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Sample records for foundry ontology development

  1. A Method for Evaluating and Standardizing Ontologies

    ERIC Educational Resources Information Center

    Seyed, Ali Patrice

    2012-01-01

    The Open Biomedical Ontology (OBO) Foundry initiative is a collaborative effort for developing interoperable, science-based ontologies. The Basic Formal Ontology (BFO) serves as the upper ontology for the domain-level ontologies of OBO. BFO is an upper ontology of types as conceived by defenders of realism. Among the ontologies developed for OBO…

  2. Foundry

    NASA Astrophysics Data System (ADS)

    Trinowski, Douglas M.

    This chapter reprises the authors' original work and covers the ubiquitous uses of phenolic resins as sand mold and core binders in the metalcasting (foundry) industry. An overview of the economic and technical significance of metalcasting is provided along with a simplified description of the process of casting. A description of all synthetic organic resins used as foundry binders is provided with an overview of the chemistry and coremaking process. Where appropriate, significant advancements made in each process are described. A new section on emissions from phenolic resins used as foundry binders is provided. Finally, comments on the future of phenolic resins in this field are described.

  3. Developing biomedical ontologies collaboratively.

    PubMed

    Noy, Natalya F; Tudorache, Tania; de Coronado, Sherri; Musen, Mark A

    2008-01-01

    The development of ontologies that define entities and relationships among them has become essential for modern work in biomedicine. Ontologies are becoming so large in their coverage that no single centralized group of people can develop them effectively and ontology development becomes a community-based enterprise. In this paper we present Collaborative Protégé-a prototype tool that supports many aspects of community-based development, such as discussions integrated with ontology-editing process, chats, and annotation of changes. We have evaluated Collaborative Protégé in the context of the NCI Thesaurus development. Users have found the tool effective for carrying out discussions and recording design rationale. PMID:18998901

  4. Data mining for ontology development.

    SciTech Connect

    Davidson, George S.; Strasburg, Jana; Stampf, David; Neymotin,Lev; Czajkowski, Carl; Shine, Eugene; Bollinger, James; Ghosh, Vinita; Sorokine, Alexandre; Ferrell, Regina; Ward, Richard; Schoenwald, David Alan

    2010-06-01

    A multi-laboratory ontology construction effort during the summer and fall of 2009 prototyped an ontology for counterfeit semiconductor manufacturing. This effort included an ontology development team and an ontology validation methods team. Here the third team of the Ontology Project, the Data Analysis (DA) team reports on their approaches, the tools they used, and results for mining literature for terminology pertinent to counterfeit semiconductor manufacturing. A discussion of the value of ontology-based analysis is presented, with insights drawn from other ontology-based methods regularly used in the analysis of genomic experiments. Finally, suggestions for future work are offered.

  5. Developing a Modular Hydrogeology Ontology Extending the SWEET Ontologies

    NASA Astrophysics Data System (ADS)

    Tripathi, A.; Babaie, H. A.

    2005-12-01

    Reengineering upper-level ontologies to make them useful for specific domains can be achieved using modular software development techniques. The challenge of manipulating complex and general, upper-level ontologies can be overcome by using ontology development tools for the purpose of analysis and design of new concepts and extension of existing concepts. As a use case representing this approach we present the reengineering of NASA's Semantic Web for Earth and Environmental Terminology (SWEET) ontologies to include part of the hydrogeology concepts. We have maintained the modular design of the SWEET ontologies for maximum extensibility and reusability. The modular reengineering of the SWEET ontologies to include hydrogeology domain involved the following steps: (1): Identify the terms and concepts relevant to the hydrogeology domain through scenarios, competency questions, and interviews with domain experts. (2): Establish the inter-relationships between concepts (e.g., vadose zone = unsaturated zone). (3): Identify the dependent concepts, such as physical properties or units, and determine their relationships to external concepts. (4): Download the OWL files from SWEET, and save them on local systems for editing. (5): Use ontology editing tools like SWOOP and Protege to analyze the structure of the existing OWL files. (6): Add new domain concepts as new classes in the OWL files, or as subclasses of already existing classes in the SWEET ontologies. The step involved changing the relationships (properties) and/or adding new relationships where they were required in the domain. Sometimes the entire structure of the existing concepts needed to be changed to represent the domain concept more meaningfully. (7): Test the consistency of concepts using appropriate tools (e.g., Protege, which uses the Racer reasoner to check consistency of concepts). (8) Add individuals to the new concepts to test the modified ontologies. We present an example of a simple RDQL query to test

  6. Ontology Research and Development. Part 2 - A Review of Ontology Mapping and Evolving.

    ERIC Educational Resources Information Center

    Ding, Ying; Foo, Schubert

    2002-01-01

    Reviews ontology research and development, specifically ontology mapping and evolving. Highlights include an overview of ontology mapping projects; maintaining existing ontologies and extending them as appropriate when new information or knowledge is acquired; and ontology's role and the future of the World Wide Web, or Semantic Web. (Contains 55…

  7. Developing a semantically rich ontology for the biobank-administration domain

    PubMed Central

    2013-01-01

    Background Biobanks are a critical resource for translational science. Recently, semantic web technologies such as ontologies have been found useful in retrieving research data from biobanks. However, recent research has also shown that there is a lack of data about the administrative aspects of biobanks. These data would be helpful to answer research-relevant questions such as what is the scope of specimens collected in a biobank, what is the curation status of the specimens, and what is the contact information for curators of biobanks. Our use cases include giving researchers the ability to retrieve key administrative data (e.g. contact information, contact's affiliation, etc.) about the biobanks where specific specimens of interest are stored. Thus, our goal is to provide an ontology that represents the administrative entities in biobanking and their relations. We base our ontology development on a set of 53 data attributes called MIABIS, which were in part the result of semantic integration efforts of the European Biobanking and Biomolecular Resources Research Infrastructure (BBMRI). The previous work on MIABIS provided the domain analysis for our ontology. We report on a test of our ontology against competency questions that we derived from the initial BBMRI use cases. Future work includes additional ontology development to answer additional competency questions from these use cases. Results We created an open-source ontology of biobank administration called Ontologized MIABIS (OMIABIS) coded in OWL 2.0 and developed according to the principles of the OBO Foundry. It re-uses pre-existing ontologies when possible in cooperation with developers of other ontologies in related domains, such as the Ontology of Biomedical Investigation. OMIABIS provides a formalized representation of biobanks and their administration. Using the ontology and a set of Description Logic queries derived from the competency questions that we identified, we were able to retrieve test data

  8. The zebrafish anatomy and stage ontologies: representing the anatomy and development of Danio rerio

    PubMed Central

    2014-01-01

    Background The Zebrafish Anatomy Ontology (ZFA) is an OBO Foundry ontology that is used in conjunction with the Zebrafish Stage Ontology (ZFS) to describe the gross and cellular anatomy and development of the zebrafish, Danio rerio, from single cell zygote to adult. The zebrafish model organism database (ZFIN) uses the ZFA and ZFS to annotate phenotype and gene expression data from the primary literature and from contributed data sets. Results The ZFA models anatomy and development with a subclass hierarchy, a partonomy, and a developmental hierarchy and with relationships to the ZFS that define the stages during which each anatomical entity exists. The ZFA and ZFS are developed utilizing OBO Foundry principles to ensure orthogonality, accessibility, and interoperability. The ZFA has 2860 classes representing a diversity of anatomical structures from different anatomical systems and from different stages of development. Conclusions The ZFA describes zebrafish anatomy and development semantically for the purposes of annotating gene expression and anatomical phenotypes. The ontology and the data have been used by other resources to perform cross-species queries of gene expression and phenotype data, providing insights into genetic relationships, morphological evolution, and models of human disease. PMID:24568621

  9. Developing Domain Ontologies for Course Content

    ERIC Educational Resources Information Center

    Boyce, Sinead; Pahl, Claus

    2007-01-01

    Ontologies have the potential to play an important role in instructional design and the development of course content. They can be used to represent knowledge about content, supporting instructors in creating content or learners in accessing content in a knowledge-guided way. While ontologies exist for many subject domains, their quality and…

  10. A Knowledge Engineering Approach to Develop Domain Ontology

    ERIC Educational Resources Information Center

    Yun, Hongyan; Xu, Jianliang; Xiong, Jing; Wei, Moji

    2011-01-01

    Ontologies are one of the most popular and widespread means of knowledge representation and reuse. A few research groups have proposed a series of methodologies for developing their own standard ontologies. However, because this ontological construction concerns special fields, there is no standard method to build domain ontology. In this paper,…

  11. The Gene Ontology (GO) Cellular Component Ontology: integration with SAO (Subcellular Anatomy Ontology) and other recent developments

    PubMed Central

    2013-01-01

    Background The Gene Ontology (GO) (http://www.geneontology.org/) contains a set of terms for describing the activity and actions of gene products across all kingdoms of life. Each of these activities is executed in a location within a cell or in the vicinity of a cell. In order to capture this context, the GO includes a sub-ontology called the Cellular Component (CC) ontology (GO-CCO). The primary use of this ontology is for GO annotation, but it has also been used for phenotype annotation, and for the annotation of images. Another ontology with similar scope to the GO-CCO is the Subcellular Anatomy Ontology (SAO), part of the Neuroscience Information Framework Standard (NIFSTD) suite of ontologies. The SAO also covers cell components, but in the domain of neuroscience. Description Recently, the GO-CCO was enriched in content and links to the Biological Process and Molecular Function branches of GO as well as to other ontologies. This was achieved in several ways. We carried out an amalgamation of SAO terms with GO-CCO ones; as a result, nearly 100 new neuroscience-related terms were added to the GO. The GO-CCO also contains relationships to GO Biological Process and Molecular Function terms, as well as connecting to external ontologies such as the Cell Ontology (CL). Terms representing protein complexes in the Protein Ontology (PRO) reference GO-CCO terms for their species-generic counterparts. GO-CCO terms can also be used to search a variety of databases. Conclusions In this publication we provide an overview of the GO-CCO, its overall design, and some recent extensions that make use of additional spatial information. One of the most recent developments of the GO-CCO was the merging in of the SAO, resulting in a single unified ontology designed to serve the needs of GO annotators as well as the specific needs of the neuroscience community. PMID:24093723

  12. Developing an Ontology for Ocean Biogeochemistry Data

    NASA Astrophysics Data System (ADS)

    Chandler, C. L.; Allison, M. D.; Groman, R. C.; West, P.; Zednik, S.; Maffei, A. R.

    2010-12-01

    Semantic Web technologies offer great promise for enabling new and better scientific research. However, significant challenges must be met before the promise of the Semantic Web can be realized for a discipline as diverse as oceanography. Evolving expectations for open access to research data combined with the complexity of global ecosystem science research themes present a significant challenge, and one that is best met through an informatics approach. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the National Science Foundation Division of Ocean Sciences to work with ocean biogeochemistry researchers to improve access to data resulting from their respective programs. In an effort to improve data access, BCO-DMO staff members are collaborating with researchers from the Tetherless World Constellation (Rensselaer Polytechnic Institute) to develop an ontology that formally describes the concepts and relationships in the data managed by the BCO-DMO. The project required transforming a legacy system of human-readable, flat files of metadata to well-ordered controlled vocabularies to a fully developed ontology. To improve semantic interoperability, terms from the BCO-DMO controlled vocabularies are being mapped to controlled vocabulary terms adopted by other oceanographic data management organizations. While the entire process has proven to be difficult, time-consuming and labor-intensive, the work has been rewarding and is a necessary prerequisite for the eventual incorporation of Semantic Web tools. From the beginning of the project, development of the ontology has been guided by a use case based approach. The use cases were derived from data access related requests received from members of the research community served by the BCO-DMO. The resultant ontology satisfies the requirements of the use cases and reflects the information stored in the metadata database. The BCO-DMO metadata database currently contains information that

  13. Developing Learning Materials Using an Ontology of Mathematical Logic

    ERIC Educational Resources Information Center

    Boyatt, Russell; Joy, Mike

    2012-01-01

    Ontologies describe a body of knowledge and give formal structure to a domain by describing concepts and their relationships. The construction of an ontology provides an opportunity to develop a shared understanding and a consistent vocabulary to be used for a given activity. This paper describes the construction of an ontology for an area of…

  14. Pre-SPC Math for Foundry Workers. A Lesson Developed for Robinson Foundry and Bodine-Robinson as Part of a National Workplace Literacy Program.

    ERIC Educational Resources Information Center

    Rasmussen, Bonnie

    Developed as part of a National Workplace Literacy Program, this lesson focuses on terms and mathematical operations associated with Statistical Process Control (SPC) in the foundry industry. With appropriate assistance and preparatory work, workers testing between grades 4 and 9 on the Test of Adult Basic Education Locator should be able to use…

  15. Foundry Industry Training Committee

    ERIC Educational Resources Information Center

    Industrial Training Journal, 1974

    1974-01-01

    The Foundry Industry Training Committee has encouraged the foundry industry in developing systematic manpower training and development programs at all levels. Features developed include competitions as a technique of standard setting, recommendations for technician training, and a widely used manpower information system. (MW)

  16. Representing Kidney Development Using the Gene Ontology

    PubMed Central

    Alam-Faruque, Yasmin; Hill, David P.; Dimmer, Emily C.; Harris, Midori A.; Foulger, Rebecca E.; Tweedie, Susan; Attrill, Helen; Howe, Douglas G.; Thomas, Stephen Randall; Davidson, Duncan; Woolf, Adrian S.; Blake, Judith A.; Mungall, Christopher J.; O’Donovan, Claire; Apweiler, Rolf; Huntley, Rachael P.

    2014-01-01

    Gene Ontology (GO) provides dynamic controlled vocabularies to aid in the description of the functional biological attributes and subcellular locations of gene products from all taxonomic groups (www.geneontology.org). Here we describe collaboration between the renal biomedical research community and the GO Consortium to improve the quality and quantity of GO terms describing renal development. In the associated annotation activity, the new and revised terms were associated with gene products involved in renal development and function. This project resulted in a total of 522 GO terms being added to the ontology and the creation of approximately 9,600 kidney-related GO term associations to 940 UniProt Knowledgebase (UniProtKB) entries, covering 66 taxonomic groups. We demonstrate the impact of these improvements on the interpretation of GO term analyses performed on genes differentially expressed in kidney glomeruli affected by diabetic nephropathy. In summary, we have produced a resource that can be utilized in the interpretation of data from small- and large-scale experiments investigating molecular mechanisms of kidney function and development and thereby help towards alleviating renal disease. PMID:24941002

  17. Developing an Ontology for Ocean Biogeochemical Data

    NASA Astrophysics Data System (ADS)

    Allison, M. D.; Chandler, C. L.; Groman, R. C.

    2009-12-01

    We could be on the verge of realizing the promise of the Semantic Web for oceanography. One of the challenges that remains is to develop ontologies that can be used to semantically enable data system interfaces for improved data discovery and usability. Evolving expectations for open access to research data combined with the informatics challenge presented by global ecosystem science themes, may result in more frustration than satisfaction if we are unable to develop efficient data discovery tools; ones that perform at least as well as the familiar telephone. The Biological and Chemical Oceanography Data Management Office (BCO-DMO) is funded by the National Science Foundation to work with ocean biogeochemistry researchers to improve access to data resulting from their respective programs. BCO-DMO staff members have begun the process of developing an ontology to represent the metadata associated with several legacy databases managed by the BCO-DMO. We will describe the challenges encountered thus far, the technologies selected, and the strategies associated with this use case based approach.

  18. Agile development of ontologies through conversation

    NASA Astrophysics Data System (ADS)

    Braines, Dave; Bhattal, Amardeep; Preece, Alun D.; de Mel, Geeth

    2016-05-01

    Ontologies and semantic systems are necessarily complex but offer great potential in terms of their ability to fuse information from multiple sources in support of situation awareness. Current approaches do not place the ontologies directly into the hands of the end user in the field but instead hide them away behind traditional applications. We have been experimenting with human-friendly ontologies and conversational interactions to enable non-technical business users to interact with and extend these dynamically. In this paper we outline our approach via a worked example, covering: OWL ontologies, ITA Controlled English, Sensor/mission matching and conversational interactions between human and machine agents.

  19. Ontology for Vector Surveillance and Management

    PubMed Central

    LOZANO-FUENTES, SAUL; BANDYOPADHYAY, ARITRA; COWELL, LINDSAY G.; GOLDFAIN, ALBERT; EISEN, LARS

    2013-01-01

    Ontologies, which are made up by standardized and defined controlled vocabulary terms and their interrelationships, are comprehensive and readily searchable repositories for knowledge in a given domain. The Open Biomedical Ontologies (OBO) Foundry was initiated in 2001 with the aims of becoming an “umbrella” for life-science ontologies and promoting the use of ontology development best practices. A software application (OBO-Edit; *.obo file format) was developed to facilitate ontology development and editing. The OBO Foundry now comprises over 100 ontologies and candidate ontologies, including the NCBI organismal classification ontology (NCBITaxon), the Mosquito Insecticide Resistance Ontology (MIRO), the Infectious Disease Ontology (IDO), the IDOMAL malaria ontology, and ontologies for mosquito gross anatomy and tick gross anatomy. We previously developed a disease data management system for dengue and malaria control programs, which incorporated a set of information trees built upon ontological principles, including a “term tree” to promote the use of standardized terms. In the course of doing so, we realized that there were substantial gaps in existing ontologies with regards to concepts, processes, and, especially, physical entities (e.g., vector species, pathogen species, and vector surveillance and management equipment) in the domain of surveillance and management of vectors and vector-borne pathogens. We therefore produced an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems. The Vector Surveillance and Management Ontology (VSMO) includes >2,200 unique terms, of which the vast majority (>80%) were newly generated during the development of this ontology. One core feature of the VSMO is the linkage

  20. Ontology for vector surveillance and management.

    PubMed

    Lozano-Fuentes, Saul; Bandyopadhyay, Aritra; Cowell, Lindsay G; Goldfain, Albert; Eisen, Lars

    2013-01-01

    Ontologies, which are made up by standardized and defined controlled vocabulary terms and their interrelationships, are comprehensive and readily searchable repositories for knowledge in a given domain. The Open Biomedical Ontologies (OBO) Foundry was initiated in 2001 with the aims of becoming an "umbrella" for life-science ontologies and promoting the use of ontology development best practices. A software application (OBO-Edit; *.obo file format) was developed to facilitate ontology development and editing. The OBO Foundry now comprises over 100 ontologies and candidate ontologies, including the NCBI organismal classification ontology (NCBITaxon), the Mosquito Insecticide Resistance Ontology (MIRO), the Infectious Disease Ontology (IDO), the IDOMAL malaria ontology, and ontologies for mosquito gross anatomy and tick gross anatomy. We previously developed a disease data management system for dengue and malaria control programs, which incorporated a set of information trees built upon ontological principles, including a "term tree" to promote the use of standardized terms. In the course of doing so, we realized that there were substantial gaps in existing ontologies with regards to concepts, processes, and, especially, physical entities (e.g., vector species, pathogen species, and vector surveillance and management equipment) in the domain of surveillance and management of vectors and vector-borne pathogens. We therefore produced an ontology for vector surveillance and management, focusing on arthropod vectors and vector-borne pathogens with relevance to humans or domestic animals, and with special emphasis on content to support operational activities through inclusion in databases, data management systems, or decision support systems. The Vector Surveillance and Management Ontology (VSMO) includes >2,200 unique terms, of which the vast majority (>80%) were newly generated during the development of this ontology. One core feature of the VSMO is the linkage, through

  1. Modeling a microbial community and biodiversity assay with OBO Foundry ontologies: the interoperability gains of a modular approach.

    PubMed

    Rocca-Serra, Philippe; Walls, Ramona; Parnell, Jacob; Gallery, Rachel; Zheng, Jie; Sansone, Susanna-Assunta; Gonzalez-Beltran, Alejandra

    2015-01-01

    The advent of affordable sequencing technology provides for a new generation of explorers who probe the world's microbial diversity. Projects such as Tara Oceans, Moorea Biocode Project and Gut Microbiome rely on sequencing technologies to probe community diversity. Either targeted gene surveys (also known as community surveys) or complete metagenomes are evaluated. The former, being the less costly of the two methods, relies on the identification of specific genomic regions, which can be used as a proxy to estimate genetic distance between related species in a Phylum. For instance, 16 S ribosomal RNA gene surveys are used to probe bacterial communities while internal transcribed spacer surveys, for example, can be used for probing fungal communities. With the explosion of projects and frenzy to explore new domains of life, scientists in the field have issued guidelines to report minimal information (following a checklist), ensuring that information is contextualized in a meaningful way. Yet the semantics of a checklist are not explicit. We demonstrate here how a tabular template can be used to collect information on microbial diversity using an explicit representation in the Resource Description Framework that is consistent with community agreed-upon knowledge representation patterns found in the Ontology for Biomedical Investigations. PMID:25632945

  2. Surreptitious, Evolving and Participative Ontology Development: An End-User Oriented Ontology Development Methodology

    ERIC Educational Resources Information Center

    Bachore, Zelalem

    2012-01-01

    Ontology not only is considered to be the backbone of the semantic web but also plays a significant role in distributed and heterogeneous information systems. However, ontology still faces limited application and adoption to date. One of the major problems is that prevailing engineering-oriented methodologies for building ontologies do not…

  3. Ontology Driven Development and Science Information System Interoperability

    NASA Astrophysics Data System (ADS)

    Hughes, J. S.; Crichton, D. J.; Joyner, R. S.; Rye, E. D.; Pds4 Data Standards Team Leads

    2010-12-01

    A domain ontology can be used to drive the development of a science information system and enable system interoperability and science data correlation. A domain ontology defines the data structures, the metadata for the science interpretation of the data, and the metadata that describes the context within which the data was captured, processed, and archived. In addition the ontology defines the organization of the data and their relationships. These definitions can be used to configure a registry-base information system from generic system components, generate schemas for data labeling and validation, and write standards documents for a variety of audiences. The resulting information system catalogs and tracks ingested data and allows the periodic harvesting of the registered metadata for sophisticated web-based search applications. An independent ontology and the data driven paradigm also allow the evolution of the domain’s information model independent from the system’s infrastructure. The Planetary Data System (PDS) is executing a plan to move the PDS to a fully online, federated system. This plan addresses new demands on the system including increasing data volume and complexity and number of missions. This poster provides an overview of the planetary science ontology and the data driven paradigm being used to development the PDS 2010 information system.

  4. Ontology Development and Evolution in the Accident Investigation Domain

    NASA Technical Reports Server (NTRS)

    Carvalho, Robert; Berrios, Dan; Williams, James

    2004-01-01

    InvestiigationOrganizer (IO) is a collaborative semantic web system designed to support the conduct of mishap investigations. IO provides a common repository for a wide range of mishap related information, allowing investigators to integrate evidence, causal models, and investigation results. IO has been used to support investigations ranging from a small property damage case to the loss of the Space Shuttle Columbia. Through IO'S use in these investigations, we have learned significant lessons? about the application of ontologies and semantic systems to solving real-world problems. This paper will describe the development of the ontology within IO, from the initial development, its growth in response to user requests during use in investigations, and the recent work that was done to control the results of that growth. This paper will also describe the lessons learned from this experience and how they may apply to the implementaton of future ontologies and semantic systems.

  5. 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

  6. Ion Channel ElectroPhysiology Ontology (ICEPO) – a case study of text mining assisted ontology development

    PubMed Central

    Elayavilli, Ravikumar Komandur; Liu, Hongfang

    2016-01-01

    Background Computational modeling of biological cascades is of great interest to quantitative biologists. Biomedical text has been a rich source for quantitative information. Gathering quantitative parameters and values from biomedical text is one significant challenge in the early steps of computational modeling as it involves huge manual effort. While automatically extracting such quantitative information from bio-medical text may offer some relief, lack of ontological representation for a subdomain serves as impedance in normalizing textual extractions to a standard representation. This may render textual extractions less meaningful to the domain experts. Methods In this work, we propose a rule-based approach to automatically extract relations involving quantitative data from biomedical text describing ion channel electrophysiology. We further translated the quantitative assertions extracted through text mining to a formal representation that may help in constructing ontology for ion channel events using a rule based approach. We have developed Ion Channel ElectroPhysiology Ontology (ICEPO) by integrating the information represented in closely related ontologies such as, Cell Physiology Ontology (CPO), and Cardiac Electro Physiology Ontology (CPEO) and the knowledge provided by domain experts. Results The rule-based system achieved an overall F-measure of 68.93% in extracting the quantitative data assertions system on an independently annotated blind data set. We further made an initial attempt in formalizing the quantitative data assertions extracted from the biomedical text into a formal representation that offers potential to facilitate the integration of text mining into ontological workflow, a novel aspect of this study. Conclusions This work is a case study where we created a platform that provides formal interaction between ontology development and text mining. We have achieved partial success in extracting quantitative assertions from the biomedical text

  7. Ontology Research and Development. Part 1-A Review of Ontology Generation.

    ERIC Educational Resources Information Center

    Ding, Ying; Foo, Schubert

    2002-01-01

    Discusses the role of ontology in knowledge representation, including enabling content-based access, interoperability, communications, and new levels of service on the Semantic Web; reviews current ontology generation studies and projects as well as problems facing such research; and discusses ontology mapping, information extraction, natural…

  8. Reactive Leadership: Divining, Developing, and Demonstrating Community Ontologies

    NASA Astrophysics Data System (ADS)

    Graybeal, J.

    2008-12-01

    The Marine Metadata Interoperability Project (known as MMI, on the web at http://marinemetadata.org) was formed to provide leadership in metadata practices to the marine science community. In 2004 this meant finding and writing about resources and best practices, which until then were all but invisible. In 2008 the scope is far wider, encompassing comprehensive guidance, collaborative community environments, and introduction and demonstration of advanced technologies to an increasingly interested scientific domain. MMI's technical leadership, based on experiences gained in the hydrologic community, emphasized the role ontologies could play in marine science. An early MMI workshop successfully incorporated a large number of community vocabularies, tools to harmonize them in a common ontological format, and the mapping of terms from vocabularies expressed in that format. That 2005 workshop demonstrated the connections to be made among different community vocabularies, and was well regarded by participants, but did not lead to widespread adoption of the tools, technologies, or even the vocabularies. Ontology development efforts for marine sensors and platforms showed intermittent progress, but again were not adopted or pushed toward completion. It is now 2008, and the marine community is increasingly attentive to a wide range of interoperability issues. A large part of the community has at least heard of "semantic interoperability", and many understand its critical role in finding and working with data. Demand for specific solutions, and for workable approaches, is becoming more vocal in the marine community. Yet there is still no encompassing model in place for achieving semantic interoperability, only simple operational registries have been set up for oceanographic community vocabularies, and only a few isolated applications demonstrate how semantic barriers can be overcome. Why has progress been so slow? Are good answers on the horizon? And if we build it, will the

  9. JPL Innovation Foundry

    NASA Astrophysics Data System (ADS)

    Sherwood, Brent; McCleese, Daniel

    2013-08-01

    Space science missions are increasingly challenged today: in ambition, by increasingly sophisticated hypotheses tested; in development, by the increasing complexity of advanced technologies; in budgeting, by the decline of flagship-class mission opportunities; in management, by expectations for breakthrough science despite a risk-averse programmatic climate; and in planning, by increasing competition for scarce resources. How are the space-science missions of tomorrow being formulated? The paper describes the JPL Innovation Foundry, created in 2011, to respond to this evolving context. The Foundry integrates methods, tools, and experts that span the mission concept lifecycle. Grounded in JPL's heritage of missions, flight instruments, mission proposals, and concept innovation, the Foundry seeks to provide continuity of support and cost-effective, on-call access to the right domain experts at the right time, as science definition teams and Principal Investigators mature mission ideas from "cocktail napkin" to PDR. The Foundry blends JPL capabilities in proposal development and concurrent engineering, including Team X, with new approaches for open-ended concept exploration in earlier, cost-constrained phases, and with ongoing research and technology projects. It applies complexity and cost models, project-formulation lessons learned, and strategy analyses appropriate to each level of concept maturity. The Foundry is organizationally integrated with JPL formulation program offices; staffed by JPL's line organizations for engineering, science, and costing; and overseen by senior Laboratory leaders to assure experienced coordination and review. Incubation of each concept is tailored depending on its maturity and proposal history, and its highest-leverage modeling and analysis needs.

