivot to bridge between the rare disease terminologies. We compare our results to a mapping obtained through manually established cross-references to OMIM. Results Our mapping has a precision of 94%, a recall of 63% and an F1-score of 76%. Our automatic mapping should help facilitate the development of more complete and consistent cross-references between GARD and Orphanet, and is applicable to other rare disease information sources as well. PMID:23920611

Enzymatic production of α-ketoglutaric acid from l-glutamic acid via l-glutamate oxidase.

PubMed

Niu, Panqing; Dong, Xiaoxiang; Wang, Yuancai; Liu, Liming

2014-06-10

In this study, a novel strategy for α-ketoglutaric acid (α-KG) production from l-glutamic acid using recombinant l-glutamate oxidase (LGOX) was developed. First, by analyzing the molecular structure characteristics of l-glutamic acid and α-KG, LGOX was found to be the best catalyst for oxidizing the amino group of l-glutamic acid to a ketonic group without the need for exogenous cofactor. Then the LGOX gene was expressed in Escherichia coli BL21 (DE3) in a soluble and active form, and the recombinant LGOX activity reached to a maximum value of 0.59U/mL at pH 6.5, 30°C. Finally, the maximum α-KG concentration reached 104.7g/L from 110g/L l-glutamic acid in 24h, under the following optimum conditions: 1.5U/mL LGOX, 250U/mL catalase, 3mM MnCl2, 30°C, and pH 6.5. Copyright © 2014. Published by Elsevier B.V.

Performance of the commercially available SERION ELISA classic Echinococcus IgG test for the detection of cystic echinococcosis in clinical practice.

PubMed

Sarink, M J; Koelewijn, R; Slingerland, B C G C; Tielens, A G M; van Genderen, P J J; van Hellemond, J J

2018-06-28

Diagnosis of cystic echinococcosis (CE) is at present mainly based on imaging techniques. Serology has a complementary role, partly due to the small number of standardized and commercially available assays. Therefore we examined the clinical performance of the SERION ELISA classic Echinococcus IgG test. Using 10 U/ml as a cut-off point, and serum samples from 50 CE patients and 105 healthy controls, the sensitivity and specificity were 98.0% and 96.2%, respectively. If patients with other infectious diseases were used as negative controls, the specificity decreased to 76.9%, which causes poor positive predictive values. However, if results between 10 and 15 U/ml are classified as indecisive, the specificity of positive results (≥15 U/ml) increased to 92.5% without greatly affecting the sensitivity (92.0%). Using this approach in combination with imaging studies, the SERION ELISA classic Echinococcosis IgG test can be a useful aid in the diagnosis of CE.