  10. JPL Innovation Foundry

    NASA Technical Reports Server (NTRS)

    Sherwood, Brent; McCleese, Daniel

    2012-01-01

    Space science missions are increasingly challenged today: in ambition, by increasingly sophisticated hypotheses tested; in development, by the increasing complexity of advanced technologies; in budgeting, by the decline of flagship-class mission opportunities; in management, by expectations for breakthrough science despite a risk-averse programmatic climate; and in planning, by increasing competition for scarce resources. How are the space-science missions of tomorrow being formulated? The paper describes the JPL Innovation Foundry, created in 2011, to respond to this evolving context. The Foundry integrates methods, tools, and experts that span the mission concept lifecycle. Grounded in JPL's heritage of missions, flight instruments, mission proposals, and concept innovation, the Foundry seeks to provide continuity of support and cost-effective, on-call access to the right domain experts at the right time, as science definition teams and Principal Investigators mature mission ideas from "cocktail napkin" to PDR. The Foundry blends JPL capabilities in proposal development and concurrent engineering, including Team X, with new approaches for open-ended concept exploration in earlier, cost-constrained phases, and with ongoing research and technology projects. It applies complexity and cost models, projectformulation lessons learned, and strategy analyses appropriate to each level of concept maturity. The Foundry is organizationally integrated with JPL formulation program offices; staffed by JPL's line organizations for engineering, science, and costing; and overseen by senior Laboratory leaders to assure experienced coordination and review. Incubation of each concept is tailored depending on its maturity and proposal history, and its highest leverage modeling and analysis needs.

  11. Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia.

    PubMed

    Ong, Edison; He, Yongqun

    2016-01-01

    Hundreds of biological and biomedical ontologies have been developed to support data standardization, integration and analysis. Although ontologies are typically developed for community usage, community efforts in ontology development are limited. To support ontology visualization, distribution, and community-based annotation and development, we have developed Ontokiwi, an ontology extension to the MediaWiki software. Ontokiwi displays hierarchical classes and ontological axioms. Ontology classes and axioms can be edited and added using Ontokiwi form or MediaWiki source editor. Ontokiwi also inherits MediaWiki features such as Wikitext editing and version control. Based on the Ontokiwi/MediaWiki software package, we have developed Ontobedia, which targets to support community-based development and annotations of biological and biomedical ontologies. As demonstrations, we have loaded the Ontology of Adverse Events (OAE) and the Cell Line Ontology (CLO) into Ontobedia. Our studies showed that Ontobedia was able to achieve expected Ontokiwi features. PMID:27570653

  12. Community-based Ontology Development, Annotation and Discussion with MediaWiki extension Ontokiwi and Ontokiwi-based Ontobedia

    PubMed Central

    Ong, Edison; He, Yongqun

    2016-01-01

    Hundreds of biological and biomedical ontologies have been developed to support data standardization, integration and analysis. Although ontologies are typically developed for community usage, community efforts in ontology development are limited. To support ontology visualization, distribution, and community-based annotation and development, we have developed Ontokiwi, an ontology extension to the MediaWiki software. Ontokiwi displays hierarchical classes and ontological axioms. Ontology classes and axioms can be edited and added using Ontokiwi form or MediaWiki source editor. Ontokiwi also inherits MediaWiki features such as Wikitext editing and version control. Based on the Ontokiwi/MediaWiki software package, we have developed Ontobedia, which targets to support community-based development and annotations of biological and biomedical ontologies. As demonstrations, we have loaded the Ontology of Adverse Events (OAE) and the Cell Line Ontology (CLO) into Ontobedia. Our studies showed that Ontobedia was able to achieve expected Ontokiwi features. PMID:27570653

  13. Semiconductor foundry, lithography, and partners

    NASA Astrophysics Data System (ADS)

    Lin, Burn J.

    2002-07-01

    The semiconductor foundry took off in 1990 with an annual capacity of less than 0.1M 8-inch-equivalent wafers at the 2-mm node. In 2000, the annual capacity rose to more than 10M. Initially, the technology practiced at foundries was 1 to 2 generations behind that at integrated device manufacturers (IDMs). Presently, the progress in 0.13-mm manufacturing goes hand-in-hand with any of the IDMs. There is a two-order of magnitude rise in output and the progress of technology development outpaces IDMs. What are the reasons of the success? Is it possible to sustain the pace? This paper shows the quick rise of foundries in capacity, sales, and market share. It discusses the their uniqueness which gives rise to advantages in conjunction with challenges. It also shows the role foundries take with their customer partners and supplier partners, their mutual dependencies, as well as expectations. What role then does lithography play in the foundries? What are the lithographic challenges to sustain the pace of technology? The experience of technology development and transfer, at one of the major foundries, is used to illustrate the difficulties and progresses made. Looking into the future, as semiconductor manufacturing will become even more expensive and capital investment more prohibitive, we will make an attempt to suggest possible solutions.

  14. Process modeling and control in foundry operations

    NASA Astrophysics Data System (ADS)

    Piwonka, T. S.

    1989-02-01

    Initial uses of process modeling were limited to phenomenological descriptions of the physical processes in foundry operations, with the aim of decreasing scrap and rework. It is now clear that process modeling can be used to select, design and optimize foundry processes so that on-line process control can be achieved. Computational, analogue and empirical process models have been developed for sand casting operations, and they are being applied in the foundry with beneficial effects.

  15. An ontological approach for the development of shareable guidelines.

    PubMed Central

    de Clercq, P. A.

    2000-01-01

    Computer-based clinical guidelines and protocols are being increasingly applied in diverse areas. Although there is still little standardization to facilitate sharing, various parties are engaged in the development of shareable guideline representation formalisms and corresponding decision support systems. This paper mentions some of these developed representations, discusses their pros en cons, and demonstrates and discusses a new approach, which combines common elements from earlier-developed formalisms with new ones to improve the reusability and shareability of developed guidelines. An ontological representation is presented that formalizes guidelines in terms of domain-specific knowledge and employed generic strategies that use this domain-specific knowledge in order to solve particular guideline tasks. Furthermore, a framework is described that supports this representation and three examples are shown of guidelines of various granularity and complexity that were developed by means of this approach. PMID:11079866

  16. An ontological approach for the development of shareable guidelines.

    PubMed

    de Clercq, P A

    2000-01-01

    Computer-based clinical guidelines and protocols are being increasingly applied in diverse areas. Although there is still little standardization to facilitate sharing, various parties are engaged in the development of shareable guideline representation formalisms and corresponding decision support systems. This paper mentions some of these developed representations, discusses their pros en cons, and demonstrates and discusses a new approach, which combines common elements from earlier-developed formalisms with new ones to improve the reusability and shareability of developed guidelines. An ontological representation is presented that formalizes guidelines in terms of domain-specific knowledge and employed generic strategies that use this domain-specific knowledge in order to solve particular guideline tasks. Furthermore, a framework is described that supports this representation and three examples are shown of guidelines of various granularity and complexity that were developed by means of this approach.

  17. Toward an Ontology-Based Framework for Clinical Research Databases

    PubMed Central

    Kong, Y. Megan; Dahlke, Carl; Xiang, Qun; Qian, Yu; Karp, David; Scheuermann, Richard H.

    2010-01-01

    Clinical research includes a wide range of study designs from focused observational studies to complex interventional studies with multiple study arms, treatment and assessment events, and specimen procurement procedures. Participant characteristics from case report forms need to be integrated with molecular characteristics from mechanistic experiments on procured specimens. In order to capture and manage this diverse array of data, we have developed the Ontology-Based eXtensible conceptual model (OBX) to serve as a framework for clinical research data in the Immunology Database and Analysis Portal (ImmPort). By designing OBX around the logical structure of the Basic Formal Ontology (BFO) and the Ontology for Biomedical Investigations (OBI), we have found that a relatively simple conceptual model can represent the relatively complex domain of clinical research. In addition, the common framework provided by BFO makes it straightforward to develop data dictionaries based on reference and application ontologies from the OBO Foundry. PMID:20460173

  18. Brucellosis Ontology (IDOBRU) as an extension of the Infectious Disease Ontology

    PubMed Central

    2011-01-01

    Background Caused by intracellular Gram-negative bacteria Brucella spp., brucellosis is the most common bacterial zoonotic disease. Extensive studies in brucellosis have yielded a large number of publications and data covering various topics ranging from basic Brucella genetic study to vaccine clinical trials. To support data interoperability and reasoning, a community-based brucellosis-specific biomedical ontology is needed. Results The Brucellosis Ontology (IDOBRU: http://sourceforge.net/projects/idobru), a biomedical ontology in the brucellosis domain, is an extension ontology of the core Infectious Disease Ontology (IDO-core) and follows OBO Foundry principles. Currently IDOBRU contains 1503 ontology terms, which includes 739 Brucella-specific terms, 414 IDO-core terms, and 350 terms imported from 10 existing ontologies. IDOBRU has been used to model different aspects of brucellosis, including host infection, zoonotic disease transmission, symptoms, virulence factors and pathogenesis, diagnosis, intentional release, vaccine prevention, and treatment. Case studies are typically used in our IDOBRU modeling. For example, diurnal temperature variation in Brucella patients, a Brucella-specific PCR method, and a WHO-recommended brucellosis treatment were selected as use cases to model brucellosis symptom, diagnosis, and treatment, respectively. Developed using OWL, IDOBRU supports OWL-based ontological reasoning. For example, by performing a Description Logic (DL) query in the OWL editor Protégé 4 or a SPARQL query in an IDOBRU SPARQL server, a check of Brucella virulence factors showed that eight of them are known protective antigens based on the biological knowledge captured within the ontology. Conclusions IDOBRU is the first reported bacterial infectious disease ontology developed to represent different disease aspects in a formal logical format. It serves as a brucellosis knowledgebase and supports brucellosis data integration and automated reasoning. PMID

  19. CLO: The cell line ontology

    PubMed Central

    2014-01-01

    Background Cell lines have been widely used in biomedical research. The community-based Cell Line Ontology (CLO) is a member of the OBO Foundry library that covers the domain of cell lines. Since its publication two years ago, significant updates have been made, including new groups joining the CLO consortium, new cell line cells, upper level alignment with the Cell Ontology (CL) and the Ontology for Biomedical Investigation, and logical extensions. Construction and content Collaboration among the CLO, CL, and OBI has established consensus definitions of cell line-specific terms such as ‘cell line’, ‘cell line cell’, ‘cell line culturing’, and ‘mortal’ vs. ‘immortal cell line cell’. A cell line is a genetically stable cultured cell population that contains individual cell line cells. The hierarchical structure of the CLO is built based on the hierarchy of the in vivo cell types defined in CL and tissue types (from which cell line cells are derived) defined in the UBERON cross-species anatomy ontology. The new hierarchical structure makes it easier to browse, query, and perform automated classification. We have recently added classes representing more than 2,000 cell line cells from the RIKEN BRC Cell Bank to CLO. Overall, the CLO now contains ~38,000 classes of specific cell line cells derived from over 200 in vivo cell types from various organisms. Utility and discussion The CLO has been applied to different biomedical research studies. Example case studies include annotation and analysis of EBI ArrayExpress data, bioassays, and host-vaccine/pathogen interaction. CLO’s utility goes beyond a catalogue of cell line types. The alignment of the CLO with related ontologies combined with the use of ontological reasoners will support sophisticated inferencing to advance translational informatics development. PMID:25852852

  20. Developing ontological model of computational linear algebra - preliminary considerations

    NASA Astrophysics Data System (ADS)

    Wasielewska, K.; Ganzha, M.; Paprzycki, M.; Lirkov, I.

    2013-10-01

    The aim of this paper is to propose a method for application of ontologically represented domain knowledge to support Grid users. The work is presented in the context provided by the Agents in Grid system, which aims at development of an agent-semantic infrastructure for efficient resource management in the Grid. Decision support within the system should provide functionality beyond the existing Grid middleware, specifically, help the user to choose optimal algorithm and/or resource to solve a problem from a given domain. The system assists the user in at least two situations. First, for users without in-depth knowledge about the domain, it should help them to select the method and the resource that (together) would best fit the problem to be solved (and match the available resources). Second, if the user explicitly indicates the method and the resource configuration, it should "verify" if her choice is consistent with the expert recommendations (encapsulated in the knowledge base). Furthermore, one of the goals is to simplify the use of the selected resource to execute the job; i.e., provide a user-friendly method of submitting jobs, without required technical knowledge about the Grid middleware. To achieve the mentioned goals, an adaptable method of expert knowledge representation for the decision support system has to be implemented. The selected approach is to utilize ontologies and semantic data processing, supported by multicriterial decision making. As a starting point, an area of computational linear algebra was selected to be modeled, however, the paper presents a general approach that shall be easily extendable to other domains.

  1. OntoFox: web-based support for ontology reuse

    PubMed Central

    2010-01-01

    Background Ontology development is a rapidly growing area of research, especially in the life sciences domain. To promote collaboration and interoperability between different projects, the OBO Foundry principles require that these ontologies be open and non-redundant, avoiding duplication of terms through the re-use of existing resources. As current options to do so present various difficulties, a new approach, MIREOT, allows specifying import of single terms. Initial implementations allow for controlled import of selected annotations and certain classes of related terms. Findings OntoFox http://ontofox.hegroup.org/ is a web-based system that allows users to input terms, fetch selected properties, annotations, and certain classes of related terms from the source ontologies and save the results using the RDF/XML serialization of the Web Ontology Language (OWL). Compared to an initial implementation of MIREOT, OntoFox allows additional and more easily configurable options for selecting and rewriting annotation properties, and for inclusion of all or a computed subset of terms between low and top level terms. Additional methods for including related classes include a SPARQL-based ontology term retrieval algorithm that extracts terms related to a given set of signature terms and an option to extract the hierarchy rooted at a specified ontology term. OntoFox's output can be directly imported into a developer's ontology. OntoFox currently supports term retrieval from a selection of 15 ontologies accessible via SPARQL endpoints and allows users to extend this by specifying additional endpoints. An OntoFox application in the development of the Vaccine Ontology (VO) is demonstrated. Conclusions OntoFox provides a timely publicly available service, providing different options for users to collect terms from external ontologies, making them available for reuse by import into client OWL ontologies. PMID:20569493

  2. Open Biomedical Ontology-based Medline exploration

    PubMed Central

    Xuan, Weijian; Dai, Manhong; Mirel, Barbara; Song, Jean; Athey, Brian; Watson, Stanley J; Meng, Fan

    2009-01-01

    Background Effective Medline database exploration is critical for the understanding of high throughput experimental results and the development of novel hypotheses about the mechanisms underlying the targeted biological processes. While existing solutions enhance Medline exploration through different approaches such as document clustering, network presentations of underlying conceptual relationships and the mapping of search results to MeSH and Gene Ontology trees, we believe the use of multiple ontologies from the Open Biomedical Ontology can greatly help researchers to explore literature from different perspectives as well as to quickly locate the most relevant Medline records for further investigation. Results We developed an ontology-based interactive Medline exploration solution called PubOnto to enable the interactive exploration and filtering of search results through the use of multiple ontologies from the OBO foundry. The PubOnto program is a rich internet application based on the FLEX platform. It contains a number of interactive tools, visualization capabilities, an open service architecture, and a customizable user interface. It is freely accessible at: . PMID:19426463

  3. Ontological realism: A methodology for coordinated evolution of scientific ontologies

    PubMed Central

    Smith, Barry; Ceusters, Werner

    2011-01-01

    Since 2002 we have been testing and refining a methodology for ontology development that is now being used by multiple groups of researchers in different life science domains. Gary Merrill, in a recent paper in this journal, describes some of the reasons why this methodology has been found attractive by researchers in the biological and biomedical sciences. At the same time he assails the methodology on philosophical grounds, focusing specifically on our recommendation that ontologies developed for scientific purposes should be constructed in such a way that their terms are seen as referring to what we call universals or types in reality. As we show, Merrill’s critique is of little relevance to the success of our realist project, since it not only reveals no actual errors in our work but also criticizes views on universals that we do not in fact hold. However, it nonetheless provides us with a valuable opportunity to clarify the realist methodology, and to show how some of its principles are being applied, especially within the framework of the OBO (Open Biomedical Ontologies) Foundry initiative. PMID:21637730

  4. Semi-automated ontology generation within OBO-Edit

    PubMed Central

    Wächter, Thomas; Schroeder, Michael

    2010-01-01

    Motivation: Ontologies and taxonomies have proven highly beneficial for biocuration. The Open Biomedical Ontology (OBO) Foundry alone lists over 90 ontologies mainly built with OBO-Edit. Creating and maintaining such ontologies is a labour-intensive, difficult, manual process. Automating parts of it is of great importance for the further development of ontologies and for biocuration. Results: We have developed the Dresden Ontology Generator for Directed Acyclic Graphs (DOG4DAG), a system which supports the creation and extension of OBO ontologies by semi-automatically generating terms, definitions and parent–child relations from text in PubMed, the web and PDF repositories. DOG4DAG is seamlessly integrated into OBO-Edit. It generates terms by identifying statistically significant noun phrases in text. For definitions and parent–child relations it employs pattern-based web searches. We systematically evaluate each generation step using manually validated benchmarks. The term generation leads to high-quality terms also found in manually created ontologies. Up to 78% of definitions are valid and up to 54% of child–ancestor relations can be retrieved. There is no other validated system that achieves comparable results. By combining the prediction of high-quality terms, definitions and parent–child relations with the ontology editor OBO-Edit we contribute a thoroughly validated tool for all OBO ontology engineers. Availability: DOG4DAG is available within OBO-Edit 2.1 at http://www.oboedit.org Contact: thomas.waechter@biotec.tu-dresden.de; Supplementary Information: Supplementary data are available at Bioinformatics online. PMID:20529942

  5. Consistency and Development of Teachers' Epistemological and Ontological World Views

    ERIC Educational Resources Information Center

    Olafson, Lori; Schraw, Gregory; Vander Veldt, Michelle

    2010-01-01

    We examined epistemological and ontological world views using self-report surveys, brief written reflections, and an extended written action research project for a sample of 16 graduate students enrolled in an education class at a large university on the West coast of the USA. We made two predictions. We anticipated that the majority of students…

  6. OMIT: Dynamic, Semi-Automated Ontology Development for the microRNA Domain

    PubMed Central

    Huang, Jingshan; Dang, Jiangbo; Borchert, Glen M.; Eilbeck, Karen; Zhang, He; Xiong, Min; Jiang, Weijian; Wu, Hao; Blake, Judith A.; Natale, Darren A.; Tan, Ming

    2014-01-01

    As a special class of short non-coding RNAs, microRNAs (a.k.a. miRNAs or miRs) have been reported to perform important roles in various biological processes by regulating respective target genes. However, significant barriers exist during biologists' conventional miR knowledge discovery. Emerging semantic technologies, which are based upon domain ontologies, can render critical assistance to this problem. Our previous research has investigated the construction of a miR ontology, named Ontology for MIcroRNA Target Prediction (OMIT), the very first of its kind that formally encodes miR domain knowledge. Although it is unavoidable to have a manual component contributed by domain experts when building ontologies, many challenges have been identified for a completely manual development process. The most significant issue is that a manual development process is very labor-intensive and thus extremely expensive. Therefore, we propose in this paper an innovative ontology development methodology. Our contributions can be summarized as: (i) We have continued the development and critical improvement of OMIT, solidly based on our previous research outcomes. (ii) We have explored effective and efficient algorithms with which the ontology development can be seamlessly combined with machine intelligence and be accomplished in a semi-automated manner, thus significantly reducing large amounts of human efforts. A set of experiments have been conducted to thoroughly evaluate our proposed methodology. PMID:25025130

  7. A generic organ based ontology system, applied to vertebrate heart anatomy, development and physiology.

    PubMed

    Bertens, Laura M F; Slob, Joris; Verbeek, Fons J

    2011-09-08

    We present a novel approach to modelling biological information using ontologies. The system interlinks three ontologies, comprising anatomical, developmental and taxonomical information, and includes instances of structures for different species. The framework is constructed for comparative analyses in the field of evolutionary development. We have applied the approach to the vertebrate heart and present four case studies of the functionality of the system, focusing on cross-species comparisons, developmental studies, physiological studies and 3D visualisation.

  8. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

    PubMed

    Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Ó Tuama, Éamonn; Schildhauer, Mark; Smith, Barry; Stucky, Brian J; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

    2014-01-01

    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers.

  9. Semantics in Support of Biodiversity Knowledge Discovery: An Introduction to the Biological Collections Ontology and Related Ontologies

    PubMed Central

    Baskauf, Steve; Blum, Stanley; Bowers, Shawn; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Tuama, Éamonn Ó.; Schildhauer, Mark; Smith, Barry; Stucky, Brian J.; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

    2014-01-01

    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers

  10. Semantics in support of biodiversity knowledge discovery: an introduction to the biological collections ontology and related ontologies.

    PubMed

    Walls, Ramona L; Deck, John; Guralnick, Robert; Baskauf, Steve; Beaman, Reed; Blum, Stanley; Bowers, Shawn; Buttigieg, Pier Luigi; Davies, Neil; Endresen, Dag; Gandolfo, Maria Alejandra; Hanner, Robert; Janning, Alyssa; Krishtalka, Leonard; Matsunaga, Andréa; Midford, Peter; Morrison, Norman; Ó Tuama, Éamonn; Schildhauer, Mark; Smith, Barry; Stucky, Brian J; Thomer, Andrea; Wieczorek, John; Whitacre, Jamie; Wooley, John

    2014-01-01

    The study of biodiversity spans many disciplines and includes data pertaining to species distributions and abundances, genetic sequences, trait measurements, and ecological niches, complemented by information on collection and measurement protocols. A review of the current landscape of metadata standards and ontologies in biodiversity science suggests that existing standards such as the Darwin Core terminology are inadequate for describing biodiversity data in a semantically meaningful and computationally useful way. Existing ontologies, such as the Gene Ontology and others in the Open Biological and Biomedical Ontologies (OBO) Foundry library, provide a semantic structure but lack many of the necessary terms to describe biodiversity data in all its dimensions. In this paper, we describe the motivation for and ongoing development of a new Biological Collections Ontology, the Environment Ontology, and the Population and Community Ontology. These ontologies share the aim of improving data aggregation and integration across the biodiversity domain and can be used to describe physical samples and sampling processes (for example, collection, extraction, and preservation techniques), as well as biodiversity observations that involve no physical sampling. Together they encompass studies of: 1) individual organisms, including voucher specimens from ecological studies and museum specimens, 2) bulk or environmental samples (e.g., gut contents, soil, water) that include DNA, other molecules, and potentially many organisms, especially microbes, and 3) survey-based ecological observations. We discuss how these ontologies can be applied to biodiversity use cases that span genetic, organismal, and ecosystem levels of organization. We argue that if adopted as a standard and rigorously applied and enriched by the biodiversity community, these ontologies would significantly reduce barriers to data discovery, integration, and exchange among biodiversity resources and researchers

  11. Unintended consequences of existential quantifications in biomedical ontologies

    PubMed Central

    2011-01-01

    Background The Open Biomedical Ontologies (OBO) Foundry is a collection of freely available ontologically structured controlled vocabularies in the biomedical domain. Most of them are disseminated via both the OBO Flatfile Format and the semantic web format Web Ontology Language (OWL), which draws upon formal logic. Based on the interpretations underlying OWL description logics (OWL-DL) semantics, we scrutinize the OWL-DL releases of OBO ontologies to assess whether their logical axioms correspond to the meaning intended by their authors. Results We analyzed ontologies and ontology cross products available via the OBO Foundry site http://www.obofoundry.org for existential restrictions (someValuesFrom), from which we examined a random sample of 2,836 clauses. According to a rating done by four experts, 23% of all existential restrictions in OBO Foundry candidate ontologies are suspicious (Cohens' κ = 0.78). We found a smaller proportion of existential restrictions in OBO Foundry cross products are suspicious, but in this case an accurate quantitative judgment is not possible due to a low inter-rater agreement (κ = 0.07). We identified several typical modeling problems, for which satisfactory ontology design patterns based on OWL-DL were proposed. We further describe several usability issues with OBO ontologies, including the lack of ontological commitment for several common terms, and the proliferation of domain-specific relations. Conclusions The current OWL releases of OBO Foundry (and Foundry candidate) ontologies contain numerous assertions which do not properly describe the underlying biological reality, or are ambiguous and difficult to interpret. The solution is a better anchoring in upper ontologies and a restriction to relatively few, well defined relation types with given domain and range constraints. PMID:22115278

  12. Analysis and Prediction of User Editing Patterns in Ontology Development Projects

    PubMed Central

    Wang, Hao; Tudorache, Tania; Dou, Dejing; Noy, Natalya F.; Musen, Mark A.

    2014-01-01

    The development of real-world ontologies is a complex undertaking, commonly involving a group of domain experts with different expertise that work together in a collaborative setting. These ontologies are usually large scale and have complex structures. To assist in the authoring process, ontology tools are key at making the editing process as streamlined as possible. Being able to predict confidently what the users are likely to do next as they edit an ontology will enable us to focus and structure the user interface accordingly and to facilitate more efficient interaction and information discovery. In this paper, we use data mining, specifically the association rule mining, to investigate whether we are able to predict the next editing operation that a user will make based on the change history. We simulated and evaluated continuous prediction across time using sliding window model. We used the association rule mining to generate patterns from the ontology change logs in the training window and tested these patterns on logs in the adjacent testing window. We also evaluated the impact of different training and testing window sizes on the prediction accuracies. At last, we evaluated our prediction accuracies across different user groups and different ontologies. Our results indicate that we can indeed predict the next editing operation a user is likely to make. We will use the discovered editing patterns to develop a recommendation module for our editing tools, and to design user interface components that better fit with the user editing behaviors. PMID:26052350

  13. Simple Ontology Format (SOFT)

    SciTech Connect

    Sorokine, Alexandre

    2011-10-01

    Simple Ontology Format (SOFT) library and file format specification provides a set of simple tools for developing and maintaining ontologies. The library, implemented as a perl module, supports parsing and verification of the files in SOFt format, operations with ontologies (adding, removing, or filtering of entities), and converting of ontologies into other formats. SOFT allows users to quickly create ontologies using only a basic text editor, verify it, and portray it in a graph layout system using customized styles.

  14. Generating application ontologies from reference ontologies.

    PubMed

    Shaw, Marianne; Detwiler, Landon T; Brinkley, James F; Suciu, Dan

    2008-01-01

    The semantic web provides the possiblity of linking together large numbers of biomedical ontologies. Unfortunately, many of the biomedical ontologies that have been developed are domain-specific and do not share a common structure that will allow them to be easily combined. Reference ontologies provide the necessary ontological framework for linking together these smaller, specialized ontologies. We present extensions to the semantic web query language SparQL that will allow researchers to develop application ontologies that are derived from reference ontologies. We have modified the ARQ query processor to support subqueries, recursive subqueries, and Skolem functions for node creation. We demonstrate the utility of these extensions by deriving an application ontology from the Foundational Model of Anatomy.

  15. The Design and Engineering of Mobile Data Services: Developing an Ontology Based on Business Model Thinking

    NASA Astrophysics Data System (ADS)

    Al-Debei, Mutaz M.; Fitzgerald, Guy

    This paper addresses the design and engineering problem related to mobile data services. The aim of the research is to inform and advise mobile service design and engineering by looking at this issue from a rigorous and holistic perspective. To this aim, this paper develops an ontology based on business model thinking. The developed ontology identifies four primary dimensions in designing business models of mobile data services: value proposition, value network, value architecture, and value finance. Within these dimensions, 15 key design concepts are identified along with their interrelationships and rules in the telecommunication service business model domain and unambiguous semantics are produced. The developed ontology is of value to academics and practitioners alike, particularly those interested in strategic-oriented IS/IT and business developments in telecommunications. Employing the developed ontology would systemize mobile service engineering functions and make them more manageable, effective, and creative. The research approach to building the mobile service business model ontology essentially follows the design science paradigm. Within this paradigm, we incorporate a number of different research methods, so the employed methodology might be better characterized as a pluralist approach.

  16. JPL Innovation Foundry

    NASA Technical Reports Server (NTRS)

    Sherwood, Brent; McCleese, Daniel J.

    2012-01-01

    NASA supports the community of mission principal investigators by helping them ideate, mature, and propose concepts for new missions. As NASA's Federally Funded Research and Development Center (FFRDC), JPL is a primary resource for providing this service. The environmental context for the formulation lifecycle evolves continuously. Contemporary trends include: more competitors; more-complex mission ideas; scarcer formulation resources; and higher standards for technical evaluation. Derived requirements for formulation support include: stable, clear, reliable methods tailored for each stage of the formulation lifecycle; on-demand access to standout technical and programmatic subject-matter experts; optimized, outfitted facilities; smart access to learning embodied in a vast oeuvre of prior formulation work; hands-on method coaching. JPL has retooled its provision of integrated formulation lifecycle support to PIs, teams, and program offices in response to this need. This mission formulation enterprise is the JPL Innovation Foundry.

  17. CONGAS: A COllaborative Ontology Development Framework Based on Named GrAphS

    NASA Astrophysics Data System (ADS)

    Bagni, Daniele; Cappella, Marco; Pazienza, Maria Teresa; Stellato, Armando

    The process of ontology development involves a range of skills and know-how often requiring team work of different people, each of them with his own way of contributing to the definition and formalization of the domain representation. For this reason, collaborative development is an important feature for ontology editing tools, and should take into account the different characteristics of team participants, provide them with a dedicated working environment allowing to express their ideas and creativity, still protecting integrity of the shared work. In this paper we present CONGAS, a collaborative version of the Knowledge Management and Acquisition platform Semantic Turkey which, exploiting the potentialities brought by recent introduction of context management into RDF triple graphs, offers a collaborative environment where proposals for ontology evolution can emerge and coexist, be evaluated by team users, trusted across different perspectives and eventually converged into the main development stream.

  18. An illustrated anatomical ontology of the developing mouse lower urogenital tract

    PubMed Central

    Georgas, Kylie M.; Armstrong, Jane; Keast, Janet R.; Larkins, Christine E.; McHugh, Kirk M.; Southard-Smith, E. Michelle; Cohn, Martin J.; Batourina, Ekatherina; Dan, Hanbin; Schneider, Kerry; Buehler, Dennis P.; Wiese, Carrie B.; Brennan, Jane; Davies, Jamie A.; Harding, Simon D.; Baldock, Richard A.; Little, Melissa H.; Vezina, Chad M.; Mendelsohn, Cathy

    2015-01-01

    Malformation of the urogenital tract represents a considerable paediatric burden, with many defects affecting the lower urinary tract (LUT), genital tubercle and associated structures. Understanding the molecular basis of such defects frequently draws on murine models. However, human anatomical terms do not always superimpose on the mouse, and the lack of accurate and standardised nomenclature is hampering the utility of such animal models. We previously developed an anatomical ontology for the murine urogenital system. Here, we present a comprehensive update of this ontology pertaining to mouse LUT, genital tubercle and associated reproductive structures (E10.5 to adult). Ontology changes were based on recently published insights into the cellular and gross anatomy of these structures, and on new analyses of epithelial cell types present in the pelvic urethra and regions of the bladder. Ontology changes include new structures, tissue layers and cell types within the LUT, external genitalia and lower reproductive structures. Representative illustrations, detailed text descriptions and molecular markers that selectively label muscle, nerves/ganglia and epithelia of the lower urogenital system are also presented. The revised ontology will be an important tool for researchers studying urogenital development/malformation in mouse models and will improve our capacity to appropriately interpret these with respect to the human situation. PMID:25968320

  19. Foundry energy conservation workbook

    SciTech Connect

    Not Available

    1990-01-01

    The foundry industry is a significant user of energy, and therefore, a natural candidate for efforts to save energy and improve efficiency by both governmental agencies and technical/trade associations. These efforts are designed to both improve the national energy position and improve the industry's efficiency and profitability. Increased energy cost and the reduced availability of fossil fuels at certain times have provided the incentive to curb waste and to utilize purchased energy wisely. Energy costs now approach and sometimes exceed 10% of the sales dollar of many foundries. Although energy use by foundries has gradually decreased on a per/ton basis in recent years, the foundry industry must continue to find ways to utilize energy more efficiently. This workbook provides ways to achieve this goal.

  20. Datamining with Ontologies.

    PubMed

    Hoehndorf, Robert; Gkoutos, Georgios V; Schofield, Paul N

    2016-01-01

    The use of ontologies has increased rapidly over the past decade and they now provide a key component of most major databases in biology and biomedicine. Consequently, datamining over these databases benefits from considering the specific structure and content of ontologies, and several methods have been developed to use ontologies in datamining applications. Here, we discuss the principles of ontology structure, and datamining methods that rely on ontologies. The impact of these methods in the biological and biomedical sciences has been profound and is likely to increase as more datasets are becoming available using common, shared ontologies.

  1. Datamining with Ontologies.

    PubMed

    Hoehndorf, Robert; Gkoutos, Georgios V; Schofield, Paul N

    2016-01-01

    The use of ontologies has increased rapidly over the past decade and they now provide a key component of most major databases in biology and biomedicine. Consequently, datamining over these databases benefits from considering the specific structure and content of ontologies, and several methods have been developed to use ontologies in datamining applications. Here, we discuss the principles of ontology structure, and datamining methods that rely on ontologies. The impact of these methods in the biological and biomedical sciences has been profound and is likely to increase as more datasets are becoming available using common, shared ontologies. PMID:27115643

  2. Dust exposure and impairment of lung function at a small iron foundry in a rapidly developing country

    PubMed Central

    Gomes, J; Lloyd, O; Norman, N; Pahwa, P

    2001-01-01

    OBJECTIVES—A cross sectional prospective study was carried out among iron foundry workers (exposed) and soft drink bottling and supply company workers (unexposed) to assess their occupational exposure to ambient respiratory dust in their work environment and its effect on their lung function profile.
PARTICIPANTS—Lung function was measured in 81 exposed and 113 unexposed workers. Personal respirable dust concentrations were measured for all the exposed and the unexposed workers. Information on respiratory signs and symptoms was also collected from the participants.
RESULTS—Among the exposed workers, midexpiratory flow (FEF25-75), forced expiratory volume in 1 second (FEV1), peak expiratory flow (PEF), FEV1/FVC, and FEV1/VC ratios were significantly lower whereas the vital capacity (VC) and forced vital capacity (FVC) were non-significantly higher. Job at the iron foundry was a significant predictor of lung function. Exposure to high concentration of respirable dust at the iron foundry was also a significant predictor. Workers working in high exposure areas (general works, furnace, continuous casting areas, and fabrication workshop) had lower lung function values than workers in medium and low exposure areas. Smoking did not enhance the effects of exposure to dust on lung function.
CONCLUSIONS—Exposure to respirable dust was higher among the iron foundry workers; and among these, general, furnace, rolling mill, and fabrication workers had higher exposures to dust than did workers in continuous casting, the mechanical workshop, and the bottling plant. Job type and exposure to dust were significant predictors of lung function. Implementation of industrial hygiene and proper and efficient use of personal protection equipment while at work could help to protect the respiratory health of industrial workers.


Keywords: lung function; dust exposure; foundry; smoking; personal protection PMID:11555687

  3. An Ontological Informatics Framework for Pharmaceutical Product Development: Milling as a Case Study

    ERIC Educational Resources Information Center

    Akkisetty, Venkata Sai Pavan Kumar

    2009-01-01

    Pharmaceutical product development is an expensive, time consuming and information intensive process. Providing the right information at the right time is of great importance in pharmaceutical industry. To achieve this, knowledge management is the approach to deal with the humongous quantity of information. Ontological approach proposed in Venkat…

  4. Forming the Professional Self: Bildung and the Ontological Perspective on Professional Education and Development

    ERIC Educational Resources Information Center

    Fellenz, Martin R.

    2016-01-01

    Ontological perspectives in higher education and particularly in professional education and development have focused attention on the question of the learner's being and becoming rather than on the epistemological concern of what and how they know. This study considers the formation of the professional self in the light of the requirements for…

  5. Ontology development for provenance tracing in National Climate Assessment of the US Global Change Research Program

    NASA Astrophysics Data System (ADS)

    Ma, X.; Zheng, J. G.; Goldstein, J.; Duggan, B.; Xu, J.; Du, C.; Akkiraju, A.; Aulenbach, S.; Tilmes, C.; Fox, P. A.

    2013-12-01

    The periodical National Climate Assessment (NCA) of the US Global Change Research Program (USGCRP) [1] produces reports about findings of global climate change and the impacts of climate change on the United States. Those findings are of great public and academic concerns and are used in policy and management decisions, which make the provenance information of findings in those reports especially important. The USGCRP is developing a Global Change Information System (GCIS), in which the NCA reports and associated provenance information are the primary records. We were modeling and developing Semantic Web applications for the GCIS. By applying a use case-driven iterative methodology [2], we developed an ontology [3] to represent the content structure of a report and the associated provenance information. We also mapped the classes and properties in our ontology into the W3C PROV-O ontology [4] to realize the formal presentation of provenance. We successfully implemented the ontology in several pilot systems for a recent National Climate Assessment report (i.e., the NCA3). They provide users the functionalities to browse and search provenance information with topics of interest. Provenance information of the NCA3 has been made structured and interoperable by applying the developed ontology. Besides the pilot systems we developed, other tools and services are also able to interact with the data in the context of the 'Web of data' and thus create added values. Our research shows that the use case-driven iterative method bridges the gap between Semantic Web researchers and earth and environmental scientists and is able to be deployed rapidly for developing Semantic Web applications. Our work also provides first-hand experience for re-using the W3C PROV-O ontology in the field of earth and environmental sciences, as the PROV-O ontology is recently ratified (on 04/30/2013) by the W3C as a recommendation and relevant applications are still rare. [1] http

  6. The Foundry: the DNA synthesis and construction Foundry at Imperial College

    PubMed Central

    Chambers, Stephen; Kitney, Richard; Freemont, Paul

    2016-01-01

    The establishment of a DNA synthesis and construction foundry at Imperial College in London heralds a new chapter in the development of synthetic biology to meet new global challenges. The Foundry employs the latest technology to make the process of engineering biology easier, faster and scalable. The integration of advanced software, automation and analytics allows the rapid design, build and testing of engineered organisms. PMID:27284027

  7. The Foundry: the DNA synthesis and construction Foundry at Imperial College.

    PubMed

    Chambers, Stephen; Kitney, Richard; Freemont, Paul

    2016-06-15

    The establishment of a DNA synthesis and construction foundry at Imperial College in London heralds a new chapter in the development of synthetic biology to meet new global challenges. The Foundry employs the latest technology to make the process of engineering biology easier, faster and scalable. The integration of advanced software, automation and analytics allows the rapid design, build and testing of engineered organisms. PMID:27284027

  8. 23. LOOKING NORTH INTO FOUNDRY BUILDING WITH FOUNDRY CRANE INSIDE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    23. LOOKING NORTH INTO FOUNDRY BUILDING WITH FOUNDRY CRANE INSIDE LARGE DOOR. THE CORE ROOM IS INSIDE THE SMALL DOOR ON THE RIGHT. CARL BORGH IN MAIN DOOR WEARING WHITE SHIRT. - Knight Foundry, 13 Eureka Street, Sutter Creek, Amador County, CA

  9. Development of National Map ontologies for organization and orchestration of hydrologic observations

    NASA Astrophysics Data System (ADS)

    Lieberman, J. E.

    2014-12-01

    Feature layers in the National Map program (TNM) are a fundamental context for much of the data collection and analysis conducted by the USGS and other governmental and nongovernmental organizations. Their computational usefulness, though, has been constrained by the lack of formal relationships besides superposition between TNM layers, as well as limited means of representing how TNM datasets relate to additional attributes, datasets, and activities. In the field of Geospatial Information Science, there has been a growing recognition of the value of semantic representation and technology for addressing these limitations, particularly in the face of burgeoning information volume and heterogeneity. Fundamental to this approach is the development of formal ontologies for concepts related to that information that can be processed computationally to enhance creation and discovery of new geospatial knowledge. They offer a means of making much of the presently innate knowledge about relationships in and between TNM features accessible for machine processing and distributed computation.A full and comprehensive ontology of all knowledge represented by TNM features is still impractical. The work reported here involves elaboration and integration of a number of small ontology design patterns (ODP's) that represent limited, discrete, but commonly accepted and broadly applicable physical theories for the behavior of TNM features representing surface water bodies and landscape surfaces and the connections between them. These ontology components are validated through use in applications for discovery and aggregation of water science observational data associated with National Hydrography Data features, features from the National Elevation Dataset (NED) and Water Boundary Dataset (WBD) that constrain water occurrence in the continental US. These applications emphasize workflows which are difficult or impossible to automate using existing data structures. Evaluation of the

  10. Toxicology ontology perspectives.

    PubMed

    Hardy, Barry; Apic, Gordana; Carthew, Philip; Clark, Dominic; Cook, David; Dix, Ian; Escher, Sylvia; Hastings, Janna; Heard, David J; Jeliazkova, Nina; Judson, Philip; Matis-Mitchell, Sherri; Mitic, Dragana; Myatt, Glenn; Shah, Imran; Spjuth, Ola; Tcheremenskaia, Olga; Toldo, Luca; Watson, David; White, Andrew; Yang, Chihae

    2012-01-01

    The field of predictive toxicology requires the development of open, public, computable, standardized toxicology vocabularies and ontologies to support the applications required by in silico, in vitro, and in vivo toxicology methods and related analysis and reporting activities. In this article we review ontology developments based on a set of perspectives showing how ontologies are being used in predictive toxicology initiatives and applications. Perspectives on resources and initiatives reviewed include OpenTox, eTOX, Pistoia Alliance, ToxWiz, Virtual Liver, EU-ADR, BEL, ToxML, and Bioclipse. We also review existing ontology developments in neighboring fields that can contribute to establishing an ontological framework for predictive toxicology. A significant set of resources is already available to provide a foundation for an ontological framework for 21st century mechanistic-based toxicology research. Ontologies such as ToxWiz provide a basis for application to toxicology investigations, whereas other ontologies under development in the biological, chemical, and biomedical communities could be incorporated in an extended future framework. OpenTox has provided a semantic web framework for the implementation of such ontologies into software applications and linked data resources. Bioclipse developers have shown the benefit of interoperability obtained through ontology by being able to link their workbench application with remote OpenTox web services. Although these developments are promising, an increased international coordination of efforts is greatly needed to develop a more unified, standardized, and open toxicology ontology framework.

  11. Developing silicon strip detectors with a large-scale commercial foundry

    NASA Astrophysics Data System (ADS)

    König, A.; Bartl, U.; Bergauer, T.; Dragicevic, M.; Hacker, J.; Treberspurg, W.

    2016-07-01

    Since 2009 the Institute of High Energy Physics (HEPHY) in Vienna is developing a production process for planar silicon strip sensors on 6-in. wafers together with the semiconductor manufacturer Infineon Technologies. Four runs with several batches of wafers, each comprising six different sensors, were manufactured and characterized. A brief summary of the recently completed 6-in. campaign is given. Milestones in sensor development as well as techniques to improve the sensor quality are discussed. Particular emphasis is placed on a failure causing areas of defective strips which accompanied the whole campaign. Beam tests at different irradiation facilities were conducted to validate the key capability of particle detection. Another major aspect is to prove the radiation hardness of sensors produced by Infineon. Therefore, neutron irradiation studies were performed.

  12. Ontologies in biological data visualization.

    PubMed

    Carpendale, Sheelagh; Chen, Min; Evanko, Daniel; Gehlenborg, Nils; Gorg, Carsten; Hunter, Larry; Rowland, Francis; Storey, Margaret-Anne; Strobelt, Hendrik

    2014-01-01

    In computer science, an ontology is essentially a graph-based knowledge representation in which each node corresponds to a concept and each edge specifies a relation between two concepts. Ontological development in biology can serve as a focus to discuss the challenges and possible research directions for ontologies in visualization. The principle challenges are the dynamic and evolving nature of ontologies, the ever-present issue of scale, the diversity and richness of the relationships in ontologies, and the need to better understand the relationship between ontologies and the data analysis tasks scientists wish to support. Research directions include visualizing ontologies; visualizing semantically or ontologically annotated texts, documents, and corpora; automated generation of visualizations using ontologies; and visualizing ontological context to support search. Although this discussion uses issues of ontologies in biological data visualization as a springboard, these topics are of general relevance to visualization. PMID:24808195

  13. TRAK ontology: defining standard care for the rehabilitation of knee conditions.

    PubMed

    Button, Kate; van Deursen, Robert W; Soldatova, Larisa; Spasić, Irena

    2013-08-01

    In this paper we discuss the design and development of TRAK (Taxonomy for RehAbilitation of Knee conditions), an ontology that formally models information relevant for the rehabilitation of knee conditions. TRAK provides the framework that can be used to collect coded data in sufficient detail to support epidemiologic studies so that the most effective treatment components can be identified, new interventions developed and the quality of future randomized control trials improved to incorporate a control intervention that is well defined and reflects clinical practice. TRAK follows design principles recommended by the Open Biomedical Ontologies (OBO) Foundry. TRAK uses the Basic Formal Ontology (BFO) as the upper-level ontology and refers to other relevant ontologies such as Information Artifact Ontology (IAO), Ontology for General Medical Science (OGMS) and Phenotype And Trait Ontology (PATO). TRAK is orthogonal to other bio-ontologies and represents domain-specific knowledge about treatments and modalities used in rehabilitation of knee conditions. Definitions of typical exercises used as treatment modalities are supported with appropriate illustrations, which can be viewed in the OBO-Edit ontology editor. The vast majority of other classes in TRAK are cross-referenced to the Unified Medical Language System (UMLS) to facilitate future integration with other terminological sources. TRAK is implemented in OBO, a format widely used by the OBO community. TRAK is available for download from http://www.cs.cf.ac.uk/trak. In addition, its public release can be accessed through BioPortal, where it can be browsed, searched and visualized. PMID:23665300

  14. Examples of Ontology

    NASA Astrophysics Data System (ADS)

    Gaševic, Dragan; Djuric, Dragan; Devedžic, Vladan

    In the previous chapters we introduced the basic concepts of MOF-based languages for developing ontologies, such as the Ontology Definition Metamodel (ODM) and the Ontology UML Profile (OUP). We also discussed mappings between those languages and the OWL language. The purpose of this chapter is to illustrate the use of MOF-based languages for developing real-world ontologies. Here we discuss two different ontologies that we developed in different domains. The first example is a Petri net ontology that formalizes the representation of Petri nets, a well-known tool for modeling, simulation, and analysis of systems and processes. This Petri net ontology overcomes the syntactic constraints of the present XMLbased standard for sharing Petri net models, namely Petri Net Markup Language.

  15. Simple Ontology Format (SOFT)

    2011-10-01

    Simple Ontology Format (SOFT) library and file format specification provides a set of simple tools for developing and maintaining ontologies. The library, implemented as a perl module, supports parsing and verification of the files in SOFt format, operations with ontologies (adding, removing, or filtering of entities), and converting of ontologies into other formats. SOFT allows users to quickly create ontologies using only a basic text editor, verify it, and portray it in a graph layoutmore » system using customized styles.« less

  16. Interdisciplinary perspectives on the development, integration, and application of cognitive ontologies

    PubMed Central

    Hastings, Janna; Frishkoff, Gwen A.; Smith, Barry; Jensen, Mark; Poldrack, Russell A.; Lomax, Jane; Bandrowski, Anita; Imam, Fahim; Turner, Jessica A.; Martone, Maryann E.

    2014-01-01

    We discuss recent progress in the development of cognitive ontologies and summarize three challenges in the coordinated development and application of these resources. Challenge 1 is to adopt a standardized definition for cognitive processes. We describe three possibilities and recommend one that is consistent with the standard view in cognitive and biomedical sciences. Challenge 2 is harmonization. Gaps and conflicts in representation must be resolved so that these resources can be combined for mark-up and interpretation of multi-modal data. Finally, Challenge 3 is to test the utility of these resources for large-scale annotation of data, search and query, and knowledge discovery and integration. As term definitions are tested and revised, harmonization should enable coordinated updates across ontologies. However, the true test of these definitions will be in their community-wide adoption which will test whether they support valid inferences about psychological and neuroscientific data. PMID:24999329

  17. Foundry energy conservation workbook

    SciTech Connect

    Not Available

    1990-12-31

    This report discusses methods for promoting energy conservation in foundries. Use of electric power, natural gas, and coke are evaluated. Waste heat recovery systems are considered. Energy consumption in the specific processes of electric melting, natural gas melting, heat treatments, ladle melting, and coke fuel melting is described. An example energy analysis is included. (GHH)

  18. Foundry energy conservation workbook

    SciTech Connect

    1990-10-01

    This report discusses methods for promoting energy conservation in foundries. Use of electric power, natural gas, and coke are evaluated. Waste heat recovery systems are considered. Energy consumption in the specific processes of electric melting, natural gas melting, heat treatments, ladle melting, and coke fuel melting is described. An example energy analysis is included. (GHH)

  19. The role of collaborative ontology development in the knowledge negotiation process

    NASA Astrophysics Data System (ADS)

    Rivera, Norma

    Interdisciplinary research (IDR) collaboration can be defined as the process of integrating experts' knowledge, perspectives, and resources to advance scientific discovery. The flourishing of more complex research problems, together with the growth of scientific and technical knowledge has resulted in the need for researchers from diverse fields to provide different expertise and points of view to tackle these problems. These collaborations, however, introduce a new set of "culture" barriers as participating experts are trained to communicate in discipline-specific languages, theories, and research practices. We propose that building a common knowledge base for research using ontology development techniques can provide a starting point for interdisciplinary knowledge exchange, negotiation, and integration. The goal of this work is to extend ontology development techniques to support the knowledge negotiation process in IDR groups. Towards this goal, this work presents a methodology that extends previous work in collaborative ontology development and integrates learning strategies and tools to enhance interdisciplinary research practices. We evaluate the effectiveness of applying such methodology in three different scenarios that cover educational and research settings. The results of this evaluation confirm that integrating learning strategies can, in fact, be advantageous to overall collaborative practices in IDR groups.

  20. Ontology Languages and Engineering

    NASA Astrophysics Data System (ADS)

    Horrocks, Ian

    Ontologies and ontology based systems are rapidly becoming mainstream technologies, with RDF and OWL now being deployed in diverse application domains, and with major technology vendors starting to augment their existing systems with ontological reasoning. For example, Oracle Inc. recently enhanced its well-known database management system with modules that use RDF/OWL ontologies to support "semantic data management", and their product brochure lists numerous application areas that can benefit from this technology, including Enterprise Information Integration, KnowledgeMining, Finance, Compliance Management and Life Science Research. The design of the high quality ontologies needed to support such applications is, however, still extremely challenging. In this talk I will describe the design of OWL, show how it facilitates the development of ontology engineering tools, describe the increasingly wide range of available tools, and explain how such tools can be used to support the entire design, deployment and maintenance ontology life-cycle.

  1. 77 FR 32998 - Foundry Coke From China

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-04

    ... The Commission instituted this review on December 1, 2011 (76 FR 74810) and determined on March 5, 2012 that it would conduct an expedited review (77 FR 15123, March 14, 2012). The Commission... COMMISSION Foundry Coke From China Determination On the basis of the record \\1\\ developed in the subject...

  2. Development of an Ontology-Directed Signal Processing Toolbox

    SciTech Connect

    Stephen W. Lang

    2011-05-27

    This project was focused on the development of tools for the automatic configuration of signal processing systems. The goal is to develop tools that will be useful in a variety of Government and commercial areas and useable by people who are not signal processing experts. In order to get the most benefit from signal processing techniques, deep technical expertise is often required in order to select appropriate algorithms, combine them into a processing chain, and tune algorithm parameters for best performance on a specific problem. Therefore a significant benefit would result from the assembly of a toolbox of processing algorithms that has been selected for their effectiveness in a group of related problem areas, along with the means to allow people who are not signal processing experts to reliably select, combine, and tune these algorithms to solve specific problems. Defining a vocabulary for problem domain experts that is sufficiently expressive to drive the configuration of signal processing functions will allow the expertise of signal processing experts to be captured in rules for automated configuration. In order to test the feasibility of this approach, we addressed a lightning classification problem, which was proposed by DOE as a surrogate for problems encountered in nuclear nonproliferation data processing. We coded a toolbox of low-level signal processing algorithms for extracting features of RF waveforms, and demonstrated a prototype tool for screening data. We showed examples of using the tool for expediting the generation of ground-truth metadata, for training a signal recognizer, and for searching for signals with particular characteristics. The public benefits of this approach, if successful, will accrue to Government and commercial activities that face the same general problem - the development of sensor systems for complex environments. It will enable problem domain experts (e.g. analysts) to construct signal and image processing chains without

  3. European MEMS foundries

    NASA Astrophysics Data System (ADS)

    Salomon, Patric R.

    2003-01-01

    According to the latest release of the NEXUS market study, the market for MEMS or Microsystems Technology (MST) is predicted to grow to $68B by the year 2005, with systems containing these components generating even higher revenues and growth. The latest advances in MST/MEMS technology have enabled the design of a new generation of microsystems that are smaller, cheaper, more reliable, and consume less power. These integrated systems bring together numerous analog/mixed signal microelectronics blocks and MEMS functions on a single chip or on two or more chips assembled within an integrated package. In spite of all these advances in technology and manufacturing, a system manufacturer either faces a substantial up-front R&D investment to create his own infrastructure and expertise, or he can use design and foundry services to get the initial product into the marketplace fast and with an affordable investment. Once he has a viable product, he can still think about his own manufacturing efforts and investments to obtain an optimized high volume manufacturing for the specific product. One of the barriers to successful exploitation of MEMS/MST technology has been the lack of access to industrial foundries capable of producing certified microsystems devices in commercial quantities, including packaging and test. This paper discusses Multi-project wafer (MPW) runs, requirements for foundries and gives some examples of foundry business models. Furthermore, this paper will give an overview on MST/MEMS services that are available in Europe, including pure commercial activities, European project activities (e.g. Europractice), and some academic services.

  4. 8. VIEW OF FOUNDRY INDUCTION FURNACES, MODULE J. THE FOUNDRY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    8. VIEW OF FOUNDRY INDUCTION FURNACES, MODULE J. THE FOUNDRY CASTING PROCESS WAS CONDUCTED IN A VACUUM. PLUTONIUM METAL WAS MELTED IN ONE OF FOUR ELECTRIC INDUCTION FURNACES TO FORM INGOTS. - Rocky Flats Plant, Plutonium Manufacturing Facility, North-central section of Plant, just south of Building 776/777, Golden, Jefferson County, CO

  5. 4. VIEW OF THE FOUNDRY. IN THE FOUNDRY, ENRICHED URANIUM ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. VIEW OF THE FOUNDRY. IN THE FOUNDRY, ENRICHED URANIUM WAS CAST INTO SLABS OR INGOTS FROM WHICH WEAPONS COMPONENTS WERE FABRICATED. (5/17/62). - Rocky Flats Plant, General Manufacturing, Support, Records-Central Computing, Southern portion of Plant, Golden, Jefferson County, CO

  6. 5. VIEW OF THE FOUNDRY. IN THE FOUNDRY, ENRICHED URANIUM ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    5. VIEW OF THE FOUNDRY. IN THE FOUNDRY, ENRICHED URANIUM WAS CAST INTO SLABS OR INGOTS FROM WHICH WEAPONS COMPONENTS WERE FABRICATED. (4/4/66) - Rocky Flats Plant, General Manufacturing, Support, Records-Central Computing, Southern portion of Plant, Golden, Jefferson County, CO

  7. Evolution of the Sequence Ontology terms and relationships

    PubMed Central

    Mungall, Christopher J.; Batchelor, Colin; Eilbeck, Karen

    2010-01-01

    The Sequence Ontology is an established ontology, with a large user community, for the purpose of genomic annotation. We are reforming the ontology to provide better terms and relationships to describe the features of biological sequence, for both genomic and derived sequence. The SO is working within the guidelines of the OBO Foundry to provide interoperability between SO and the other related OBO ontologies. Here we report changes and improvements made to SO including new relationships to better define the mereological, spatial and temporal aspects of biological sequence. PMID:20226267

  8. Cognitive Foundry 2.0

    2007-12-18

    Cognitive Foundry is a software framework designed for cognitive modeling, machine learning, and pattern recognition. This software has a graphical user interface that can be used to visualize graphical structures and build models graphically. Cognitive Foundry models are created using with a collection of application-specific modules, which can be reused from previous applcations or designed for a particular algorithm to incorporate.

  9. From relational ontology to transformative activist stance on development and learning: expanding Vygotsky's (CHAT) project

    NASA Astrophysics Data System (ADS)

    Stetsenko, Anna

    2008-07-01

    This paper offers steps towards overcoming current fragmentation within sociocultural approaches by expansively reconstructing a broad dialectical view on human development and learning (drawing on Vygotsky's project) underwritten by ideology of social justice. The common foundation for sociocultural approaches is developed by dialectically supplanting relational ontology with the notion that collaborative purposeful transformation of the world is the core of human nature and the principled grounding for learning and development. An activist transformative stance suggests that people come to know themselves and their world as well as ultimately come to be human in and through (not in addition to) the processes of collaboratively transforming the world in view of their goals. This means that all human activities (including psychological processes and the self) are instantiations of contributions to collaborative transformative practices that are contingent on both the past and the vision for the future and therefore are profoundly imbued with ideology, ethics, and values. And because acting, being, and knowing are seen from a transformative activist stance as all rooted in, derivative of, and instrumental within a collaborative historical becoming, this stance cuts across and bridges the gaps (a) between individual and social and (b) among ontological, epistemological, and moral-ethical (ideological) dimensions of activity.

  10. Performing ontology.

    PubMed

    Aspers, Patrik

    2015-06-01

    Ontology, and in particular, the so-called ontological turn, is the topic of a recent themed issue of Social Studies of Science (Volume 43, Issue 3, 2013). Ontology, or metaphysics, is in philosophy concerned with what there is, how it is, and forms of being. But to what is the science and technology studies researcher turning when he or she talks of ontology? It is argued that it is unclear what is gained by arguing that ontology also refers to constructed elements. The 'ontological turn' comes with the risk of creating a pseudo-debate or pseudo-activity, in which energy is used for no end, at the expense of empirical studies. This text rebuts the idea of an ontological turn as foreshadowed in the texts of the themed issue. It argues that there is no fundamental qualitative difference between the ontological turn and what we know as constructivism. PMID:26477201

  11. Quantum ontologies

    SciTech Connect

    Stapp, H.P.

    1988-12-01

    Quantum ontologies are conceptions of the constitution of the universe that are compatible with quantum theory. The ontological orientation is contrasted to the pragmatic orientation of science, and reasons are given for considering quantum ontologies both within science, and in broader contexts. The principal quantum ontologies are described and evaluated. Invited paper at conference: Bell's Theorem, Quantum Theory, and Conceptions of the Universe, George Mason University, October 20-21, 1988. 16 refs.

  12. Synergy of the Developed 6D BIM Framework and Conception of the nD BIM Framework and nD BIM Process Ontology

    ERIC Educational Resources Information Center

    O'Keeffe, Shawn Edward

    2013-01-01

    The author developed a unified nD framework and process ontology for Building Information Modeling (BIM). The research includes a framework developed for 6D BIM, nD BIM, and nD ontology that defines the domain and sub-domain constructs for future nD BIM dimensions. The nD ontology defines the relationships of kinds within any new proposed…

  13. Benefits of Enterprise Ontology for the Development of ICT-Based Value Networks

    NASA Astrophysics Data System (ADS)

    Albani, Antonia; Dietz, Jan L. G.

    The competitiveness of value networks is highly dependent on the cooperation between business partners and the interoperability of their information systems. Innovations in information and communication technology (ICT), primarily the emergence of the Internet, offer possibilities to increase the interoperability of information systems and therefore enable inter-enterprise cooperation. For the design of inter-enterprise information systems, the concept of business component appears to be very promising. However, the identification of business components is strongly dependent on the appropriateness and the quality of the underlying business domain model. The ontological model of an enterprise - or an enterprise network - as presented in this article, is a high-quality and very adequate business domain model. It provides all essential information that is necessary for the design of the supporting information systems, and at a level of abstraction that makes it also understandable for business people. The application of enterprise ontology for the identification of business components is clarified. To exemplify our approach, a practical case is taken from the domain of strategic supply network development. By doing this, a widespread problem of the practical application of inter-enterprise information systems is being addressed.

  14. Ayurveda research: Ontological challenges.

    PubMed

    Nayak, Jayakrishna

    2012-01-01

    Collaborative research involving Ayurveda and the current sciences is undoubtedly an imperative and is emerging as an exciting horizon, particularly in basic sciences. Some work in this direction is already going on and outcomes are awaited with bated breath. For instance the 'ASIIA (A Science Initiative In Ayurveda)' projects of Dept of Science and Technology, Govt of India, which include studies such as Ayurvedic Prakriti and Genetics. Further intense and sustained collaborative research needs to overcome a subtle and fundamental challenge-the ontologic divide between Ayurveda and all the current sciences. Ontology, fundamentally, means existence; elaborated, ontology is a particular perspective of an object of existence and the vocabulary developed to share that perspective. The same object of existence is susceptible to several ontologies. Ayurveda and modern biomedical as well as other sciences belong to different ontologies, and as such, collaborative research cannot be carried out at required levels until a mutually acceptable vocabulary is developed. PMID:22529675

  15. Ayurveda research: Ontological challenges.

    PubMed

    Nayak, Jayakrishna

    2012-01-01

    Collaborative research involving Ayurveda and the current sciences is undoubtedly an imperative and is emerging as an exciting horizon, particularly in basic sciences. Some work in this direction is already going on and outcomes are awaited with bated breath. For instance the 'ASIIA (A Science Initiative In Ayurveda)' projects of Dept of Science and Technology, Govt of India, which include studies such as Ayurvedic Prakriti and Genetics. Further intense and sustained collaborative research needs to overcome a subtle and fundamental challenge-the ontologic divide between Ayurveda and all the current sciences. Ontology, fundamentally, means existence; elaborated, ontology is a particular perspective of an object of existence and the vocabulary developed to share that perspective. The same object of existence is susceptible to several ontologies. Ayurveda and modern biomedical as well as other sciences belong to different ontologies, and as such, collaborative research cannot be carried out at required levels until a mutually acceptable vocabulary is developed.

  16. Ayurveda research: Ontological challenges

    PubMed Central

    Nayak, Jayakrishna

    2012-01-01

    Collaborative research involving Ayurveda and the current sciences is undoubtedly an imperative and is emerging as an exciting horizon, particularly in basic sciences. Some work in this direction is already going on and outcomes are awaited with bated breath. For instance the ‘ASIIA (A Science Initiative In Ayurveda)’ projects of Dept of Science and Technology, Govt of India, which include studies such as Ayurvedic Prakriti and Genetics. Further intense and sustained collaborative research needs to overcome a subtle and fundamental challenge-the ontologic divide between Ayurveda and all the current sciences. Ontology, fundamentally, means existence; elaborated, ontology is a particular perspective of an object of existence and the vocabulary developed to share that perspective. The same object of existence is susceptible to several ontologies. Ayurveda and modern biomedical as well as other sciences belong to different ontologies, and as such, collaborative research cannot be carried out at required levels until a mutually acceptable vocabulary is developed. PMID:22529675

  17. Combinatorial optimization in foundry practice

    NASA Astrophysics Data System (ADS)

    Antamoshkin, A. N.; Masich, I. S.

    2016-04-01

    The multicriteria mathematical model of foundry production capacity planning is suggested in the paper. The model is produced in terms of pseudo-Boolean optimization theory. Different search optimization methods were used to solve the obtained problem.

  18. Excess foundry sand characterization and experimental investigation in controlled low-strength material

    NASA Astrophysics Data System (ADS)

    Deng, An

    The objective of this dissertation is to provide support with technical data for the reuse of excess foundry sand. The dissertation addresses two topics: a statistical sound evaluation of the characterization of foundry waste streams, and a laboratory investigation to qualify excess foundry sand as a major component in controlled low-strength material (CLSM). The survival analysis statistical technique is developed for processing censored characterization data with significant confidence. Using this methodology, supported by abundant characterization datasets, foundry waste streams are characterized in full spectrum of general chemical parameters, metallic elements and organic compounds regarding bulk analysis and leachate characterization. Not limited to characterization and environmental impact, foundry waste streams are evaluated by factor analyses, which contributes to proper selection of factor and maximization of reuse marketplace of foundry waste streams. Excavatable CLSM and structural CLSM containing different types of excess foundry sands are investigated through laboratory experiments. Technical data regarding physical characteristics of excess foundry sands, design, behavior, performance and environmental impact of fresh and hardened CLSM are presented in details. Wide span of parameters are analyzed to evaluate the qualification of integrating excess foundry sands into CLSM.

  19. Development and Application of Ontologies in Support of Earth and Space Science Education

    NASA Astrophysics Data System (ADS)

    Fox, S. P.; Manduca, C. A.; Iverson, E.

    2007-12-01

    Through its work in supporting improved science education the Science Education Resource Center (SERC) has developed and applied a set of Earth and Space Science vocabularies. These controlled vocabularies play a central role in supporting user exploration of our educational materials. The set of over 50 vocabularies run the gamut from small vocabularies with a narrowly targeted use, to broader vocabularies that span multiple disciplines and are applied across multiple projects and collections. Typical specialized vocabularies cover disciplinary themes such as tectonic setting (with terms such as mid-ocean ridge, passive margin, and craton) as well as interdisciplinary work such as geology and human health (with terms such as radionuclides and airborne transport processes). To support project-specific customization of vocabularies while retaining the benefits of cross-project reuse our systems allow for dynamic mapping of terms among multiple vocabularies based on semantic equivalencies. The end result is a weaving of related vocabularies into an ontological network that is exposed as specific vocabularies that employ the natural language of the collections and communities that use them. Our process for vocabulary development is community driven and reflects our experiences in aligning terminology with disciplinary-specific expectations. These experiences include rectifying language differences across disciplines in building a Geoscience Quantitative Skills vocabulary through work with both the Mathematics and Geoscience communities, as well as the iterative development of a vocabulary spanning Earth and Space science through the aggregation of smaller vocabularies, each developed by scientists for use within their own discipline. The vocabularies are exposed as key navigational features in over 100 faceted search interfaces within the web sites of a dozen Earth and Space Science Education projects. Within these faceted search interfaces the terms in the

  20. Ontology-Oriented Programming for Biomedical Informatics.

    PubMed

    Lamy, Jean-Baptiste

    2016-01-01

    Ontologies are now widely used in the biomedical domain. However, it is difficult to manipulate ontologies in a computer program and, consequently, it is not easy to integrate ontologies with databases or websites. Two main approaches have been proposed for accessing ontologies in a computer program: traditional API (Application Programming Interface) and ontology-oriented programming, either static or dynamic. In this paper, we will review these approaches and discuss their appropriateness for biomedical ontologies. We will also present an experience feedback about the integration of an ontology in a computer software during the VIIIP research project. Finally, we will present OwlReady, the solution we developed. PMID:27071878

  1. Ontology-Oriented Programming for Biomedical Informatics.

    PubMed

    Lamy, Jean-Baptiste

    2016-01-01

    Ontologies are now widely used in the biomedical domain. However, it is difficult to manipulate ontologies in a computer program and, consequently, it is not easy to integrate ontologies with databases or websites. Two main approaches have been proposed for accessing ontologies in a computer program: traditional API (Application Programming Interface) and ontology-oriented programming, either static or dynamic. In this paper, we will review these approaches and discuss their appropriateness for biomedical ontologies. We will also present an experience feedback about the integration of an ontology in a computer software during the VIIIP research project. Finally, we will present OwlReady, the solution we developed.

  2. Developing packages and integrating ontologies for Volcanoes, Plate Tectonics and Atmospheric Science Data Integration

    NASA Astrophysics Data System (ADS)

    Sinha, K.; Raskin, R.; McGuinness, D.; Fox, P.

    2007-12-01

    In support of a NASA-funded scientific application (SESDI; Semantically Enabled Science Data Integration Project; that needs to share volcano and climate data to investigate relationships between volcanism and global climate, we have generated a volcano and plate tectonic ontologies and leveraged and augmented the existing SWEET (Semantic Web for Earth and Environmental Terminology) ontoloy. Our goal is to create a package for integrating the relevant ontologies (meant to be shared and reused by a broad community of users) to provide access to the key volcanology, plate tectonic and atmospheric related databases. We present how we have put ontologies to work in this science application setting, and the methodologies employed to create the ontologies, map them to the underlying data and implement them for use by scientists. SESDI is an NASA/ESTO/ACCESS-funded project involving the High Altitude Observatory at the National Center for Atmospheric Research (NCAR), McGuinness Associates Consulting, NASA/JPL and Virginia Polytechnic University.

  3. Ambient Findability: Developing a Flowsheet Ontology for i2B2

    PubMed Central

    Warren, Judith J.; Manos, E. LaVerne; Connolly, Daniel W.; Waitman, Lemuel R.

    2012-01-01

    The process of moving from the locally defined flowsheet ontology containing redundancy and jargon to one understandable by researchers is described. Over 250 million nursing flowsheet observations were imported into a data repository that uses the i2b2 framework. Focus groups were used to derive a new ontology model--18 templates were identified. One hundred measures, 50% of all patient observations over 36 months, were encoded in SNOMED CT©. 78% of the concepts were mapped. PMID:24199136

  4. Development of an informatics infrastructure for data exchange of biomolecular simulations: architecture, data models and ontology$

    PubMed Central

    Thibault, J. C.; Roe, D. R.; Eilbeck, K.; Cheatham, T. E.; Facelli, J. C.

    2015-01-01

    Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data – both within the same organization and among different ones – remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations. PMID:26387907

  5. Development of an informatics infrastructure for data exchange of biomolecular simulations: Architecture, data models and ontology.

    PubMed

    Thibault, J C; Roe, D R; Eilbeck, K; Cheatham Iii, T E; Facelli, J C

    2015-01-01

    Biomolecular simulations aim to simulate structure, dynamics, interactions, and energetics of complex biomolecular systems. With the recent advances in hardware, it is now possible to use more complex and accurate models, but also reach time scales that are biologically significant. Molecular simulations have become a standard tool for toxicology and pharmacology research, but organizing and sharing data - both within the same organization and among different ones - remains a substantial challenge. In this paper we review our recent work leading to the development of a comprehensive informatics infrastructure to facilitate the organization and exchange of biomolecular simulations data. Our efforts include the design of data models and dictionary tools that allow the standardization of the metadata used to describe the biomedical simulations, the development of a thesaurus and ontology for computational reasoning when searching for biomolecular simulations in distributed environments, and the development of systems based on these models to manage and share the data at a large scale (iBIOMES), and within smaller groups of researchers at laboratory scale (iBIOMES Lite), that take advantage of the standardization of the meta data used to describe biomolecular simulations. PMID:26387907

  6. Developing an ontological explosion knowledge base for business continuity planning purposes.

    PubMed

    Mohammadfam, Iraj; Kalatpour, Omid; Golmohammadi, Rostam; Khotanlou, Hasan

    2013-01-01

    Industrial accidents are among the most known challenges to business continuity. Many organisations have lost their reputation following devastating accidents. To manage the risks of such accidents, it is necessary to accumulate sufficient knowledge regarding their roots, causes and preventive techniques. The required knowledge might be obtained through various approaches, including databases. Unfortunately, many databases are hampered by (among other things) static data presentations, a lack of semantic features, and the inability to present accident knowledge as discrete domains. This paper proposes the use of Protégé software to develop a knowledge base for the domain of explosion accidents. Such a structure has a higher capability to improve information retrieval compared with common accident databases. To accomplish this goal, a knowledge management process model was followed. The ontological explosion knowledge base (EKB) was built for further applications, including process accident knowledge retrieval and risk management. The paper will show how the EKB has a semantic feature that enables users to overcome some of the search constraints of existing accident databases. PMID:24113639

  7. Development and use of Ontologies Inside the Neuroscience Information Framework: A Practical Approach.

    PubMed

    Imam, Fahim T; Larson, Stephen D; Bandrowski, Anita; Grethe, Jeffery S; Gupta, Amarnath; Martone, Maryann E

    2012-01-01

    An initiative of the NIH Blueprint for neuroscience research, the Neuroscience Information Framework (NIF) project advances neuroscience by enabling discovery and access to public research data and tools worldwide through an open source, semantically enhanced search portal. One of the critical components for the overall NIF system, the NIF Standardized Ontologies (NIFSTD), provides an extensive collection of standard neuroscience concepts along with their synonyms and relationships. The knowledge models defined in the NIFSTD ontologies enable an effective concept-based search over heterogeneous types of web-accessible information entities in NIF's production system. NIFSTD covers major domains in neuroscience, including diseases, brain anatomy, cell types, sub-cellular anatomy, small molecules, techniques, and resource descriptors. Since the first production release in 2008, NIF has grown significantly in content and functionality, particularly with respect to the ontologies and ontology-based services that drive the NIF system. We present here on the structure, design principles, community engagement, and the current state of NIFSTD ontologies.

  8. Identification of Anchor Genes during Kidney Development Defines Ontological Relationships, Molecular Subcompartments and Regulatory Pathways

    PubMed Central

    Lesieur, Emmanuelle; Chiu, Han Sheng; Taylor, Darrin; Tang, Dave T. P.; Grimmond, Sean M.; Little, Melissa H.

    2011-01-01

    The development of the mammalian kidney is well conserved from mouse to man. Despite considerable temporal and spatial data on gene expression in mammalian kidney development, primarily in rodent species, there is a paucity of genes whose expression is absolutely specific to a given anatomical compartment and/or developmental stage, defined here as ‘anchor’ genes. We previously generated an atlas of gene expression in the developing mouse kidney using microarray analysis of anatomical compartments collected via laser capture microdissection. Here, this data is further analysed to identify anchor genes via stringent bioinformatic filtering followed by high resolution section in situ hybridisation performed on 200 transcripts selected as specific to one of 11 anatomical compartments within the midgestation mouse kidney. A total of 37 anchor genes were identified across 6 compartments with the early proximal tubule being the compartment richest in anchor genes. Analysis of minimal and evolutionarily conserved promoter regions of this set of 25 anchor genes identified enrichment of transcription factor binding sites for Hnf4a and Hnf1b, RbpJ (Notch signalling), PPARγ:RxRA and COUP-TF family transcription factors. This was reinforced by GO analyses which also identified these anchor genes as targets in processes including epithelial proliferation and proximal tubular function. As well as defining anchor genes, this large scale validation of gene expression identified a further 92 compartment-enriched genes able to subcompartmentalise key processes during murine renal organogenesis spatially or ontologically. This included a cohort of 13 ureteric epithelial genes revealing previously unappreciated compartmentalisation of the collecting duct system and a series of early tubule genes suggesting that segmentation into proximal tubule, loop of Henle and distal tubule does not occur until the onset of glomerular vascularisation. Overall, this study serves to illuminate

  9. Molecular Foundry, Berkeley, California (Revised)

    SciTech Connect

    Carlisle, N.

    2008-03-01

    This case study provides information on the Molecular Foundry, which incorporates Labs21 principles in its design and construction. The design includes many of the strategies researched at Lawrence Berkeley Laboratory for energy efficient cleanroom and data centers. The result is an energy efficient high-performing sustainable laboratory.

  10. Dust exposure in Finnish foundries.

    PubMed

    Siltanen, E; Koponen, M; Kokko, A; Engström, B; Reponen, J

    1976-01-01

    Dust measurements were made in 51 iron, 9 steel, and 8 nonferrous foundries, at which 4,316 foundrymen were working. The sampling lasted at least two entire shifts or work days continuously during various operations in each foundry. The dust samples were collected at fixed sites or in the breathing zones of the workers. The mass concentration was determined by weighing and the respirable dust fraction was separated by liquid sedimentation. The free silica content was determined by X-ray diffraction. In the study a total of 3,188 samples were collected in the foundries and 6,505 determinations were made in the laboratory. The results indicated a definite difference in the dust exposure during various operations. The highest dust exposures were found during furnace, cupola, and pouring ladle repair. During cleaning work, sand mixing, and shake-out operations excessive silica dust concentrations were also measured. The lowest dust concentrations were measured during melting and pouring operations. Moderate dust concentrations were measured during coremaking and molding operations. The results obtained during the same operations of iron and steel foundries were similar. The distribution of the workers into various exposure categories, the content of respirable dust and quartz, the correlation between respirable dust and total dust, and the correlation between respirable silica and total dust concentrations are discussed. Observations concerning dust suppression and control methods are briefly considered.

  11. Cognitive Foundry v. 3.0 (OSS)

    2009-11-18

    The Cognitive Foundry is a unified collection of tools designed for research and applications that use cognitive modeling, machine learning, or pattern recognition. The software library contains design patterns, interface definitions, and default implementations of reusable software components and algorithms designed to support a wide variety of research and development needs. The library contains three main software packages: the Common package that contains basic utilities and linear algebraic methods, the Cognitive Framework package that containsmore » tools to assist in implementing and analyzing theories of cognition, and the Machine Learning package that provides general algorithms and methods for populating Cognitive Framework components from domain-relevant data.« less

  12. Cognitive Foundry v. 3.0 (OSS)

    SciTech Connect

    Basilico, Justin; Dixon, Kevin; McClain, Jonathan; Benz, Zachary; & Warrender, Christina

    2009-11-18

    The Cognitive Foundry is a unified collection of tools designed for research and applications that use cognitive modeling, machine learning, or pattern recognition. The software library contains design patterns, interface definitions, and default implementations of reusable software components and algorithms designed to support a wide variety of research and development needs. The library contains three main software packages: the Common package that contains basic utilities and linear algebraic methods, the Cognitive Framework package that contains tools to assist in implementing and analyzing theories of cognition, and the Machine Learning package that provides general algorithms and methods for populating Cognitive Framework components from domain-relevant data.

  13. MEMS/MOEMS foundry services at INO

    NASA Astrophysics Data System (ADS)

    García-Blanco, Sonia; Ilias, Samir; Williamson, Fraser; Généreux, Francis; Le Noc, Loïc; Poirier, Michel; Proulx, Christian; Tremblay, Bruno; Provençal, Francis; Desroches, Yan; Caron, Jean-Sol; Larouche, Carl; Beaupré, Patrick; Fortin, Benoit; Topart, Patrice; Picard, Francis; Alain, Christine; Pope, Timothy; Jerominek, Hubert

    2010-06-01

    In the MEMS manufacturing world, the "fabless" model is getting increasing importance in recent years as a way for MEMS manufactures and startups to minimize equipment costs and initial capital investment. In order for this model to be successful, the fabless company needs to work closely with a MEMS foundry service provider. Due to the lack of standardization in MEMS processes, as opposed to CMOS microfabrication, the experience in MEMS development processes and the flexibility of the MEMS foundry are of vital importance. A multidisciplinary team together with a complete microfabrication toolset allows INO to offer unique MEMS foundry services to fabless companies looking for low to mid-volume production. Companies that benefit from their own microfabrication facilities can also be interested in INO's assistance in conducting their research and development work during periods where production runs keep their whole staff busy. Services include design, prototyping, fabrication, packaging, and testing of various MEMS and MOEMS devices on wafers fully compatible with CMOS integration. Wafer diameters ranging typically from 1 inch to 6 inches can be accepted while 8-inch wafers can be processed in some instances. Standard microfabrication techniques such as metal, dielectric, and semiconductor film deposition and etching as well as photolithographic pattern transfer are available. A stepper permits reduction of the critical dimension to around 0.4 μm. Metals deposited by vacuum deposition methods include Au, Ag, Al, Al alloys, Ti, Cr, Cu, Mo, MoCr, Ni, Pt, and V with thickness varying from 5 nm to 2 μm. Electroplating of several materials including Ni, Au and In is also available. In addition, INO has developed and built a gold black deposition facility to answer customer's needs for broadband microbolometric detectors. The gold black deposited presents specular reflectance of less than 10% in the wavelength range from 0.2 μm to 100 μm with thickness ranging from

  14. Building biological foundries for next-generation synthetic biology.

    PubMed

    Chao, Ran; Yuan, YongBo; Zhao, HuiMin

    2015-07-01

    Synthetic biology is an interdisciplinary field that takes top-down approaches to understand and engineer biological systems through design-build-test cycles. A number of advances in this relatively young field have greatly accelerated such engineering cycles. Specifically, various innovative tools were developed for in silico biosystems design, DNA de novo synthesis and assembly, construct verification, as well as metabolite analysis, which have laid a solid foundation for building biological foundries for rapid prototyping of improved or novel biosystems. This review summarizes the state-of-the-art technologies for synthetic biology and discusses the challenges to establish such biological foundries. PMID:25985756

  15. NORTHEAST VIEW OF FOUNDRY FROM TOP OF GREY IRON CUPOLA ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    NORTHEAST VIEW OF FOUNDRY FROM TOP OF GREY IRON CUPOLA SHOWING CORE ROOM ROOF DIRECTLY NORTHEAST, GREY IRON FOUNDRY TO THE RIGHT, MALLEABLE IRON CUPOLAS AND FOUNDRY NORTHEAST OF GREY IRON FOUNDRY WITH THE BRASS FOUNDRY IN THE REAR. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  16. An Ontological Model of Evaluation: A Dynamic Model for Aiding Organizational Development.

    ERIC Educational Resources Information Center

    Peper, John B.

    Evaluation models imply or assume theories of organization, behavior, and decision-making. Seldom does an evaluation model specify these assumptions. As a result, program evaluators often choose mechanistic models and their resultant information is either inadequate or inappropriate for most of the client's purposes. The Ontological Evaluation…

  17. An Application of Structural Equation Modeling for Developing Good Teaching Characteristics Ontology

    ERIC Educational Resources Information Center

    Phiakoksong, Somjin; Niwattanakul, Suphakit; Angskun, Thara

    2013-01-01

    Ontology is a knowledge representation technique which aims to make knowledge explicit by defining the core concepts and their relationships. The Structural Equation Modeling (SEM) is a statistical technique which aims to explore the core factors from empirical data and estimates the relationship between these factors. This article presents an…

  18. The 18 mm[superscript 2] Laboratory: Teaching MEMS Development with the SUMMiT Foundry Process

    ERIC Educational Resources Information Center

    Dallas, T.; Berg, J. M.; Gale, R. O.

    2012-01-01

    This paper describes the goals, pedagogical system, and educational outcomes of a three-semester curriculum in microelectromechanical systems (MEMS). The sequence takes engineering students with no formal MEMS training and gives them the skills to participate in cutting-edge MEMS research and development. The evolution of the curriculum from…

  19. Microtox(TM) characterization of foundry sand residuals

    USGS Publications Warehouse

    Bastian, K.C.; Alleman, J.E.

    1998-01-01

    Although foundry residuals, consisting mostly of waste Sands, represent a potentially attractive, high-volume resource for beneficial reuse applications (e.g. highway embankment construction), prospective end users are understandably concerned about unforeseen liabilities stemming from the use of these residuals. This paper, therefore, focuses on the innovative use of a microbial bioassay as a means of developing a characterization of environmental suitability extending beyond the analytical coverage already provided by mandated chemical-specific tests (i.e., TCLP, etc.). Microtox(TM) bioassays were conducted on leachates derived from residuals obtained at a wide range of facilities, including: 11 gray and ductile iron foundries plus one each steel and aluminum foundries. In addition, virgin sand samples were used to establish a relative 'natural' benchmark against which the waste foundry sands could then be compared in terms of their apparent quality. These bioassay tests were able to effectively 'fingerprint' those residuals whose bioassay behavior was comparable to that of virgin materials. In fact, the majority of gray and ductile iron foundry residuals tested during this reported study elicited Microtox(TM) response levels which fell within or below the virgin sand response range, consequently providing another quantifiable layer of Support for this industry's claim that their sands are 'cleaner than dirt.' However, negative Microtox(TM) responses beyond that of the virgin sands were observed with a number of foundry samples (i.e. four of the 11 gray or ductile iron sands plus both non-iron sands). Therefore, the latter results would suggest that these latter residuals be excluded from beneficial reuse for the immediate future, at least until the cause and nature of this negative response has been further identified.

  20. Determination of concept technology - the ontology of the concept as a component of the knowledge development in caring science.

    PubMed

    Korhonen, Eila-Sisko; Nordman, Tina; Eriksson, Katie

    2014-12-01

    The purpose of this study is to determine the ontology of the concept of technology from the perspective of caring science. The aim is to increase knowledge of the concept in caring science and to answer the research question concerning what the concept of technology is in caring science. In literature, the concept of technology is used diversely referring it to caring technology, nursing technology, wellbeing technology, information technology, telenursing and technology in care named by a specific device or an area of nursing or medicine. The definition of the concept of technology and its ontology has not been determined from the viewpoint of caring science. Eriksson's model of concept determination provides a method to explore the ontology of the concept. This includes an etymological and semantic analysis as well as a determination of essence and basic category of the concept. The results showed that the concept of technology is multidimensional. It has evolved and altered over the centuries. The origin of the concept formulated from the Greek word 'techne', which has wider ontological dimensions. It is universal, it can be taught and it depends on the substance. Subsequently, the concept was introduced an ethical dimension, and it also developed more to the direction of engineering, mechanics and technical know-how. The semantic analysis revealed synonyms of the concept: art, equipment and knowledge. These introduced concepts such as craft, skill, treatment, engineering, science, study method and way. The nuances of the concept framed its nature. On the one hand, it stands out as practical and advanced, but on the other hand, it is difficult and conventional. The knowledge gained in this study will help to understand the phenomenon of technology in caring science. PMID:24506411

  1. Determination of concept technology - the ontology of the concept as a component of the knowledge development in caring science.

    PubMed

    Korhonen, Eila-Sisko; Nordman, Tina; Eriksson, Katie

    2014-12-01

    The purpose of this study is to determine the ontology of the concept of technology from the perspective of caring science. The aim is to increase knowledge of the concept in caring science and to answer the research question concerning what the concept of technology is in caring science. In literature, the concept of technology is used diversely referring it to caring technology, nursing technology, wellbeing technology, information technology, telenursing and technology in care named by a specific device or an area of nursing or medicine. The definition of the concept of technology and its ontology has not been determined from the viewpoint of caring science. Eriksson's model of concept determination provides a method to explore the ontology of the concept. This includes an etymological and semantic analysis as well as a determination of essence and basic category of the concept. The results showed that the concept of technology is multidimensional. It has evolved and altered over the centuries. The origin of the concept formulated from the Greek word 'techne', which has wider ontological dimensions. It is universal, it can be taught and it depends on the substance. Subsequently, the concept was introduced an ethical dimension, and it also developed more to the direction of engineering, mechanics and technical know-how. The semantic analysis revealed synonyms of the concept: art, equipment and knowledge. These introduced concepts such as craft, skill, treatment, engineering, science, study method and way. The nuances of the concept framed its nature. On the one hand, it stands out as practical and advanced, but on the other hand, it is difficult and conventional. The knowledge gained in this study will help to understand the phenomenon of technology in caring science.

  2. How granularity issues concern biomedical ontology integration.

    PubMed

    Schulz, Stefan; Boeker, Martin; Stenzhorn, Holger

    2008-01-01

    The application of upper ontologies has been repeatedly advocated for supporting interoperability between domain ontologies in order to facilitate shared data use both within and across disciplines. We have developed BioTop as a top-domain ontology to integrate more specialized ontologies in the biomolecular and biomedical domain. In this paper, we report on concrete integration problems of this ontology with the domain-independent Basic Formal Ontology (BFO) concerning the issue of fiat and aggregated objects in the context of different granularity levels. We conclude that the third BFO level must be ignored in order not to obviate cross-granularity integration.

  3. The Drosophila phenotype ontology

    PubMed Central

    2013-01-01

    Background Phenotype ontologies are queryable classifications of phenotypes. They provide a widely-used means for annotating phenotypes in a form that is human-readable, programatically accessible and that can be used to group annotations in biologically meaningful ways. Accurate manual annotation requires clear textual definitions for terms. Accurate grouping and fruitful programatic usage require high-quality formal definitions that can be used to automate classification. The Drosophila phenotype ontology (DPO) has been used to annotate over 159,000 phenotypes in FlyBase to date, but until recently lacked textual or formal definitions. Results We have composed textual definitions for all DPO terms and formal definitions for 77% of them. Formal definitions reference terms from a range of widely-used ontologies including the Phenotype and Trait Ontology (PATO), the Gene Ontology (GO) and the Cell Ontology (CL). We also describe a generally applicable system, devised for the DPO, for recording and reasoning about the timing of death in populations. As a result of the new formalisations, 85% of classifications in the DPO are now inferred rather than asserted, with much of this classification leveraging the structure of the GO. This work has significantly improved the accuracy and completeness of classification and made further development of the DPO more sustainable. Conclusions The DPO provides a set of well-defined terms for annotating Drosophila phenotypes and for grouping and querying the resulting annotation sets in biologically meaningful ways. Such queries have already resulted in successful function predictions from phenotype annotation. Moreover, such formalisations make extended queries possible, including cross-species queries via the external ontologies used in formal definitions. The DPO is openly available under an open source license in both OBO and OWL formats. There is good potential for it to be used more broadly by the Drosophila

  4. Space Technology for the Iron Foundry

    NASA Technical Reports Server (NTRS)

    1990-01-01

    Electric Power Research Institute (EPRI) initiated development of a plasma melter intended to solve a major problem in the U.S. foundry industry. EPRI is a non-profit organization that manages research and development for some 600 electric utility member companies. For the plasma melter program, EPRI enlisted as co-sponsors Westinghouse Electric's Environmental Systems and Services Division, General Motors Corporation, and Modern Equipment Company, supplier of equipment and services to the foundry industry. General Motor's plasma melter, first in the U.S., is an advanced technology system designed to improve the efficiency of coke-burning cupolas that melt iron to produce automotive castings. The key elements are six Westinghouse plasma torches. Electrically-powered plasma torch creates an ionized gas that superheats air entering the cupola to 10,000 degrees Fahrenheit. That great heat, three times higher than that attainable by oil or natural gas systems, is the key to making iron cheaper, cleaner, and faster. System offers an environmental bonus in reduced cupola emissions. Plasma torches increase GM's electric bill at Defiance, but that cost is more than compensated by the savings in charge material. The EPRI-sponsored Center for Materials Production (CMP) is evaluating the potential of plasma cupola technology.

  5. From famous foundry to 'supersurgery'.

    PubMed

    Mann, Steve

    2014-02-01

    Dr Steve Mann, a partner at the Worcester Street Medical Practice in Stourbridge, describes how he and a number of his GP colleagues have worked with architects, Abacus Architects, and main contractor, Amphion Construction, as well as with a number of local NHS and local authority bodies, to co-ordinate construction of a new GP 'supersurgery' - the realisation of a dream - on the former site of what is believed to be one of England's oldest foundries in the West Midlands town. The architects' view on the scheme, one of the key goals of which is to retain both much of the character, and the unusual original metal sub-structure, of the former foundry, is also given. PMID:24620493

  6. From famous foundry to 'supersurgery'.

    PubMed

    Mann, Steve

    2014-02-01

    Dr Steve Mann, a partner at the Worcester Street Medical Practice in Stourbridge, describes how he and a number of his GP colleagues have worked with architects, Abacus Architects, and main contractor, Amphion Construction, as well as with a number of local NHS and local authority bodies, to co-ordinate construction of a new GP 'supersurgery' - the realisation of a dream - on the former site of what is believed to be one of England's oldest foundries in the West Midlands town. The architects' view on the scheme, one of the key goals of which is to retain both much of the character, and the unusual original metal sub-structure, of the former foundry, is also given.

  7. An ontological case base engineering methodology for diabetes management.

    PubMed

    El-Sappagh, Shaker H; El-Masri, Samir; Elmogy, Mohammed; Riad, A M; Saddik, Basema

    2014-08-01

    Ontology engineering covers issues related to ontology development and use. In Case Based Reasoning (CBR) system, ontology plays two main roles; the first as case base and the second as domain ontology. However, the ontology engineering literature does not provide adequate guidance on how to build, evaluate, and maintain ontologies. This paper proposes an ontology engineering methodology to generate case bases in the medical domain. It mainly focuses on the research of case representation in the form of ontology to support the case semantic retrieval and enhance all knowledge intensive CBR processes. A case study on diabetes diagnosis case base will be provided to evaluate the proposed methodology.

  8. The ontology life cycle: Integrated tools for editing, publishing, peer review, and evolution of ontologies.

    PubMed

    Noy, Natalya; Tudorache, Tania; Nyulas, Csongor; Musen, Mark

    2010-11-13

    Ontologies have become a critical component of many applications in biomedical informatics. However, the landscape of the ontology tools today is largely fragmented, with independent tools for ontology editing, publishing, and peer review: users develop an ontology in an ontology editor, such as Protégé; and publish it on a Web server or in an ontology library, such as BioPortal, in order to share it with the community; they use the tools provided by the library or mailing lists and bug trackers to collect feedback from users. In this paper, we present a set of tools that bring the ontology editing and publishing closer together, in an integrated platform for the entire ontology lifecycle. This integration streamlines the workflow for collaborative development and increases integration between the ontologies themselves through the reuse of terms.

  9. From disease ontology to disease-ontology lite: statistical methods to adapt a general-purpose ontology for the test of gene-ontology associations.

    PubMed

    Du, Pan; Feng, Gang; Flatow, Jared; Song, Jie; Holko, Michelle; Kibbe, Warren A; Lin, Simon M

    2009-06-15

    Subjective methods have been reported to adapt a general-purpose ontology for a specific application. For example, Gene Ontology (GO) Slim was created from GO to generate a highly aggregated report of the human-genome annotation. We propose statistical methods to adapt the general purpose, OBO Foundry Disease Ontology (DO) for the identification of gene-disease associations. Thus, we need a simplified definition of disease categories derived from implicated genes. On the basis of the assumption that the DO terms having similar associated genes are closely related, we group the DO terms based on the similarity of gene-to-DO mapping profiles. Two types of binary distance metrics are defined to measure the overall and subset similarity between DO terms. A compactness-scalable fuzzy clustering method is then applied to group similar DO terms. To reduce false clustering, the semantic similarities between DO terms are also used to constrain clustering results. As such, the DO terms are aggregated and the redundant DO terms are largely removed. Using these methods, we constructed a simplified vocabulary list from the DO called Disease Ontology Lite (DOLite). We demonstrated that DOLite results in more interpretable results than DO for gene-disease association tests. The resultant DOLite has been used in the Functional Disease Ontology (FunDO) Web application at http://www.projects.bioinformatics.northwestern.edu/fundo.

  10. Ontology-driven health information systems architectures.

    PubMed

    Blobel, Bernd; Oemig, Frank

    2009-01-01

    Following an architecture vision such as the Generic Component Model (GCM) architecture framework, health information systems for supporting personalized care have to be based on a component-oriented architecture. Representing concepts and their interrelations, the GCM perspectives system architecture, domains, and development process can be described by the domains' ontologies. The paper introduces ontology principles, ontology references to the GCM as well as some practical aspects of ontology-driven approaches to semantically interoperable and sustainable health information systems.

  11. Automatic generation of warehouse mediators using an ontology engine

    SciTech Connect

    Critchlow, T., LLNL

    1998-03-04

    The Data Foundry research project at LLNL is investigating data warehousing in highly dynamic scientific environments. Specifically, we are developing a data warehouse to aid structural biologists in genetics research. Upon completion, this warehouse will present a uniform view of data obtained from several heterogeneous data sources containing distinct but related data from various genetics domains. Our warehouse uses a mediated data warehouse architecture in which only some data is represented explicitly in the warehouse; remote access is required to obtain the non-materialized data. Mediators are used to convert data from the data source representation to the warehouse representation and make it available to the warehouse. The major challenge we face is reducing the impact of source schema changes on warehouse availability and reliability: based upon previous efforts, we anticipate one source schema modification every 2-4 weeks once all of the desired sources have been integrated. Incorporating these modifications into the mediators using brute force results in an unacceptable amount of warehouse down-time. We believe that extensive use of a carefully designed ontology will allow us to overcome this problem, while providing a useful knowledge base for other applications. In addition to automatically generating the transformation between the data sources and the warehouse, the ontology will be used to guide automatic schema evolution, and provide a high level interface to the warehouse. This paper focuses on the use of the ontology to automatically generate mediators, because reducing the effect of source changes is a critical step in providing reliable access to heterogeneous data sources.

  12. Ontological engineering versus metaphysics

    NASA Astrophysics Data System (ADS)

    Tataj, Emanuel; Tomanek, Roman; Mulawka, Jan

    2011-10-01

    It has been recognized that ontologies are a semantic version of world wide web and can be found in knowledge-based systems. A recent time survey of this field also suggest that practical artificial intelligence systems may be motivated by this research. Especially strong artificial intelligence as well as concept of homo computer can also benefit from their use. The main objective of this contribution is to present and review already created ontologies and identify the main advantages which derive such approach for knowledge management systems. We would like to present what ontological engineering borrows from metaphysics and what a feedback it can provide to natural language processing, simulations and modelling. The potential topics of further development from philosophical point of view is also underlined.

  13. A Unified Framework for Biomedical Terminologies and Ontologies

    PubMed Central

    Ceusters, Werner; Smith, Barry

    2011-01-01

    The goal of the OBO (Open Biomedical Ontologies) Foundry initiative is to create and maintain an evolving collection of non-overlapping interoperable ontologies that will offer unambiguous representations of the types of entities in biological and biomedical reality. These ontologies are designed to serve non-redundant annotation of data and scientific text. To achieve these ends, the Foundry imposes strict requirements upon the ontologies eligible for inclusion. While these requirements are not met by most existing biomedical terminologies, the latter may nonetheless support the Foundry’s goal of consistent and non-redundant annotation if appropriate mappings of data annotated with their aid can be achieved. To construct such mappings in reliable fashion, however, it is necessary to analyze terminological resources from an ontologically realistic perspective in such a way as to identify the exact import of the ‘concepts’ and associated terms which they contain. We propose a framework for such analysis that is designed to maximize the degree to which legacy terminologies and the data coded with their aid can be successfully used for information-driven clinical and translational research. PMID:20841844

  14. CONTROLLING ODOROUS EMISSIONS FROM IRON FOUNDRIES

    EPA Science Inventory

    The report discusses the control of odorous emissions from iron foundries. he main process sources of odors in iron foundries are mold and core making, casting, and sand shakeout. he odors are usually caused by chemicals, which may be present as binders and other additives to the...

  15. Development of a Knowledge-based Application Utilizing Ontologies for the Continuing Site-specific JJ1017 Master Maintenance.

    PubMed

    Kobayashi, Tatsuaki; Tsuji, Shintaro; Yagahara, Ayako; Tanikawa, Takumi; Umeda, Tokuo

    2015-07-01

    The purpose of this study was to develop the JJ1017 Knowledge-based Application (JKA) to support the continuing maintenance of a site-specific JJ1017 master defined by the JJ1017 guideline as a standard radiologic procedure master for medical information systems that are being adopted by some medical facilities in Japan. The method consisted of the following three steps: (1) construction of the JJ1017 Ontology (JJOnt) as a knowledge base using the Hozo (an environment for building/using ontologies); (2) development of modules (operation, I/O, graph modules) that are required to continue the maintenance of a site-specific JJ1017 master; and (3) unit testing of the JKA that consists of the JJOnt and the modules. As a result, the number of classes included in the JJOnt was 21,697. Within the radiologic procedure classes included in the above, the ratio of a JJ1017 master code for an external beam radiotherapy was the highest (51%). In unit testing of the JKA, we checked the main operations (e.g., keyword search of a JJ1017 master code/code meaning, editing the description of classes, etc.). The JJOnt is a knowledge base for implementing features that medical technologists find necessary in medical information systems. To enable medical technologists to exchange/retrieve semantically accurate information while using medical information systems in the future, we expect the JKA to support the maintenance and improvement of the site-specific JJ1017 master.

  16. A Marketplace for Ontologies and Ontology-Based Tools and Applications in the Life Sciences

    SciTech Connect

    McEntire, R; Goble, C; Stevens, R; Neumann, E; Matuszek, P; Critchlow, T; Tarczy-Hornoch, P

    2005-06-30

    This paper describes a strategy for the development of ontologies in the life sciences, tools to support the creation and use of those ontologies, and a framework whereby these ontologies can support the development of commercial applications within the field. At the core of these efforts is the need for an organization that will provide a focus for ontology work that will engage researchers as well as drive forward the commercial aspects of this effort.

  17. Plasma on a foundry cupola

    NASA Astrophysics Data System (ADS)

    Pineau, Didier

    An experiment of a plasma torch on a production foundry cupola is reported. The test runs were conducted on a hot blast cupola, the blast temperature in the absence of plasma being 400 C. With the torch, the temperature of the blast was increased to 1000 C. The experiment was conducted for the manufacture of car engines with a 2.5 MW transportable plasma system. The cupola was boosted with a 4 MW torch and results included an increase in production of 45 percent, a decrease in coke rate and no more new iron in the loads. The plasma torch and hot air cupola furnace are described.

  18. Research-IQ: Development and Evaluation of an Ontology-anchored Integrative Query Tool

    PubMed Central

    Borlawsky, Tara B.; Lele, Omkar; Payne, Philip R. O.

    2011-01-01

    Investigators in the translational research and systems medicine domains require highly usable, efficient and integrative tools and methods that allow for the navigation of and reasoning over emerging large-scale data sets. Such resources must cover a spectrum of granularity from bio-molecules to population phenotypes. Given such information needs, we report upon the initial design and evaluation of an ontology-anchored integrative query tool, Research-IQ, which employs a combination of conceptual knowledge engineering and information retrieval techniques to enable the intuitive and rapid construction of queries, in terms of semi-structured textual propositions, that can subsequently be applied to integrative data sets. Our initial results, based upon both quantitative and qualitative evaluations of the efficacy and usability of Research-IQ, demonstrate its potential to increase clinical and translational research throughput. PMID:21821150

  19. Ontologies as integrative tools for plant science

    PubMed Central

    Walls, Ramona L.; Athreya, Balaji; Cooper, Laurel; Elser, Justin; Gandolfo, Maria A.; Jaiswal, Pankaj; Mungall, Christopher J.; Preece, Justin; Rensing, Stefan; Smith, Barry; Stevenson, Dennis W.

    2012-01-01

    Premise of the study Bio-ontologies are essential tools for accessing and analyzing the rapidly growing pool of plant genomic and phenomic data. Ontologies provide structured vocabularies to support consistent aggregation of data and a semantic framework for automated analyses and reasoning. They are a key component of the semantic web. Methods This paper provides background on what bio-ontologies are, why they are relevant to botany, and the principles of ontology development. It includes an overview of ontologies and related resources that are relevant to plant science, with a detailed description of the Plant Ontology (PO). We discuss the challenges of building an ontology that covers all green plants (Viridiplantae). Key results Ontologies can advance plant science in four keys areas: (1) comparative genetics, genomics, phenomics, and development; (2) taxonomy and systematics; (3) semantic applications; and (4) education. Conclusions Bio-ontologies offer a flexible framework for comparative plant biology, based on common botanical understanding. As genomic and phenomic data become available for more species, we anticipate that the annotation of data with ontology terms will become less centralized, while at the same time, the need for cross-species queries will become more common, causing more researchers in plant science to turn to ontologies. PMID:22847540

  20. Mortality among ferrous foundry workers.

    PubMed

    Silverstein, M; Maizlish, N; Park, R; Silverstein, B; Brodsky, L; Mirer, F

    1986-01-01

    Mortality analyses were carried out for 278 male hourly workers who were employed for at least 10 years at a gray iron foundry and who died between January 1, 1970 and December 31, 1981. Statistically significant excess proportional mortality due to non-malignant respiratory disease (SPMR = 177), lung cancer (SPMR = 148), and leukemia (SPMR = 284) was found among the 221 white males. Among nonwhite males there was a significant excess in proportional mortality due to circulatory diseases (SPMR = 143). White males in the Finishing classification experienced a significant excess of proportional mortality due to nonmalignant respiratory disease (SPMR = 279) and lung cancer (SPMR = 179). White males in the Core Room classification experienced an excess of proportional mortality due to nonmalignant respiratory disease (SPMR = 321). Case-control studies demonstrated a significant association between nonmalignant respiratory disease and the Finishing classification after controlling for the effects of age, prior occupations in coal mining or foundries, and smoking. A positive but nonsignificant association between lung cancer and Finishing was also found after controlling for age, prior work history, and smoking in case control studies.

  1. The Drosophila anatomy ontology

    PubMed Central

    2013-01-01

    Background Anatomy ontologies are query-able classifications of anatomical structures. They provide a widely-used means for standardising the annotation of phenotypes and expression in both human-readable and programmatically accessible forms. They are also frequently used to group annotations in biologically meaningful ways. Accurate annotation requires clear textual definitions for terms, ideally accompanied by images. Accurate grouping and fruitful programmatic usage requires high-quality formal definitions that can be used to automate classification and check for errors. The Drosophila anatomy ontology (DAO) consists of over 8000 classes with broad coverage of Drosophila anatomy. It has been used extensively for annotation by a range of resources, but until recently it was poorly formalised and had few textual definitions. Results We have transformed the DAO into an ontology rich in formal and textual definitions in which the majority of classifications are automated and extensive error checking ensures quality. Here we present an overview of the content of the DAO, the patterns used in its formalisation, and the various uses it has been put to. Conclusions As a result of the work described here, the DAO provides a high-quality, queryable reference for the wild-type anatomy of Drosophila melanogaster and a set of terms to annotate data related to that anatomy. Extensive, well referenced textual definitions make it both a reliable and useful reference and ensure accurate use in annotation. Wide use of formal axioms allows a large proportion of classification to be automated and the use of consistency checking to eliminate errors. This increased formalisation has resulted in significant improvements to the completeness and accuracy of classification. The broad use of both formal and informal definitions make further development of the ontology sustainable and scalable. The patterns of formalisation used in the DAO are likely to be useful to developers of other

  2. Towards Ontology-Driven Information Systems: Guidelines to the Creation of New Methodologies to Build Ontologies

    ERIC Educational Resources Information Center

    Soares, Andrey

    2009-01-01

    This research targeted the area of Ontology-Driven Information Systems, where ontology plays a central role both at development time and at run time of Information Systems (IS). In particular, the research focused on the process of building domain ontologies for IS modeling. The motivation behind the research was the fact that researchers have…

  3. [Environmental toxicity of waste foundry sand].

    PubMed

    Zhang, Hai-Feng; Wang, Yu-Jue; Wang, Jin-Lin; Huang, Tian-You; Xiong, Ying

    2013-03-01

    The metal leaching characteristics and volatile organic compounds (VOCs) of five different types of waste foundry sands were analyzed with the toxicity characteristic leaching procedure (TCLP) and head space-gas chromatography (HS-GC). Microtox and soil dehydrogenase activity (DHA) tests were then used to evaluate the bio-effects of these waste sands. The results showed that due to the different metals poured and casting materials used to make the sand molds, there was significant difference among the five waste foundry sands in the compositions and concentrations of metal and organic pollutants. The concentrations of Fe in the leachates of iron and steel casting waste foundry sand exceeded the maximal allowable concentrations specified in the National Standard of Drinking Water Quality, whereas the As concentration in the leachate of aluminum casting waste foundry sand exceeded the standard. The five waste foundry sands had quite different compositions and levels of VOCs, which resulted in different levels of inhibition effects on the luminescent bacteria (30% and 95%). Additionally, the soil DHA tests suggested that metal pollutants in waste foundry sands may inhibit the soil microbial activity, whereas organics in the sands may slightly promote the microbial activity. The results of this study indicated that the waste foundry sands may pose considerable threat to the environment when improperly disposed. PMID:23745431

  4. [Environmental toxicity of waste foundry sand].

    PubMed

    Zhang, Hai-Feng; Wang, Yu-Jue; Wang, Jin-Lin; Huang, Tian-You; Xiong, Ying

    2013-03-01

    The metal leaching characteristics and volatile organic compounds (VOCs) of five different types of waste foundry sands were analyzed with the toxicity characteristic leaching procedure (TCLP) and head space-gas chromatography (HS-GC). Microtox and soil dehydrogenase activity (DHA) tests were then used to evaluate the bio-effects of these waste sands. The results showed that due to the different metals poured and casting materials used to make the sand molds, there was significant difference among the five waste foundry sands in the compositions and concentrations of metal and organic pollutants. The concentrations of Fe in the leachates of iron and steel casting waste foundry sand exceeded the maximal allowable concentrations specified in the National Standard of Drinking Water Quality, whereas the As concentration in the leachate of aluminum casting waste foundry sand exceeded the standard. The five waste foundry sands had quite different compositions and levels of VOCs, which resulted in different levels of inhibition effects on the luminescent bacteria (30% and 95%). Additionally, the soil DHA tests suggested that metal pollutants in waste foundry sands may inhibit the soil microbial activity, whereas organics in the sands may slightly promote the microbial activity. The results of this study indicated that the waste foundry sands may pose considerable threat to the environment when improperly disposed.

  5. Gene Ontology Consortium: going forward

    PubMed Central

    2015-01-01

    The Gene Ontology (GO; http://www.geneontology.org) is a community-based bioinformatics resource that supplies information about gene product function using ontologies to represent biological knowledge. Here we describe improvements and expansions to several branches of the ontology, as well as updates that have allowed us to more efficiently disseminate the GO and capture feedback from the research community. The Gene Ontology Consortium (GOC) has expanded areas of the ontology such as cilia-related terms, cell-cycle terms and multicellular organism processes. We have also implemented new tools for generating ontology terms based on a set of logical rules making use of templates, and we have made efforts to increase our use of logical definitions. The GOC has a new and improved web site summarizing new developments and documentation, serving as a portal to GO data. Users can perform GO enrichment analysis, and search the GO for terms, annotations to gene products, and associated metadata across multiple species using the all-new AmiGO 2 browser. We encourage and welcome the input of the research community in all biological areas in our continued effort to improve the Gene Ontology. PMID:25428369

  6. Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.

    PubMed

    Ochs, Christopher; He, Zhe; Zheng, Ling; Geller, James; Perl, Yehoshua; Hripcsak, George; Musen, Mark A

    2016-06-01

    An Abstraction Network is a compact summary of an ontology's structure and content. In previous research, we showed that Abstraction Networks support quality assurance (QA) of biomedical ontologies. The development of an Abstraction Network and its associated QA methodologies, however, is a labor-intensive process that previously was applicable only to one ontology at a time. To improve the efficiency of the Abstraction-Network-based QA methodology, we introduced a QA framework that uses uniform Abstraction Network derivation techniques and QA methodologies that are applicable to whole families of structurally similar ontologies. For the family-based framework to be successful, it is necessary to develop a method for classifying ontologies into structurally similar families. We now describe a structural meta-ontology that classifies ontologies according to certain structural features that are commonly used in the modeling of ontologies (e.g., object properties) and that are important for Abstraction Network derivation. Each class of the structural meta-ontology represents a family of ontologies with identical structural features, indicating which types of Abstraction Networks and QA methodologies are potentially applicable to all of the ontologies in the family. We derive a collection of 81 families, corresponding to classes of the structural meta-ontology, that enable a flexible, streamlined family-based QA methodology, offering multiple choices for classifying an ontology. The structure of 373 ontologies from the NCBO BioPortal is analyzed and each ontology is classified into multiple families modeled by the structural meta-ontology. PMID:26988001

  7. Where to Publish and Find Ontologies? A Survey of Ontology Libraries

    PubMed Central

    d'Aquin, Mathieu; Noy, Natalya F.

    2011-01-01

    One of the key promises of the Semantic Web is its potential to enable and facilitate data interoperability. The ability of data providers and application developers to share and reuse ontologies is a critical component of this data interoperability: if different applications and data sources use the same set of well defined terms for describing their domain and data, it will be much easier for them to “talk” to one another. Ontology libraries are the systems that collect ontologies from different sources and facilitate the tasks of finding, exploring, and using these ontologies. Thus ontology libraries can serve as a link in enabling diverse users and applications to discover, evaluate, use, and publish ontologies. In this paper, we provide a survey of the growing—and surprisingly diverse—landscape of ontology libraries. We highlight how the varying scope and intended use of the libraries a ects their features, content, and potential exploitation in applications. From reviewing eleven ontology libraries, we identify a core set of questions that ontology practitioners and users should consider in choosing an ontology library for finding ontologies or publishing their own. We also discuss the research challenges that emerge from this survey, for the developers of ontology libraries to address. PMID:22408576

  8. Where to Publish and Find Ontologies? A Survey of Ontology Libraries.

    PubMed

    d'Aquin, Mathieu; Noy, Natalya F

    2012-03-01

    One of the key promises of the Semantic Web is its potential to enable and facilitate data interoperability. The ability of data providers and application developers to share and reuse ontologies is a critical component of this data interoperability: if different applications and data sources use the same set of well defined terms for describing their domain and data, it will be much easier for them to "talk" to one another. Ontology libraries are the systems that collect ontologies from different sources and facilitate the tasks of finding, exploring, and using these ontologies. Thus ontology libraries can serve as a link in enabling diverse users and applications to discover, evaluate, use, and publish ontologies. In this paper, we provide a survey of the growing-and surprisingly diverse-landscape of ontology libraries. We highlight how the varying scope and intended use of the libraries a ects their features, content, and potential exploitation in applications. From reviewing eleven ontology libraries, we identify a core set of questions that ontology practitioners and users should consider in choosing an ontology library for finding ontologies or publishing their own. We also discuss the research challenges that emerge from this survey, for the developers of ontology libraries to address.

  9. How Ontologies are Made: Studying the Hidden Social Dynamics Behind Collaborative Ontology Engineering Projects.

    PubMed

    Strohmaier, Markus; Walk, Simon; Pöschko, Jan; Lamprecht, Daniel; Tudorache, Tania; Nyulas, Csongor; Musen, Mark A; Noy, Natalya F

    2013-05-01

    Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ontologies as a product. In this paper, we aim to shed light on the process of ontology engineering construction by introducing and applying a set of measures to analyze hidden social dynamics. We argue that especially for ontologies which are constructed collaboratively, understanding the social processes that have led to its construction is critical not only in understanding but consequently also in evaluating the ontology. With the work presented in this paper, we aim to expose the texture of collaborative ontology engineering processes that is otherwise left invisible. Using historical change-log data, we unveil qualitative differences and commonalities between different collaborative ontology engineering projects. Explaining and understanding these differences will help us to better comprehend the role and importance of social factors in collaborative ontology engineering projects. We hope that our analysis will spur a new line of evaluation techniques that view ontologies not as the static result of deliberations among domain experts, but as a dynamic, collaborative and iterative process that needs to be understood, evaluated and managed in itself. We believe that advances in this direction would help our community to expand the existing arsenal of ontology evaluation techniques towards more holistic approaches.

  10. Ontology Reuse in Geoscience Semantic Applications

    NASA Astrophysics Data System (ADS)

    Mayernik, M. S.; Gross, M. B.; Daniels, M. D.; Rowan, L. R.; Stott, D.; Maull, K. E.; Khan, H.; Corson-Rikert, J.

    2015-12-01

    The tension between local ontology development and wider ontology connections is fundamental to the Semantic web. It is often unclear, however, what the key decision points should be for new semantic web applications in deciding when to reuse existing ontologies and when to develop original ontologies. In addition, with the growth of semantic web ontologies and applications, new semantic web applications can struggle to efficiently and effectively identify and select ontologies to reuse. This presentation will describe the ontology comparison, selection, and consolidation effort within the EarthCollab project. UCAR, Cornell University, and UNAVCO are collaborating on the EarthCollab project to use semantic web technologies to enable the discovery of the research output from a diverse array of projects. The EarthCollab project is using the VIVO Semantic web software suite to increase discoverability of research information and data related to the following two geoscience-based communities: (1) the Bering Sea Project, an interdisciplinary field program whose data archive is hosted by NCAR's Earth Observing Laboratory (EOL), and (2) diverse research projects informed by geodesy through the UNAVCO geodetic facility and consortium. This presentation will outline of EarthCollab use cases, and provide an overview of key ontologies being used, including the VIVO-Integrated Semantic Framework (VIVO-ISF), Global Change Information System (GCIS), and Data Catalog (DCAT) ontologies. We will discuss issues related to bringing these ontologies together to provide a robust ontological structure to support the EarthCollab use cases. It is rare that a single pre-existing ontology meets all of a new application's needs. New projects need to stitch ontologies together in ways that fit into the broader semantic web ecosystem.

  11. Final Scientific Report Steel Foundry Refractory Lining Optimization

    SciTech Connect

    Smith, J.D.; Peaslee, K.D.

    2002-12-02

    The overall objective of the program was to optimize refractory materials and foundry processing used in casting steel. This objective was to be met by completing the following: (1) Surveying the steel foundries both through paper/electronic surveys sent to North American steel foundries as well as plant visits to participants. Information concerning refractory selection and performance as well as refractory and steelmaking practices provides a baseline for future comparison and to identify opportunities for substantial improvement in energy efficiency. (2) Conducting post-mortem analysis of materials from existing refractory/steelmaking practices to determine wear/failure mechanisms. (3) Identify areas for research on developing refractories for use in steel foundry furnaces, adjusting steelmaking practices to improve efficiency and modifying slag practices to improve refractory performance. The overall objective of the steel foundry refractory lining optimization program was to review established refractory and steelmaking practices to identify opportunities for improvements that would yield substantial energy savings for steel foundries. Energy savings were expected to arise from improved efficiency of the electric arc furnaces and from reductions in the post-casting welding and grinding that are normally required. Ancillary energy savings related to a reduction in the amount of refractories currently produced to meet the needs of the steel foundry industry, and a shift from pre-fired materials (shaped refractories) to monolithic refractories that are heat treated ''in situ'' were anticipated. A review of the complete program results indicates that techniques for achieving the overall goal were demonstrated. The main difference between the predicted and the actual achievements relates to the areas from which actual energy savings could be realized. Although reductions in furnace tap temperature would result in a reduction in the power required for melting, such

  12. Legal Ontologies and Loopholes in the Law

    NASA Astrophysics Data System (ADS)

    Lovrenčić, Sandra; Tomac, Ivorka Jurenec; Mavrek, Blaženka

    The use of ontologies is today widely spread across many different domains. The main effort today is, with the development of Semantic Web, to make them available across the Internet community with the purpose of reuse. The legal domain has also been explored concerning ontologies, both on the general as on the sub-domain level. In this paper are explored problems of formal ontology development regarding areas in specific legislation acts that are understated or unequally described across the act — popularly said: loopholes in the law. An example of such a problematic act is shown. For ontology implementation, a well-known tool, Protégé, is used. The ontology is made in formal way, using PAL — Protégé Axiom Language, for expressing constraints, where needed. Ontology is evaluated using known evaluation methods.

  13. Creating a magnetic resonance imaging ontology.

    PubMed

    Lasbleiz, Jérémy; Saint-Jalmes, Hervé; Duvauferrier, Régis; Burgun, Anita

    2011-01-01

    The goal of this work is to build an ontology of Magnetic Resonance Imaging. The MRI domain has been analysed regarding MRI simulators and the DICOM standard. Tow MRI simulators have been analysed: JEMRIS, which is developed in XML and C++, has a hierarchical organisation and SIMRI, which is developed in C, has a good representation of MRI physical processes. To build the ontology we have used Protégé 4, owl2 that allows quantitative representations. The ontology has been validated by a reasoner (Fact++) and by a good representation of DICOM headers and of MRI processes. The MRI ontology would improved MRI simulators and eased semantic interoperability. PMID:21893854

  14. Scientific Digital Libraries, Interoperability, and Ontologies

    NASA Technical Reports Server (NTRS)

    Hughes, J. Steven; Crichton, Daniel J.; Mattmann, Chris A.

    2009-01-01

    Scientific digital libraries serve complex and evolving research communities. Justifications for the development of scientific digital libraries include the desire to preserve science data and the promises of information interconnectedness, correlative science, and system interoperability. Shared ontologies are fundamental to fulfilling these promises. We present a tool framework, some informal principles, and several case studies where shared ontologies are used to guide the implementation of scientific digital libraries. The tool framework, based on an ontology modeling tool, was configured to develop, manage, and keep shared ontologies relevant within changing domains and to promote the interoperability, interconnectedness, and correlation desired by scientists.

  15. Vaccine and Drug Ontology Studies (VDOS 2014).

    PubMed

    Tao, Cui; He, Yongqun; Arabandi, Sivaram

    2016-01-01

    The "Vaccine and Drug Ontology Studies" (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat human and animal diseases. Work in both (drugs and vaccines) areas is closely related - from preclinical research and development to manufacturing, clinical trials, government approval and regulation, and post-licensure usage surveillance and monitoring. Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugs - extending existing clinical terminology systems such as SNOMED, RxNorm, NDF-RT, and MedDRA, developing new models such as the Vaccine Ontology (VO) and Ontology of Adverse Events (OAE), vernacular medical terminologies such as the Consumer Health Vocabulary (CHV). The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs and vaccines, their administration, host immune responses, adverse events, and other related topics. The five full-length papers included in this 2014 thematic issue focus on two main themes: (i) General vaccine/drug-related ontology development and exploration, and (ii) Interaction and network-related ontology studies.

  16. Development of a One-Stop Data Search and Discovery Engine using Ontologies for Semantic Mappings (HydroSeek)

    NASA Astrophysics Data System (ADS)

    Piasecki, M.; Beran, B.

    2007-12-01

    Search engines have changed the way we see the Internet. The ability to find the information by just typing in keywords was a big contribution to the overall web experience. While the conventional search engine methodology worked well for textual documents, locating scientific data remains a problem since they are stored in databases not readily accessible by search engine bots. Considering different temporal, spatial and thematic coverage of different databases, especially for interdisciplinary research it is typically necessary to work with multiple data sources. These sources can be federal agencies which generally offer national coverage or regional sources which cover a smaller area with higher detail. However for a given geographic area of interest there often exists more than one database with relevant data. Thus being able to query multiple databases simultaneously is a desirable feature that would be tremendously useful for scientists. Development of such a search engine requires dealing with various heterogeneity issues. In scientific databases, systems often impose controlled vocabularies which ensure that they are generally homogeneous within themselves but are semantically heterogeneous when moving between different databases. This defines the boundaries of possible semantic related problems making it easier to solve than with the conventional search engines that deal with free text. We have developed a search engine that enables querying multiple data sources simultaneously and returns data in a standardized output despite the aforementioned heterogeneity issues between the underlying systems. This application relies mainly on metadata catalogs or indexing databases, ontologies and webservices with virtual globe and AJAX technologies for the graphical user interface. Users can trigger a search of dozens of different parameters over hundreds of thousands of stations from multiple agencies by providing a keyword, a spatial extent, i.e. a bounding box

  17. 35. GREY IRON TUMBLERS, IN THE GREY IRON FOUNDRY ROTATE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    35. GREY IRON TUMBLERS, IN THE GREY IRON FOUNDRY ROTATE CASTINGS WITH SHOT TO REMOVE AND SURFACE OXIDES AND REMAINING EXCESS METALS. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  18. 4. INTERIOR, FOUNDRY CA. 1919 SHOWING CASTINGS READY FOR CLEANING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    4. INTERIOR, FOUNDRY CA. 1919 SHOWING CASTINGS READY FOR CLEANING AND FOUNDRY FLASKS TO RIGHT. - Hardie-Tynes Manufacturing Company, Workshop, 800 Twenty-eighth Street North, Birmingham, Jefferson County, AL

  19. 30. VIEW OF DEMOLITION OF FOUNDRY SAND BLASTING AND CLEANING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    30. VIEW OF DEMOLITION OF FOUNDRY SAND BLASTING AND CLEANING BUILDING FROM INSIDE FOUNDRY. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  20. 31. VIEW OF DEMOLITION OF FOUNDRY SAND BLASTING AND CLEANING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    31. VIEW OF DEMOLITION OF FOUNDRY SAND BLASTING AND CLEANING BUILDING FROM INSIDE FOUNDRY. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  1. ELECTRIC HOLDING FURNACE IN THE MALLEABLE FOUNDRY MAINTAINS CONSTANT TEMPERATURES ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    ELECTRIC HOLDING FURNACE IN THE MALLEABLE FOUNDRY MAINTAINS CONSTANT TEMPERATURES FOR IRON PRIOR TO FILLING MOBILE LADLES. - Stockham Pipe & Fittings Company, Malleable Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  2. BRASS FOUNDRY MACHINE ROOM USED TO MACHINE CAST BRONZE PIECES ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    BRASS FOUNDRY MACHINE ROOM USED TO MACHINE CAST BRONZE PIECES FOR VALVES AND PREPARE BRONZE VALVE BODIES FOR ASSEMBLY. - Stockham Pipe & Fittings Company, Brass Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  3. SOUTH AND EAST FACADES OF BRASS FOUNDRY, LOOKING NORTH, MORE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    SOUTH AND EAST FACADES OF BRASS FOUNDRY, LOOKING NORTH, MORE RECENTLY USED FOR STORAGE. - Carnegie Institution of Washington, Department of Terrestrial Magnetism, Brass Foundry, 5241 Broad Branch Drive Northwest, Washington, District of Columbia, DC

  4. FOUNDRY LANDSCAPE LOOKING NORTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    FOUNDRY LANDSCAPE LOOKING NORTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING THE MALLEABLE ANNEALING BUILDING AND THE BRASS FOUNDRY. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  5. 40. THIS TUMBLING MILL IN THE GREY IRON FOUNDRY IS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    40. THIS TUMBLING MILL IN THE GREY IRON FOUNDRY IS USED TO TUMBLE CASTINGS OVER EACH OTHER TO BREAK OFF RUNNERS AND SPRUES. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  6. MOLD MACHINE, BRASS FOUNDRY, USED TO COMPRESS CONDITIONED SAND IN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    MOLD MACHINE, BRASS FOUNDRY, USED TO COMPRESS CONDITIONED SAND IN FLASKS OVER PATTERNS TO CREATE MOLD CAVITIES WHICH ARE LATER FILLED WITH MOLTEN BRONZE. - Stockham Pipe & Fittings Company, Brass Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  7. Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice.

    PubMed

    Shrestha, Rosemary; Matteis, Luca; Skofic, Milko; Portugal, Arllet; McLaren, Graham; Hyman, Glenn; Arnaud, Elizabeth

    2012-01-01

    The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) is developed for the Integrated Breeding Platform (IBP) (http://www.integratedbreeding.net/) by several centers of The Consultative Group on International Agricultural Research (CGIAR): bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The CO provides validated trait names used by the crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales, and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for an automatic annotation of the phenotypic data measured in the field. The IB fieldbook provides breeders with direct access to the CO to get additional descriptive information on the traits. Ontologies and trait dictionaries are online for cassava, chickpea, common bean, groundnut, maize, Musa, potato, rice, sorghum, and wheat. Online curation and annotation tools facilitate (http://cropontology.org) direct maintenance of the trait information and production of trait dictionaries by the crop communities. An important feature is the cross referencing of CO terms with the Crop database trait ID and with their synonyms in Plant Ontology (PO) and Trait Ontology (TO). Web links between cross referenced terms in CO provide online access to data annotated with similar ontological terms, particularly the genetic data in Gramene (University of Cornell) or the evaluation and climatic data in the Global Repository of evaluation trials of the Climate Change, Agriculture and Food Security programme (CCAFS). Cross-referencing and annotation will be further applied in the IBP. PMID:22934074

  8. Bridging the phenotypic and genetic data useful for integrated breeding through a data annotation using the Crop Ontology developed by the crop communities of practice

    PubMed Central

    Shrestha, Rosemary; Matteis, Luca; Skofic, Milko; Portugal, Arllet; McLaren, Graham; Hyman, Glenn; Arnaud, Elizabeth

    2012-01-01

    The Crop Ontology (CO) of the Generation Challenge Program (GCP) (http://cropontology.org/) is developed for the Integrated Breeding Platform (IBP) (http://www.integratedbreeding.net/) by several centers of The Consultative Group on International Agricultural Research (CGIAR): bioversity, CIMMYT, CIP, ICRISAT, IITA, and IRRI. Integrated breeding necessitates that breeders access genotypic and phenotypic data related to a given trait. The CO provides validated trait names used by the crop communities of practice (CoP) for harmonizing the annotation of phenotypic and genotypic data and thus supporting data accessibility and discovery through web queries. The trait information is completed by the description of the measurement methods and scales, and images. The trait dictionaries used to produce the Integrated Breeding (IB) fieldbooks are synchronized with the CO terms for an automatic annotation of the phenotypic data measured in the field. The IB fieldbook provides breeders with direct access to the CO to get additional descriptive information on the traits. Ontologies and trait dictionaries are online for cassava, chickpea, common bean, groundnut, maize, Musa, potato, rice, sorghum, and wheat. Online curation and annotation tools facilitate (http://cropontology.org) direct maintenance of the trait information and production of trait dictionaries by the crop communities. An important feature is the cross referencing of CO terms with the Crop database trait ID and with their synonyms in Plant Ontology (PO) and Trait Ontology (TO). Web links between cross referenced terms in CO provide online access to data annotated with similar ontological terms, particularly the genetic data in Gramene (University of Cornell) or the evaluation and climatic data in the Global Repository of evaluation trials of the Climate Change, Agriculture and Food Security programme (CCAFS). Cross-referencing and annotation will be further applied in the IBP. PMID:22934074

  9. From zebrafish heart jogging genes to mouse and human orthologs: using Gene Ontology to investigate mammalian heart development.

    PubMed

    Khodiyar, Varsha K; Howe, Doug; Talmud, Philippa J; Breckenridge, Ross; Lovering, Ruth C

    2013-01-01

    For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer's vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer's vesicle determine asymmetry in the developing heart, the direction of 'heart jogging' and the direction of 'heart looping'.  'Heart jogging' is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward 'jog'. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish 'heart jogging orthologs' are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach.

  10. Measuring Incoherence in Description Logic-Based Ontologies

    NASA Astrophysics Data System (ADS)

    Qi, Guilin; Hunter, Anthony

    Ontologies play a core role in the success of the Semantic Web as they provide a shared vocabulary for different resources and applications. Developing an error-free ontology is a difficult task. A common kind of error for an ontology is logical contradiction or incoherence. In this paper, we propose some approaches to measuring incoherence in DL-based ontologies. These measures give an ontology engineer important information for maintaining and evaluating ontologies. We implement the proposed approaches using the KAON2 reasoner and provide some preliminary but encouraging empirical results.

  11. Cancer Morbidity of Foundry Workers in Korea

    PubMed Central

    Won, Jong-Uk; Park, Robert M.

    2010-01-01

    Foundry workers are potentially exposed to a number of carcinogens. This study was conducted to describe the cancer incidence associated with employment in small-sized Korean iron foundries and to compare those findings to the Korean population. Cancer morbidity in 208 Korean foundries was analyzed using the Standardized Incidence Ratio (SIR) and Standardized Rate Ratio (SRR). Overall cancer morbidity in foundry workers (SIR=1.11, 95% confidence interval [CI]=1.01-1.21) was significantly higher than that of Korean general population. Lung cancer (SIR=1.45, 95%CI=1.11-1.87) and lymphohematopoietcic cancer (SIR=1.58, 95%CI=1.00-2.37) in production workers were significantly high compared to Korean general population. Stomach cancer in fettling (SRR=2.10, 95%CI=1.10-4.01) and lung cancer in molding (SRR=3.06, 95%CI=1.22-7.64) and in fettling (SRR=2.63, 95%CI=1.01-6.84) were there significant elevations compared to office workers. In this study, statistically significant excess lung cancer was observed in production workers comparing to Korean general population and office workers. Also, cancer morbidity of overall cancer, lung cancer and stomach cancer was significantly increased with duration of employment at ten and more years comparing to Korean general population. These findings suggest in causal association between exposure to carcinogens during foundry work and cancer morbidity. PMID:21165287

  12. BRASS FOUNDRY BUILDING WHERE STOCKHAM MANUFACTURED ITS BRONZE VALVES AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    BRASS FOUNDRY BUILDING WHERE STOCKHAM MANUFACTURED ITS BRONZE VALVES AND VALVE PARTS. ALTHOUGH THE COMPANY DID NOT PRODUCE BRASS CASTINGS, ITS EQUIPMENT WAS SIMILAR TO THAT USED IN BRASS FOUNDRIES AND MAY HAVE BEEN PART OF LONG RANGE PLAN TO CAST BRASS. - Stockham Pipe & Fittings Company, Brass Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  13. Ontologies for cancer nanotechnology research.

    PubMed

    Thomas, Dennis G; Pappu, Rohit V; Baker, Nathan A

    2009-01-01

    Cancer nanotechnology research data are diverse. Ontologies that provide a unifying knowledge framework for annotation of data are necessary to facilitate the sharing and semantic integration of data for advancing the research via informatics methods. In this work, we report the development of NanoParticle Ontology (NPO) to support the terminological and informatics needs of cancer nanotechnology. The NPO is developed within the framework of the Basic Formal Ontology (BFO) using well-defined principles, and implemented in the Ontology Web Language (OWL). The NPO currently represents entities related to physical, chemical and functional descriptions of nanoparticles that are formulated and tested for applications in cancer diagnostics and therapeutics. Public releases of the NPO are available through the BioPortal web site, maintained by the National Center for Biomedical Ontology. Expansion of the scope and application of the NPO will depend on the needs of and feedback from the user community, and its adoption in nanoparticle database applications. As the NPO continues to grow, it will require a governance structure and well-organized community effort for the maintenance, review and development of the NPO.

  14. The National Center for Biomedical Ontology.

    PubMed

    Musen, Mark A; Noy, Natalya F; Shah, Nigam H; Whetzel, Patricia L; Chute, Christopher G; Story, Margaret-Anne; Smith, Barry

    2012-01-01

    The National Center for Biomedical Ontology is now in its seventh year. The goals of this National Center for Biomedical Computing are to: create and maintain a repository of biomedical ontologies and terminologies; build tools and web services to enable the use of ontologies and terminologies in clinical and translational research; educate their trainees and the scientific community broadly about biomedical ontology and ontology-based technology and best practices; and collaborate with a variety of groups who develop and use ontologies and terminologies in biomedicine. The centerpiece of the National Center for Biomedical Ontology is a web-based resource known as BioPortal. BioPortal makes available for research in computationally useful forms more than 270 of the world's biomedical ontologies and terminologies, and supports a wide range of web services that enable investigators to use the ontologies to annotate and retrieve data, to generate value sets and special-purpose lexicons, and to perform advanced analytics on a wide range of biomedical data.

  15. Revisiting the Collective in Critical Consciousness: Diverse Sociopolitical Wisdoms and Ontological Healing in Sociopolitical Development

    ERIC Educational Resources Information Center

    Sánchez Carmen, Sonia Abigail; Domínguez, Michael; Greene, Andrew Cory; Mendoza, Elizabeth; Fine, Michelle; Neville, Helen A.; Gutiérrez, Kris D.

    2015-01-01

    In this manuscript, we take up a "critical friend" perspective on sociopolitical development (SPD), seeking to expand the field's understanding of the collective, intersectional, and dialectic qualities and dimensions in which sociopolitical youth development might occur. Specifically, we contribute to thinking around how SPD is…

  16. Hydrologic Ontology for the Web

    NASA Astrophysics Data System (ADS)

    Bermudez, L. E.; Piasecki, M.

    2003-12-01

    This poster presents the conceptual development of a Hydrologic Ontology for the Web (HOW) that will facilitate data sharing among the hydrologic community. Hydrologic data is difficult to share because of its predicted vast increase in data volume, the availability of new measurement technologies and the heterogeneity of information systems used to produced, store, retrieved and used the data. The augmented capacity of the Internet and the technologies recommended by the W3C, as well as metadata standards provide sophisticated means to make data more usable and systems to be more integrated. Standard metadata is commonly used to solve interoperability issues. For the hydrologic field an explicit metadata standard does not exist, but one could be created extending metadata standards such as the FGDC-STD-001-1998 or ISO 19115. Standard metadata defines a set of elements required to describe data in a consistent manner, and their domains are sometimes restricted by a finite set of values or controlled vocabulary (e.g. code lists in ISO/DIS 19115). This controlled vocabulary is domain specific varying from one information community to another, allowing dissimilar descriptions to similar data sets. This issue is sometimes called semantic non-interoperability or semantic heterogeneity, and it is usually the main problem when sharing data. Explicit domain ontologies could be created to provide semantic interoperability among heterogeneous information communities. Domain ontologies supply the values for restricted domains of some elements in the metadata set and the semantic mapping with other domain ontologies. To achieve interoperability between applications that exchange machine-understandable information on the Web, metadata is expressed using Resource Description Framework (RDF) and domain ontologies are expressed using the Ontology Web Language (OWL), which is also based on RDF. A specific OWL ontology for hydrology is HOW. HOW presents, using a formal syntax, the

  17. Ontology and Taxonomy Design and Development for Personalised Web-Based Learning Systems

    ERIC Educational Resources Information Center

    Yalcinalp, Serpil; Gulbahar, Yasemin

    2010-01-01

    Recent developments and new directions in education have emphasised learners' needs, profile and pedagogical aspects by focusing on learner-centered approaches in educational settings. e-Learning, on the other hand, guarantees learners the opportunity of learning in their own way, and leads to new considerations in course design. e-Learning is…

  18. Evolution of biomedical ontologies and mappings: Overview of recent approaches.

    PubMed

    Groß, Anika; Pruski, Cédric; Rahm, Erhard

    2016-01-01

    Biomedical ontologies are heavily used to annotate data, and different ontologies are often interlinked by ontology mappings. These ontology-based mappings and annotations are used in many applications and analysis tasks. Since biomedical ontologies are continuously updated dependent artifacts can become outdated and need to undergo evolution as well. Hence there is a need for largely automated approaches to keep ontology-based mappings up-to-date in the presence of evolving ontologies. In this article, we survey current approaches and novel directions in the context of ontology and mapping evolution. We will discuss requirements for mapping adaptation and provide a comprehensive overview on existing approaches. We will further identify open challenges and outline ideas for future developments. PMID:27642503

  19. Ontological Annotation with WordNet

    SciTech Connect

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

    2006-06-06

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  20. Automating Ontological Annotation with WordNet

    SciTech Connect

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

    2006-01-22

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  1. Foundry air contaminants from green sand molds.

    PubMed

    Scott, W D; James, R H; Bates, C E

    1976-06-01

    The major gases evolved from foundry molds have been determined in the laboratory. The principal gases evolved during pouring and shakeout of castings include hydrogen, carbon monoxide, carbon dioxide, methane and other low molecular weight hydrocarbons with smaller amounts of ammonia, hydrogen cyanide, and sulfur dioxide. PMID:937172

  2. Use of anthracite in the foundry industry

    SciTech Connect

    Bethray, A.

    1994-12-31

    Anthracite has been used for smelting iron in North America for nearly 200 years and is still used today in cupolas. Environmental and market factors contribute to continued cost increases in foundry coke that will continue in the future. This paper reviews the availability, quality and properties of anthracite and considers some of the differences in operation when using anthracite in place of coke.

  3. The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications.

    PubMed

    Dönitz, Jürgen; Wingender, Edgar

    2012-01-01

    The semantic web depends on the use of ontologies to let electronic systems interpret contextual information. Optimally, the handling and access of ontologies should be completely transparent to the user. As a means to this end, we have developed a service that attempts to bridge the gap between experts in a certain knowledge domain, ontologists, and application developers. The ontology-based answers (OBA) service introduced here can be embedded into custom applications to grant access to the classes of ontologies and their relations as most important structural features as well as to information encoded in the relations between ontology classes. Thus computational biologists can benefit from ontologies without detailed knowledge about the respective ontology. The content of ontologies is mapped to a graph of connected objects which is compatible to the object-oriented programming style in Java. Semantic functions implement knowledge about the complex semantics of an ontology beyond the class hierarchy and "partOf" relations. By using these OBA functions an application can, for example, provide a semantic search function, or (in the examples outlined) map an anatomical structure to the organs it belongs to. The semantic functions relieve the application developer from the necessity of acquiring in-depth knowledge about the semantics and curation guidelines of the used ontologies by implementing the required knowledge. The architecture of the OBA service encapsulates the logic to process ontologies in order to achieve a separation from the application logic. A public server with the current plugins is available and can be used with the provided connector in a custom application in scenarios analogous to the presented use cases. The server and the client are freely available if a project requires the use of custom plugins or non-public ontologies. The OBA service and further documentation is available at http://www.bioinf.med.uni-goettingen.de/projects/oba. PMID

  4. The ontology-based answers (OBA) service: a connector for embedded usage of ontologies in applications.

    PubMed

    Dönitz, Jürgen; Wingender, Edgar

    2012-01-01

    The semantic web depends on the use of ontologies to let electronic systems interpret contextual information. Optimally, the handling and access of ontologies should be completely transparent to the user. As a means to this end, we have developed a service that attempts to bridge the gap between experts in a certain knowledge domain, ontologists, and application developers. The ontology-based answers (OBA) service introduced here can be embedded into custom applications to grant access to the classes of ontologies and their relations as most important structural features as well as to information encoded in the relations between ontology classes. Thus computational biologists can benefit from ontologies without detailed knowledge about the respective ontology. The content of ontologies is mapped to a graph of connected objects which is compatible to the object-oriented programming style in Java. Semantic functions implement knowledge about the complex semantics of an ontology beyond the class hierarchy and "partOf" relations. By using these OBA functions an application can, for example, provide a semantic search function, or (in the examples outlined) map an anatomical structure to the organs it belongs to. The semantic functions relieve the application developer from the necessity of acquiring in-depth knowledge about the semantics and curation guidelines of the used ontologies by implementing the required knowledge. The architecture of the OBA service encapsulates the logic to process ontologies in order to achieve a separation from the application logic. A public server with the current plugins is available and can be used with the provided connector in a custom application in scenarios analogous to the presented use cases. The server and the client are freely available if a project requires the use of custom plugins or non-public ontologies. The OBA service and further documentation is available at http://www.bioinf.med.uni-goettingen.de/projects/oba.

  5. An ontology for sensor networks

    NASA Astrophysics Data System (ADS)

    Compton, Michael; Neuhaus, Holger; Bermudez, Luis; Cox, Simon

    2010-05-01

    ontologies can be easily attached when instantiating the ontology for any particular sensors in a domain. After a review of previous work on the specification of sensors, the group is developing the ontology in conjunction with use case development. Part of the difficulty of such work is that relevant concepts from for example OGC standards and other ontologies must be identified and aligned and also placed in a consistent and logically correct way into the ontology. In terms of alignment with OGC's SWE, the ontology is intended to be able to model concepts from SensorML and O&M. Similar to SensorML and O&M, the ontology is based around concepts of systems, processes, and observations. It supports the description of the physical and processing structure of sensors. Sensors are not constrained to physical sensing devices: rather a sensor is anything that can estimate or calculate the value of a phenomenon, so a device or computational process or combination could play the role of a sensor. The representation of a sensor in the ontology links together what is measured (the domain phenomena), the sensor's physical and other properties and its functions and processing. Parts of the ontology are well aligned with SensorML and O&M, but parts are not, and the group is working to understand how differences from (and alignment with) the OGC standards affect the application of the ontology.

  6. Temporal Ontologies for Geoscience: Alignment Challenges

    NASA Astrophysics Data System (ADS)

    Cox, S. J. D.

    2014-12-01

    Time is a central concept in geoscience. Geologic histories are composed of sequences of geologic processes and events. Calibration of their timing ties a local history into a broader context, and enables correlation of events between locations. The geologic timescale is standardized in the International Chronostratigraphic Chart, which specifies interval names, and calibrations for the ages of the interval boundaries. Time is also a key concept in the world at large. A number of general purpose temporal ontologies have been developed, both stand-alone and as parts of general purpose or upper ontologies. A temporal ontology for geoscience should apply or extend a suitable general purpose temporal ontology. However, geologic time presents two challenges: Geology involves greater spans of time than in other temporal ontologies, inconsistent with the year-month-day/hour-minute-second formalization that is a basic assumption of most general purpose temporal schemes; The geologic timescale is a temporal topology. Its calibration in terms of an absolute (numeric) scale is a scientific issue in its own right supporting a significant community. In contrast, the general purpose temporal ontologies are premised on exact numeric values for temporal position, and do not allow for temporal topology as a primary structure. We have developed an ontology for the geologic timescale to account for these concerns. It uses the ISO 19108 distinctions between different types of temporal reference system, also linking to an explicit temporal topology model. Stratotypes used in the calibration process are modelled as sampling-features following the ISO 19156 Observations and Measurements model. A joint OGC-W3C harmonization project is underway, with standardization of the W3C OWL-Time ontology as one of its tasks. The insights gained from the geologic timescale ontology will assist in development of a general ontology capable of modelling a richer set of use-cases from geoscience.

  7. Automatic generation of warehouse mediators using an ontology engine

    SciTech Connect

    Critchlow, T., LLNL

    1998-04-01

    Data warehouses created for dynamic scientific environments, such as genetics, face significant challenges to their long-term feasibility One of the most significant of these is the high frequency of schema evolution resulting from both technological advances and scientific insight Failure to quickly incorporate these modifications will quickly render the warehouse obsolete, yet each evolution requires significant effort to ensure the changes are correctly propagated DataFoundry utilizes a mediated warehouse architecture with an ontology infrastructure to reduce the maintenance acquirements of a warehouse. Among the things, the ontology is used as an information source for automatically generating mediators, the methods that transfer data between the data sources and the warehouse The identification, definition and representation of the metadata required to perform this task is a primary contribution of this work.

  8. Towards an Ontology for Reef Islands

    NASA Astrophysics Data System (ADS)

    Duce, Stephanie

    Reef islands are complex, dynamic and vulnerable environments with a diverse range of stake holders. Communication and data sharing between these different groups of stake holders is often difficult. An ontology for the reef island domain would improve the understanding of reef island geomorphology and improve communication between stake holders as well as forming a platform from which to move towards interoperability and the application of Information Technology to forecast and monitor these environments. This paper develops a small, prototypical reef island domain ontology, based on informal, natural language relations, aligned to the DOLCE upper-level ontology, for 20 fundamental terms within the domain. A subset of these terms and their relations are discussed in detail. This approach reveals and discusses challenges which must be overcome in the creation of a reef island domain ontology and which could be relevant to other ontologies in dynamic geospatial domains.

  9. Technologies for decreasing the tap temperature to save energy in steel foundries

    NASA Astrophysics Data System (ADS)

    Biswas, Siddhartha

    Steel foundries are one of the most energy intensive industries. The increasing concerns over volatile energy cost and carbon dioxide emission have pushed foundries to improve efficiency and hence decrease electrical energy consumption. Statistical analysis of industrial survey data was combined with computational fluid dynamics (CFD) modeling to investigate the best industrial practices and opportunities to improve energy efficiency. Reducing tap temperature was identified as one of the important ways of reducing energy consumption. Steel foundries typically tap at 1650-1800°C (3000-3300°F) which is 100-250°C (150-450°F) higher than the pouring temperature. The steel temperature is elevated to compensate for the temperature loss associated with tapping, holding and transporting the liquid steel from the furnace to the pouring floor. Based on experimental investigations and CFD modeling of heat losses during holding in the ladle for different foundry practices, a spreadsheet calculator has been developed to calculate the optimum tap temperature for the specific foundry practices which will eliminate unnecessary superheating. The calculated results were compared and validated with industrial measurements. Improving the lining refractory is one significant way of reducing heat losses during holding of the steel in ladle. Silica sand linings are being used in steel foundries as an inexpensive and convenient material for short holding times and small volumes. The possibilities of improvements of silica sand linings by the addition of lower density cenospheres (hollow spheres), a byproduct of coal fired power plants, was studied through property measurements and laboratory trials.

  10. The SWAN biomedical discourse ontology.

    PubMed

    Ciccarese, Paolo; Wu, Elizabeth; Wong, Gwen; Ocana, Marco; Kinoshita, June; Ruttenberg, Alan; Clark, Tim

    2008-10-01

    Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. SWAN (Semantic Web Applications in Neuromedicine) is an interdisciplinary project to develop a practical, common, semantically structured, framework for biomedical discourse initially applied, but not limited, to significant problems in Alzheimer Disease (AD) research. The SWAN ontology has been developed in the context of building a series of applications for biomedical researchers, as well as in extensive discussions and collaborations with the larger bio-ontologies community. In this paper, we present and discuss the SWAN ontology of biomedical discourse. We ground its development theoretically, present its design approach, explain its main classes and their application, and show its relationship to other ongoing activities in biomedicine and bio-ontologies. PMID:18583197

  11. The SWAN biomedical discourse ontology.

    PubMed

    Ciccarese, Paolo; Wu, Elizabeth; Wong, Gwen; Ocana, Marco; Kinoshita, June; Ruttenberg, Alan; Clark, Tim

    2008-10-01

    Developing cures for highly complex diseases, such as neurodegenerative disorders, requires extensive interdisciplinary collaboration and exchange of biomedical information in context. Our ability to exchange such information across sub-specialties today is limited by the current scientific knowledge ecosystem's inability to properly contextualize and integrate data and discourse in machine-interpretable form. This inherently limits the productivity of research and the progress toward cures for devastating diseases such as Alzheimer's and Parkinson's. SWAN (Semantic Web Applications in Neuromedicine) is an interdisciplinary project to develop a practical, common, semantically structured, framework for biomedical discourse initially applied, but not limited, to significant problems in Alzheimer Disease (AD) research. The SWAN ontology has been developed in the context of building a series of applications for biomedical researchers, as well as in extensive discussions and collaborations with the larger bio-ontologies community. In this paper, we present and discuss the SWAN ontology of biomedical discourse. We ground its development theoretically, present its design approach, explain its main classes and their application, and show its relationship to other ongoing activities in biomedicine and bio-ontologies.

  12. Emotion Education without Ontological Commitment?

    ERIC Educational Resources Information Center

    Kristjansson, Kristjan

    2010-01-01

    Emotion education is enjoying new-found popularity. This paper explores the "cosy consensus" that seems to have developed in education circles, according to which approaches to emotion education are immune from metaethical considerations such as contrasting rationalist and sentimentalist views about the moral ontology of emotions. I spell out five…

  13. Crowdsourcing the Verification of Relationships in Biomedical Ontologies

    PubMed Central

    Mortensen, Jonathan M.; Musen, Mark A.; Noy, Natalya F.

    2013-01-01

    Biomedical ontologies are often large and complex, making ontology development and maintenance a challenge. To address this challenge, scientists use automated techniques to alleviate the difficulty of ontology development. However, for many ontology-engineering tasks, human judgment is still necessary. Microtask crowdsourcing, wherein human workers receive remuneration to complete simple, short tasks, is one method to obtain contributions by humans at a large scale. Previously, we developed and refined an effective method to verify ontology hierarchy using microtask crowdsourcing. In this work, we report on applying this method to find errors in the SNOMED CT CORE subset. By using crowdsourcing via Amazon Mechanical Turk with a Bayesian inference model, we correctly verified 86% of the relations from the CORE subset of SNOMED CT in which Rector and colleagues previously identified errors via manual inspection. Our results demonstrate that an ontology developer could deploy this method in order to audit large-scale ontologies quickly and relatively cheaply. PMID:24551391

  14. An ontology for description of drug discovery investigations.

    PubMed

    Qi, Da; King, Ross D; Hopkins, Andrew L; Bickerton, G Richard J; Soldatova, Larisa N

    2010-01-01

    The paper presents an ontology for the description of Drug Discovery Investigation (DDI).This has been developed through the use of a Robot Scientist "Eve", and in consultation with industry. DDI aims to define the principle entities and the relations in the research and development phase of the drug discovery pipeline. DDI is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. This enables DDI to be integrated with such related ontologies as the Vaccine Ontology, the Advancing Clinico-Genomic Trials on Cancer Master Ontology, etc. DDI is available at http://purl.org/ddi/wikipedia or http://purl.org/ddi/home.

  15. SWEET- An Upper Level Ontology for Earth System Science

    NASA Astrophysics Data System (ADS)

    Raskin, R.

    2005-12-01

    The Semantic Web for Earth and Environmental Terminology (SWEET) provides a set of upper-level ontologies constituting a concept space of Earth system science. These ontologies can be used, mapped, or extended by developers of specialized domain ontologies. SWEET components are being adopted within a diverse range of applications, including: the Geosciences Network (GEON), the Marine Metadata Initiative (MMI), the Virtual Solar Terrestrial Observatory (VSTO), and the Earth Science Markup Language (ESML). SWEET includes 12 ontologies, decomposed into component parts that can be reassembled to meet the needs of user communities. For example, the Property ontology terms (e.g., temperature, pressure) can be associated with measurable (observable) quantities of a dataset. The Substance ontology provides representations of the substance in which a property is being measured (e.g., air, water, rock). The Earth Realm ontology provides representations for the environmental regions of the Earth (e.g., atmospheric boundary layer, ocean mixed layer). The Data and Service ontology enables representations of how data are captured, stored, and accessed. The Numerics ontology entries represent 2-D and 3-D objects or spatial/temporal entities and relations. The Human Activities ontology captures the human side or applications of Earth science. The Phenomena ontology describes major geophysical or geophysical-related events. All of the ontologies are written in the OWL-DL language to give domain specialists a starting vocabulary, over which layers, synonyms, or extensions can be applied.

  16. Characterization of the Context of Drug Concepts in Research Protocols: An Empiric Study to Guide Ontology Development

    PubMed Central

    Cimino, James J.; Huser, Vojtech

    2015-01-01

    We examined a large body of research study documents (protocols) to identify mentions of drug concepts and established base concepts and roles needed to characterize the semantics of these instances. We found these concepts in three general situations: background knowledge about the drug, study procedures involving the drug, and other roles of the drug in the study. We identified 18 more specific contexts (e.g., adverse event information, administration and dosing of the drug, and interactions between the study drug and other drugs). The ontology was validated against a test set of protocol documents from NIH and ClinicalTrial.gov. The goal is to support the automated extraction of drug information from protocol documents to support functions such as study retrieval, determination of subject eligibility, generation of order sets, and creation of logic for decision support alerts and reminders. Further work is needed to formally extend existing ontologies of clinical research. PMID:26958176

  17. The Domain Shared by Computational and Digital Ontology: A Phenomenological Exploration and Analysis

    ERIC Educational Resources Information Center

    Compton, Bradley Wendell

    2009-01-01

    The purpose of this dissertation is to explore and analyze a domain of research thought to be shared by two areas of philosophy: computational and digital ontology. Computational ontology is philosophy used to develop information systems also called computational ontologies. Digital ontology is philosophy dealing with our understanding of Being…

  18. Gene Ontology annotations and resources.

    PubMed

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources.

  19. Gene Ontology annotations and resources.

    PubMed

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources. PMID:23161678

  20. An investigation of waste foundry sand in asphalt concrete mixtures.

    PubMed

    Bakis, Recep; Koyuncu, Hakan; Demirbas, Ayhan

    2006-06-01

    A laboratory study regarding the reuse of waste foundry sand in asphalt concrete production by replacing a certain portion of aggregate with WFS was undertaken. The results showed that replacement of 10% aggregates with waste foundry sand was found to be the most suitable for asphalt concrete mixtures. Furthermore, the chemical and physical properties of waste foundry sand were analysed in the laboratory to determine the potential effect on the environment. The results indicated that the investigated waste foundry sand did not significantly affect the environment around the deposition PMID:16784170

  1. Environmental factors and work performance of foundry workers.

    PubMed

    Horino, S

    1977-12-01

    Environmental factors such as atmospheric conditions, lighting, noise, and dust in foundry factories of different sizes were evaluated by direct physical measurements and a subjective rating method using an ergonomic checklist. Working postures and subjective feelings of fatigue of the workers were analyzed in various types of foundry shops. The results showed that work load was highly connected with poor working postures and unfavorable arrangement of work space as well as with poor workplace environment, particularly in terms of dust and noise. Forward bending and squatting positions, which were attributable to the manual working height on or just above the floor level, occupied 70--90% of the actual working time handling large-sized casts, while the work using a table allowed workers more frequent erect standing postures. It seemed essential to redesign the fundamental working processes and to improve the work surface height. A comparison was then made as to performance patterns and electromyographic activities of main muscles between the traditional molding work on the floor and the work at a newly developed hydraulic lift-table operated by foot pedals. The new table assured the worker of an optimal standing position and proved to be an effective means of redesigning the work space. PMID:617651

  2. Ontology Sparse Vector Learning Algorithm for Ontology Similarity Measuring and Ontology Mapping via ADAL Technology

    NASA Astrophysics Data System (ADS)

    Gao, Wei; Zhu, Linli; Wang, Kaiyun

    2015-12-01

    Ontology, a model of knowledge representation and storage, has had extensive applications in pharmaceutics, social science, chemistry and biology. In the age of “big data”, the constructed concepts are often represented as higher-dimensional data by scholars, and thus the sparse learning techniques are introduced into ontology algorithms. In this paper, based on the alternating direction augmented Lagrangian method, we present an ontology optimization algorithm for ontological sparse vector learning, and a fast version of such ontology technologies. The optimal sparse vector is obtained by an iterative procedure, and the ontology function is then obtained from the sparse vector. Four simulation experiments show that our ontological sparse vector learning model has a higher precision ratio on plant ontology, humanoid robotics ontology, biology ontology and physics education ontology data for similarity measuring and ontology mapping applications.

  3. The Ontology of Disaster.

    ERIC Educational Resources Information Center

    Thompson, Neil

    1995-01-01

    Explores some key existential or ontological concepts to show their applicability to the complex area of disaster impact as it relates to health and social welfare practice. Draws on existentialist philosophy, particularly that of John Paul Sartre, and introduces some key ontological concepts to show how they specifically apply to the experience…

  4. Constructive Ontology Engineering

    ERIC Educational Resources Information Center

    Sousan, William L.

    2010-01-01

    The proliferation of the Semantic Web depends on ontologies for knowledge sharing, semantic annotation, data fusion, and descriptions of data for machine interpretation. However, ontologies are difficult to create and maintain. In addition, their structure and content may vary depending on the application and domain. Several methods described in…

  5. Beyond the Ontology Definition Metamodel: Applications

    NASA Astrophysics Data System (ADS)

    Gaševic, Dragan; Djuric, Dragan; Devedžic, Vladan

    The previous chapters provided a detailed overview of the elements defined in the ODM specification, along with possible tool support and examples of the developed ontologies. In this chapter, we analyze the research results that go beyond the ODM specification and focus on several different applications of the ODM. We start with a description of the first implementation of ODM. Next, we analyze how the ODM-based metamodels can be used for model driven engineering of ontology reasoners. Finally, we show how the ODM is applied in collaboration with many other different languages. This includes UML, programming languages, Semantic Web ontology, and rule languages.

  6. Nuclear Nonproliferation Ontology Assessment Team Final Report

    SciTech Connect

    Strasburg, Jana D.; Hohimer, Ryan E.

    2012-01-01

    Final Report for the NA22 Simulations, Algorithm and Modeling (SAM) Ontology Assessment Team's efforts from FY09-FY11. The Ontology Assessment Team began in May 2009 and concluded in September 2011. During this two-year time frame, the Ontology Assessment team had two objectives: (1) Assessing the utility of knowledge representation and semantic technologies for addressing nuclear nonproliferation challenges; and (2) Developing ontological support tools that would provide a framework for integrating across the Simulation, Algorithm and Modeling (SAM) program. The SAM Program was going through a large assessment and strategic planning effort during this time and as a result, the relative importance of these two objectives changed, altering the focus of the Ontology Assessment Team. In the end, the team conducted an assessment of the state of art, created an annotated bibliography, and developed a series of ontological support tools, demonstrations and presentations. A total of more than 35 individuals from 12 different research institutions participated in the Ontology Assessment Team. These included subject matter experts in several nuclear nonproliferation-related domains as well as experts in semantic technologies. Despite the diverse backgrounds and perspectives, the Ontology Assessment team functioned very well together and aspects could serve as a model for future inter-laboratory collaborations and working groups. While the team encountered several challenges and learned many lessons along the way, the Ontology Assessment effort was ultimately a success that led to several multi-lab research projects and opened up a new area of scientific exploration within the Office of Nuclear Nonproliferation and Verification.

  7. Biological Model Development as an Opportunity to Provide Content Auditing for the Foundational Model of Anatomy Ontology

    PubMed Central

    Wang, Lucy L.; Grunblatt, Eli; Jung, Hyunggu; Kalet, Ira J.; Whipple, Mark E.

    2015-01-01

    Constructing a biological model using an established ontology provides a unique opportunity to perform content auditing on the ontology. We built a Markov chain model to study tumor metastasis in the regional lymphatics of patients with head and neck squamous cell carcinoma (HNSCC). The model attempts to determine regions with high likelihood for metastasis, which guides surgeons and radiation oncologists in selecting the boundaries of treatment. To achieve consistent anatomical relationships, the nodes in our model are populated using lymphatic objects extracted from the Foundational Model of Anatomy (FMA) ontology. During this process, we discovered several classes of inconsistencies in the lymphatic representations within the FMA. We were able to use this model building opportunity to audit the entities and connections in this region of interest (ROI). We found five subclasses of errors that are computationally detectable and resolvable, one subclass of errors that is computationally detectable but unresolvable, requiring the assistance of a content expert, and also errors of content, which cannot be detected through computational means. Mathematical descriptions of detectable errors along with expert review were used to discover inconsistencies and suggest concepts for addition and removal. Out of 106 organ and organ parts in the ROI, 8 unique entities were affected, leading to the suggestion of 30 concepts for addition and 4 for removal. Out of 27 lymphatic chain instances, 23 were found to have errors, with a total of 32 concepts suggested for addition and 15 concepts for removal. These content corrections are necessary for the accurate functioning of the FMA and provide benefits for future research and educational uses. PMID:26958311

  8. Types of Concepts in Geoscience Ontologies

    NASA Astrophysics Data System (ADS)

    Brodaric, B.

    2006-05-01

    Ontologies are increasingly viewed as a key enabler of scientific research in cyber-infrastructures. They provide a way of digitally representing the meaning of concepts embedded in the theories and models of geoscience, enabling such representations to be compared and contrasted computationally. This facilitates the discovery, integration and communication of digitally accessible geoscience resources, and potentially helps geoscientists attain new knowledge. As ontologies are typically built to closely reflect some aspect or viewpoint of a domain, recognizing significant ontological patterns within the domain should thus lead to more useful and robust ontologies. A key idea then motivating this work is the notion that geoscience concepts possess an ontological pattern that helps not only structure them, but also aids ontology development in disciplines where concepts are similarly abstracted from geospatial regions, such as in ecology, soil science, etc. Proposed is an ontology structure in which six basic concept types are identified, defined, and organized in increasing levels of abstraction, including a level for general concepts (e.g. 'granite') and a level for concepts specific to a geospace-time region (e.g. 'granites of Ireland'). Discussed will be the six concept types, the proposed structure that organizes them, and several examples from geoscience. Also mentioned will be the significant implementation challenges faced but not addressed by the proposed structure. In general, the proposal prioritizes conceptual granularity over its engineering deficits, but this prioritization remains to be tested in serious applications.

  9. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013.

    PubMed

    Hastings, Janna; de Matos, Paula; Dekker, Adriano; Ennis, Marcus; Harsha, Bhavana; Kale, Namrata; Muthukrishnan, Venkatesh; Owen, Gareth; Turner, Steve; Williams, Mark; Steinbeck, Christoph

    2013-01-01

    ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now 'is_a' classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization.

  10. Design of Wrapper Integration Within the DataFoundry Bioinformatics Application

    SciTech Connect

    Anderson, J; Critchlow, T

    2002-08-20

    The DataFoundry bioinformatics application was designed to enable scientists to directly interact with large datasets, gathered from multiple remote data sources, through a graphical, interactive interface. Gathering information from multiple data sources, integrating that data, and providing an interface to the accumulated data is non-trivial. Advanced techniques are required to develop a solution that adequately completes this task. One possible solution to this problem involves the use of specialized information access programs that are able to access information and transmute that information to a form usable by a single application. These information access programs, called wrappers, were decided to be the most appropriate way to extend the DataFoundry bioinformatics application to support data integration from multiple sources. By adding wrapper support into the DataFoundry application, it is hoped that this system will be able to provide a single access point to bioinformatics data for scientists. We describe some of the computer science concepts, design, and the implementation of adding wrapper support into the DataFoundry bioinformatics application, and then discuss issues of performance.

  11. TGF-beta signaling proteins and the Protein Ontology

    PubMed Central

    Arighi, Cecilia N; Liu, Hongfang; Natale, Darren A; Barker, Winona C; Drabkin, Harold; Blake, Judith A; Smith, Barry; Wu, Cathy H

    2009-01-01

    Background The Protein Ontology (PRO) is designed as a formal and principled Open Biomedical Ontologies (OBO) Foundry ontology for proteins. The components of PRO extend from a classification of proteins on the basis of evolutionary relationships at the homeomorphic level to the representation of the multiple protein forms of a gene, including those resulting from alternative splicing, cleavage and/or post-translational modifications. Focusing specifically on the TGF-beta signaling proteins, we describe the building, curation, usage and dissemination of PRO. Results PRO is manually curated on the basis of PrePRO, an automatically generated file with content derived from standard protein data sources. Manual curation ensures that the treatment of the protein classes and the internal and external relationships conform to the PRO framework. The current release of PRO is based upon experimental data from mouse and human proteins wherein equivalent protein forms are represented by single terms. In addition to the PRO ontology, the annotation of PRO terms is released as a separate PRO association file, which contains, for each given PRO term, an annotation from the experimentally characterized sub-types as well as the corresponding database identifiers and sequence coordinates. The annotations are added in the form of relationship to other ontologies. Whenever possible, equivalent forms in other species are listed to facilitate cross-species comparison. Splice and allelic variants, gene fusion products and modified protein forms are all represented as entities in the ontology. Therefore, PRO provides for the representation of protein entities and a resource for describing the associated data. This makes PRO useful both for proteomics studies where isoforms and modified forms must be differentiated, and for studies of biological pathways, where representations need to take account of the different ways in which the cascade of events may depend on specific protein

  12. Towards an Ontology-driven Framework to Enable Development of Personalized mHealth Solutions for Cancer Survivors' Engagement in Healthy Living.

    PubMed

    Myneni, Sahiti; Amith, Muhammad; Geng, Yimin; Tao, Cui

    2015-01-01

    Adolescent and Young Adult (AYA) cancer survivors manage an array of health-related issues. Survivorship Care Plans (SCPs) have the potential to empower these young survivors by providing information regarding treatment summary, late-effects of cancer therapies, healthy lifestyle guidance, coping with work-life-health balance, and follow-up care. However, current mHealth infrastructure used to deliver SCPs has been limited in terms of flexibility, engagement, and reusability. The objective of this study is to develop an ontology-driven survivor engagement framework to facilitate rapid development of mobile apps that are targeted, extensible, and engaging. The major components include ontology models, patient engagement features, and behavioral intervention technologies. We apply the proposed framework to characterize individual building blocks ("survivor digilegos"), which form the basis for mHealth tools that address user needs across the cancer care continuum. Results indicate that the framework (a) allows identification of AYA survivorship components, (b) facilitates infusion of engagement elements, and (c) integrates behavior change constructs into the design architecture of survivorship applications. Implications for design of patient-engaging chronic disease management solutions are discussed. PMID:26262021

  13. Towards an Ontology-driven Framework to Enable Development of Personalized mHealth Solutions for Cancer Survivors' Engagement in Healthy Living.

    PubMed

    Myneni, Sahiti; Amith, Muhammad; Geng, Yimin; Tao, Cui

    2015-01-01

    Adolescent and Young Adult (AYA) cancer survivors manage an array of health-related issues. Survivorship Care Plans (SCPs) have the potential to empower these young survivors by providing information regarding treatment summary, late-effects of cancer therapies, healthy lifestyle guidance, coping with work-life-health balance, and follow-up care. However, current mHealth infrastructure used to deliver SCPs has been limited in terms of flexibility, engagement, and reusability. The objective of this study is to develop an ontology-driven survivor engagement framework to facilitate rapid development of mobile apps that are targeted, extensible, and engaging. The major components include ontology models, patient engagement features, and behavioral intervention technologies. We apply the proposed framework to characterize individual building blocks ("survivor digilegos"), which form the basis for mHealth tools that address user needs across the cancer care continuum. Results indicate that the framework (a) allows identification of AYA survivorship components, (b) facilitates infusion of engagement elements, and (c) integrates behavior change constructs into the design architecture of survivorship applications. Implications for design of patient-engaging chronic disease management solutions are discussed.

  14. The Gene Ontology: enhancements for 2011.

    PubMed

    2012-01-01

    The Gene Ontology (GO) (http://www.geneontology.org) is a community bioinformatics resource that represents gene product function through the use of structured, controlled vocabularies. The number of GO annotations of gene products has increased due to curation efforts among GO Consortium (GOC) groups, including focused literature-based annotation and ortholog-based functional inference. The GO ontologies continue to expand and improve as a result of targeted ontology development, including the introduction of computable logical definitions and development of new tools for the streamlined addition of terms to the ontology. The GOC continues to support its user community through the use of e-mail lists, social media and web-based resources. PMID:22102568

  15. "Being In" and "Feeling Seen" in Professional Development as New Teachers: The Ontological Layer(ing) of Professional Development Practice

    ERIC Educational Resources Information Center

    Bills, Andrew M.; Giles, David; Rogers, Bev

    2016-01-01

    Dominant discourses on professional development for teachers internationally are increasingly geared to the priority of ensuring individual teachers are meeting prescribed standards-based performance benchmarks which we call "performativities" in this paper. While this intent is invariably played out in individualised performance…

  16. Natural Language Processing Methods and Systems for Biomedical Ontology Learning

    PubMed Central

    Liu, Kaihong; Hogan, William R.; Crowley, Rebecca S.

    2010-01-01

    While the biomedical informatics community widely acknowledges the utility of domain ontologies, there remain many barriers to their effective use. One important requirement of domain ontologies is that they must achieve a high degree of coverage of the domain concepts and concept relationships. However, the development of these ontologies is typically a manual, time-consuming, and often error-prone process. Limited resources result in missing concepts and relationships as well as difficulty in updating the ontology as knowledge changes. Methodologies developed in the fields of natural language processing, information extraction, information retrieval and machine learning provide techniques for automating the enrichment of an ontology from free-text documents. In this article, we review existing methodologies and developed systems, and discuss how existing methods can benefit the development of biomedical ontologies. PMID:20647054

  17. Meeting report: advancing practical applications of biodiversity ontologies

    PubMed Central

    2014-01-01

    We describe the outcomes of three recent workshops aimed at advancing development of the Biological Collections Ontology (BCO), the Population and Community Ontology (PCO), and tools to annotate data using those and other ontologies. The first workshop gathered use cases to help grow the PCO, agreed upon a format for modeling challenging concepts such as ecological niche, and developed ontology design patterns for defining collections of organisms and population-level phenotypes. The second focused on mapping datasets to ontology terms and converting them to Resource Description Framework (RDF), using the BCO. To follow-up, a BCO hackathon was held concurrently with the 16th Genomics Standards Consortium Meeting, during which we converted additional datasets to RDF, developed a Material Sample Core for the Global Biodiversity Information Framework, created a Web Ontology Language (OWL) file for importing Darwin Core classes and properties into BCO, and developed a workflow for converting biodiversity data among formats.

  18. NanoParticle Ontology for cancer nanotechnology research.

    PubMed

    Thomas, Dennis G; Pappu, Rohit V; Baker, Nathan A

    2011-02-01

    Data generated from cancer nanotechnology research are so diverse and large in volume that it is difficult to share and efficiently use them without informatics tools. In particular, ontologies that provide a unifying knowledge framework for annotating the data are required to facilitate the semantic integration, knowledge-based searching, unambiguous interpretation, mining and inferencing of the data using informatics methods. In this paper, we discuss the design and development of NanoParticle Ontology (NPO), which is developed within the framework of the Basic Formal Ontology (BFO), and implemented in the Ontology Web Language (OWL) using well-defined ontology design principles. The NPO was developed to represent knowledge underlying the preparation, chemical composition, and characterization of nanomaterials involved in cancer research. Public releases of the NPO are available through BioPortal website, maintained by the National Center for Biomedical Ontology. Mechanisms for editorial and governance processes are being developed for the maintenance, review, and growth of the NPO.

  19. 30. NATIONAL SHELL CORE MACHINE IN THE GREY IRON FOUNDRY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    30. NATIONAL SHELL CORE MACHINE IN THE GREY IRON FOUNDRY AUTOMATICALLY INJECTS SAND INTO CLOSED, HEATED CORE BOXES THAT SET THE RESINS AND PERMIT A HARDENED CORE TO BE REMOVED BY THE OPERATOR. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  20. 9. VIEW OF FOUNDRY FURNACE, DEPLETED URANIUM INGOTS, BERYLLIUM INGOTS, ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    9. VIEW OF FOUNDRY FURNACE, DEPLETED URANIUM INGOTS, BERYLLIUM INGOTS, AND ALUMINUM SHAPES WERE PRODUCED IN THE FOUNDRY. (10/30/56) - Rocky Flats Plant, Non-Nuclear Production Facility, South of Cottonwood Avenue, west of Seventh Avenue & east of Building 460, Golden, Jefferson County, CO

  1. BRASS FOUNDRY ROOM SHOWING GATE CUTTERS USED TO REMOVE RUNNERS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    BRASS FOUNDRY ROOM SHOWING GATE CUTTERS USED TO REMOVE RUNNERS AND SPRUES FROM BRONZE CASTINGS TOO SOFT TO BE CLEANED IN TUMBLING MILLS. ALSO SHOWN ARE MOLD MACHINES AND THE SAND DELIVERY SYSTEM USED TO CREATE GREEN SAND MOLDS, POURED AT THE OTHER END OF THE GRAVITY CONVEYORS. - Stockham Pipe & Fittings Company, Brass Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  2. 33. BENCH CORE STATION, GREY IRON FOUNDRY CORE ROOM WHERE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    33. BENCH CORE STATION, GREY IRON FOUNDRY CORE ROOM WHERE CORE MOLDS WERE HAND FILLED AND OFTEN PNEUMATICALLY COMPRESSED WITH A HAND-HELD RAMMER BEFORE THEY WERE BAKED. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  3. 34. DESPATCH CORE OVENS, GREY IRON FOUNDRY CORE ROOM, BAKES ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    34. DESPATCH CORE OVENS, GREY IRON FOUNDRY CORE ROOM, BAKES CORES THAT ARE NOT MADE ON HEATED OR COLD BOX CORE MACHINES, TO SET BINDING AGENTS MIXED WITH THE SAND CREATING CORES HARD ENOUGH TO WITHSTAND THE FLOW OF MOLTEN IRON INSIDE A MOLD. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  4. 31. PETIBONE SAND THROWING MACHINE BOX FLOOR GREY IRON FOUNDRY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    31. PETIBONE SAND THROWING MACHINE BOX FLOOR GREY IRON FOUNDRY FORCES CONDITIONED MOLDING SAND, AT HIGH VELOCITY, INTO MOLDS TOO BIG TO BE MADE ON ONE OF THE CONVEYOR SYSTEMS. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  5. Plant Availability of Metals in Waste Foundry Sands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Foundries in the United States generate several million tons of waste sand each year. These sands are no longer suitable for metalcasting processes, and about 90% are discarded in landfills. However, the majority of these waste foundry sands (WFSs) qualify as non-hazardous industrial waste and the...

  6. Foundry. Trade and Industrial Education Trade Preparatory Training Guide.

    ERIC Educational Resources Information Center

    Nebraska State Dept. of Education, Lincoln. Div. of Vocational Education.

    One of a series of curriculum guides prepared for the metals occupations cluster of the construction/fabrication occupational group, this guide identifies the essentials of the foundry trade as recommended by the successful foundry operator. An instructional program based upon the implementation of the guide is expected to prepare a student to…

  7. 17. Forge building, fuel storage shed, and foundry, 1906 Photocopied ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    17. Forge building, fuel storage shed, and foundry, 1906 Photocopied from a photograph by Thomas S. Bronson, 'Group at Whitney Factory, 5 November 1906,' NHCHSL. The most reliable view of the fuel storage sheds and foundry, together with a view of the forge building. - Eli Whitney Armory, West of Whitney Avenue, Armory Street Vicinity, Hamden, New Haven County, CT

  8. 32. LARGE LADLE, BOX FLOOR, GREY IRON FOUNDRY IS USED ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    32. LARGE LADLE, BOX FLOOR, GREY IRON FOUNDRY IS USED TO CARRY LARGE BATCHES OF IRON FROM THE CUPOLA AREAS TO THE LARGE MOLDS MADE ON BOX FLOOR AREA. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  9. Interior of rail mill, now an iron foundry; Foundrymen are ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Interior of rail mill, now an iron foundry; Foundrymen are pouring the molten iron into the ladle which will then be positioned for pouring into the molds (the final products are ingot molds) - Bethlehem Steel Corporation, South Bethlehem Works, Iron Foundry, Along Lehigh River, North of Fourth Street, West of Minsi Trail Bridge, Bethlehem, Northampton County, PA

  10. 1928 MALLEABLE FOUNDRY MOLD CONVEYOR #1 SHOWING CONVEYOR AND TRACK ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    1928 MALLEABLE FOUNDRY MOLD CONVEYOR #1 SHOWING CONVEYOR AND TRACK ARRANGEMENTS WITH OVERHEAD POURING WEIGHTS THAT REST ON A MOLD'S TOP SURFACE TO ENSURE THAT IRON DOES NOT FLOW OUT OF THE MOLD WHEN IT IS BEING POURED THROUGH THE OPENING IN THE WEIGHT. - Stockham Pipe & Fittings Company, Malleable Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  11. BRONZE FOUNDRY SCRAP STORED IN THE BINS TO THE RIGHT ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    BRONZE FOUNDRY SCRAP STORED IN THE BINS TO THE RIGHT ARE LOADED INTO THE BOTTOM DROPPING CHARGE BUCKET IN THE BACKGROUND BEFORE BEING CHARGED INTO ONE OF THE ELECTRIC ARC FURNACES. - Stockham Pipe & Fittings Company, Brass Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  12. Contemporary and futuristic views of pollution control devices in foundries.

    PubMed

    Krishnaraj, R

    2015-10-01

    Foundry practices are used in contemporary world to produce large volume of components and products. Foundry practices involve the melting of metals and pouring the molten metal into the cavities called molds. On solidification, the metals which assume the shape of molds are removed as castings. Foundries that employ these practices were growing in large number till the middle part of the twentieth century in the world. After the middle part of the twentieth century, the world community begun to realize that, foundries were emitting pollutants which were affecting the health of humans. In order to overcome this situation, several countries in the world promulgated laws stipulating the maximum level of pollutants that can emit by foundries. These laws affected the functioning and growth of foundries. In order to sustain amidst these constraints, foundries begun to install energy efficient melting technologies and pollution control devices (PCDs). In this back ground, this paper reports to assess the contemporary scenario and project the future needs for sustaining the foundries. During the conduct of this literature review, it was discernable that, research papers have reported three categories of researches. In the first category of research papers, the researches reporting the achievement of cleaner production technologies in foundries using PCDs have appeared. In the second category of research papers, the application of cleaner production technology in foundries located in different countries has been examined. In the third category of research papers, the application of efficient melting technologies and PCDs in different clusters of foundries located in different parts of world has been explored. Subsequently implementation technics of Environmental Management System in cleaner production technics in foundries has been described the analysis of the information and knowledge drawn from these three categories of papers has revealed that, researches exploring the

  13. The Gene Ontology project in 2008

    PubMed Central

    2008-01-01

    The Gene Ontology (GO) project (http://www.geneontology.org/) provides a set of structured, controlled vocabularies for community use in annotating genes, gene products and sequences (also see http://www.sequenceontology.org/). The ontologies have been extended and refined for several biological areas, and improvements to the structure of the ontologies have been implemented. To improve the quantity and quality of gene product annotations available from its public repository, the GO Consortium has launched a focused effort to provide comprehensive and detailed annotation of orthologous genes across a number of ‘reference’ genomes, including human and several key model organisms. Software developments include two releases of the ontology-editing tool OBO-Edit, and improvements to the AmiGO browser interface. PMID:17984083

  14. Alterations of neutrophil functions in foundry and pottery workers.

    PubMed

    Başaran, N; Undeğer, U; Shubair, M

    2002-11-01

    To assess the immune competence of workers occupationally exposed to mainly silica, neutrophil functions such as the chemotactic and oxidative burst activity in foundry and pottery workers were evaluated. The chemotactic activity was examined in 22 foundry and 10 pottery workers and oxidative burst activity of neutrophils were determined in 22 foundry and 6 pottery workers. Healthy subjects of comparable age, sex, and smoking habits and with no history of silica exposure were used as the control groups. Chemotaxis was carried out in Boyden chambers using Zymosan activated serum as chemotactic stimulus. Oxidative burst activity was measured using nitroblue tetrazolium (NBT) dye reduction test. Both neutrophil functions were significantly reduced in silica-exposed foundry and pottery workers (p < 0.001) compared to controls suggesting that human chronic exposure mainly to silica and other chemicals originated from foundry and pottery settings may diminish neutrophil functions in humans. PMID:12510795

  15. Alterations of neutrophil functions in foundry and pottery workers.

    PubMed

    Başaran, N; Undeğer, U; Shubair, M

    2002-11-01

    To assess the immune competence of workers occupationally exposed to mainly silica, neutrophil functions such as the chemotactic and oxidative burst activity in foundry and pottery workers were evaluated. The chemotactic activity was examined in 22 foundry and 10 pottery workers and oxidative burst activity of neutrophils were determined in 22 foundry and 6 pottery workers. Healthy subjects of comparable age, sex, and smoking habits and with no history of silica exposure were used as the control groups. Chemotaxis was carried out in Boyden chambers using Zymosan activated serum as chemotactic stimulus. Oxidative burst activity was measured using nitroblue tetrazolium (NBT) dye reduction test. Both neutrophil functions were significantly reduced in silica-exposed foundry and pottery workers (p < 0.001) compared to controls suggesting that human chronic exposure mainly to silica and other chemicals originated from foundry and pottery settings may diminish neutrophil functions in humans.

  16. The geographical ontology, LDAP, and the space information semantic grid

    NASA Astrophysics Data System (ADS)

    Cui, Wei; Li, Deren

    2005-10-01

    The research purpose is to discuss the development trend and theory of the semantic integration and interoperability of Geography Information Systems on the network ages and to point out that the geography ontology is the foregone conclusion of the development of the semantic-based integration and interoperability of Geography Information Systems. After analyzing the effect by using the various new technologies, the paper proposes new idea for the family of the ontology class based on the GIS knowledge built here. They are the basic ontology, the domain ontology and the application ontology and are very useful for the sharing and transferring of the semantic information between the complicated distributed systems and object abstracting. The main contributions of the paper are as follows: 1) For the first time taking the ontology and LDAP (Lightweight Directory Access Protocol) in creating and optimizing the architecture of Spatial Information Gird and accelerating the fusion of Geography Information System and other domain's information systems. 2) For the first time, introducing a hybrid method to build geography ontology. This hybrid method mixes the excellence of the independent domain expert and data mining. It improves the efficiency of the method of the domain expert and builds ontology semi-automatically. 3) For the first time, implementing the many-to-many relationship of integration ontology system by LDAP's reference and creating ontology-based virtual organization that could provide transparent service to guests.

  17. Best behaviour? Ontologies and the formal description of animal behaviour.

    PubMed

    Gkoutos, Georgios V; Hoehndorf, Robert; Tsaprouni, Loukia; Schofield, Paul N

    2015-10-01

    The development of ontologies for describing animal behaviour has proved to be one of the most difficult of all scientific knowledge domains. Ranging from neurological processes to human emotions, the range and scope needed for such ontologies is highly challenging, but if data integration and computational tools such as automated reasoning are to be fully applied in this important area the underlying principles of these ontologies need to be better established and development needs detailed coordination. Whilst the state of scientific knowledge is always paramount in ontology and formal description framework design, this is a particular problem with neurobehavioural ontologies where our understanding of the relationship between behaviour and its underlying biophysical basis is currently in its infancy. In this commentary, we discuss some of the fundamental problems in designing and using behaviour ontologies, and present some of the best developed tools in this domain.

  18. An Approach to Support Collaborative Ontology Construction.

    PubMed

    Tahar, Kais; Schaaf, Michael; Jahn, Franziska; Kücherer, Christian; Paech, Barbara; Herre, Heinrich; Winter, Alfred

    2016-01-01

    The increasing number of terms used in textbooks for information management (IM) in hospitals makes it difficult for medical informatics students to grasp IM concepts and their interrelations. Formal ontologies which comprehend and represent the essential content of textbooks can facilitate the learning process in IM education. The manual construction of such ontologies is time-consuming and thus very expensive [3]. Moreover, most domain experts lack skills in using a formal language like OWL [2] and usually have no experience with standard editing tools like Protégé http://protege.stanford.edu [4,5]. This paper presents an ontology modeling approach based on Excel2OWL, a self-developed tool which efficiently supports domain experts in collaboratively constructing ontologies from textbooks. This approach was applied to classic IM textbooks, resulting in an ontology called SNIK. Our method facilitates the collaboration between domain experts and ontologists in the development process. Furthermore, the proposed approach enables ontologists to detect modeling errors and also to evaluate and improve the quality of the resulting ontology rapidly. This approach allows us to visualize the modeled textbooks and to analyze their semantics automatically. Hence, it can be used for e-learning purposes, particularly in the field of IM in hospitals.

  19. An Approach to Support Collaborative Ontology Construction.

    PubMed

    Tahar, Kais; Schaaf, Michael; Jahn, Franziska; Kücherer, Christian; Paech, Barbara; Herre, Heinrich; Winter, Alfred

    2016-01-01

    The increasing number of terms used in textbooks for information management (IM) in hospitals makes it difficult for medical informatics students to grasp IM concepts and their interrelations. Formal ontologies which comprehend and represent the essential content of textbooks can facilitate the learning process in IM education. The manual construction of such ontologies is time-consuming and thus very expensive [3]. Moreover, most domain experts lack skills in using a formal language like OWL [2] and usually have no experience with standard editing tools like Protégé http://protege.stanford.edu [4,5]. This paper presents an ontology modeling approach based on Excel2OWL, a self-developed tool which efficiently supports domain experts in collaboratively constructing ontologies from textbooks. This approach was applied to classic IM textbooks, resulting in an ontology called SNIK. Our method facilitates the collaboration between domain experts and ontologists in the development process. Furthermore, the proposed approach enables ontologists to detect modeling errors and also to evaluate and improve the quality of the resulting ontology rapidly. This approach allows us to visualize the modeled textbooks and to analyze their semantics automatically. Hence, it can be used for e-learning purposes, particularly in the field of IM in hospitals. PMID:27577406

  20. Ontologies for Astronomy

    NASA Astrophysics Data System (ADS)

    Lesteven, S.; Derrière, S.; Dubois, P.; Genova, F.; Preite Martinez, A.; Hernandez, N.; Mothe, J.; Napoli, A.; Toussaint, Y.

    2007-10-01

    Ontologies are used in many application domains to organize information and described knowledge. Classifications and thesauri define concepts and relationships in a systematic manner and the ontologies are mainly used due to their ability to specify the semantics and relations between concepts and to express them in a computer understandable language. Astronomers regularly use information networks made up of electronic journal articles, databases and catalog servers. To go further, we are working on the definition of an ontology which would give intelligent access to the heterogeneous astronomical resources. This ontology will be used for different tasks such as intelligent information retrieval based on the content of documents and information manipulation for matching and comparing the content of these astronomical documents.

  1. Evaluation of occupational hazards in foundries.

    PubMed

    Zakaria, Adel M; Noweir, Kamal H; El-Maghrabi, Gamal

    2005-01-01

    The working environment of foundries is hazardous and characterized by multiple simultaneous chemical, physical and mechanical hazards exposure, which would lead to injuries of foundry workers. The aim of the present work is to evaluate occupational hazards in four foundries, two in Alexandria: El Nasr and Ramsis, and two in Behira: Misr Spinning and Weaving and Misr Rayon companies. Levels of total and respirable dust, free silica % in total dust and lead concentration in total and respirable dust; NO2, SO2 and CO concentrations; noise and heat stress levels have been determined in the present work. Occupational injuries data were analyzed in a three years period from 1998 to 2000. The results of the present work revealed; 1. The levels of total dust and respirable dust exceeded the threshold limit values at knockout and cleaning operations at El Nasr Company. 2. Free silica percentage exceeded permissible levels in all operations except pouring in El Nasr Company. 3. CO levels in Misr Spinning and Weaving Company were higher than threshold levels. 4. Noise levels in knockout and cleaning operations at the four companies were exceeding the threshold limit values. 5. Heat stress levels in melting and pouring operations in El Nasr and in pouring operation in Ramsis Company were higher than the maximum permissible levels. 6. The age group 31-40 years has recorded the highest average incidence rate of injuries of age groups (P<0.01). 7. Lower extremities and higher extremities have recorded the highest average incidence rate in the four companies (P<0.001-P<0.01 respectively). 8. Transportation and lifting was the main cause of injury in the four companies (P<0.05). 9. Faulty action and striking against was the main mean of injury in the four companies (P<0.01). 10. Ramsis Company has the highest average incidence rate in almost all injuries parameters and indices (frequency rate and severity rate) (P<0.05-P<0.001). The present work is a massive survey, which

  2. Marine Planning and Service Platform: specific ontology based semantic search engine serving data management and sustainable development

    NASA Astrophysics Data System (ADS)

    Manzella, Giuseppe M. R.; Bartolini, Andrea; Bustaffa, Franco; D'Angelo, Paolo; De Mattei, Maurizio; Frontini, Francesca; Maltese, Maurizio; Medone, Daniele; Monachini, Monica; Novellino, Antonio; Spada, Andrea

    2016-04-01

    The MAPS (Marine Planning and Service Platform) project is aiming at building a computer platform supporting a Marine Information and Knowledge System. One of the main objective of the project is to develop a repository that should gather, classify and structure marine scientific literature and data thus guaranteeing their accessibility to researchers and institutions by means of standard protocols. In oceanography the cost related to data collection is very high and the new paradigm is based on the concept to collect once and re-use many times (for re-analysis, marine environment assessment, studies on trends, etc). This concept requires the access to quality controlled data and to information that is provided in reports (grey literature) and/or in relevant scientific literature. Hence, creation of new technology is needed by integrating several disciplines such as data management, information systems, knowledge management. In one of the most important EC projects on data management, namely SeaDataNet (www.seadatanet.org), an initial example of knowledge management is provided through the Common Data Index, that is providing links to data and (eventually) to papers. There are efforts to develop search engines to find author's contributions to scientific literature or publications. This implies the use of persistent identifiers (such as DOI), as is done in ORCID. However very few efforts are dedicated to link publications to the data cited or used or that can be of importance for the published studies. This is the objective of MAPS. Full-text technologies are often unsuccessful since they assume the presence of specific keywords in the text; in order to fix this problem, the MAPS project suggests to use different semantic technologies for retrieving the text and data and thus getting much more complying results. The main parts of our design of the search engine are: • Syntactic parser - This module is responsible for the extraction of "rich words" from the text

  3. Marine Planning and Service Platform: specific ontology based semantic search engine serving data management and sustainable development

    NASA Astrophysics Data System (ADS)

    Manzella, Giuseppe M. R.; Bartolini, Andrea; Bustaffa, Franco; D'Angelo, Paolo; De Mattei, Maurizio; Frontini, Francesca; Maltese, Maurizio; Medone, Daniele; Monachini, Monica; Novellino, Antonio; Spada, Andrea

    2016-04-01

    The MAPS (Marine Planning and Service Platform) project is aiming at building a computer platform supporting a Marine Information and Knowledge System. One of the main objective of the project is to develop a repository that should gather, classify and structure marine scientific literature and data thus guaranteeing their accessibility to researchers and institutions by means of standard protocols. In oceanography the cost related to data collection is very high and the new paradigm is based on the concept to collect once and re-use many times (for re-analysis, marine environment assessment, studies on trends, etc). This concept requires the access to quality controlled data and to information that is provided in reports (grey literature) and/or in relevant scientific literature. Hence, creation of new technology is needed by integrating several disciplines such as data management, information systems, knowledge management. In one of the most important EC projects on data management, namely SeaDataNet (www.seadatanet.org), an initial example of knowledge management is provided through the Common Data Index, that is providing links to data and (eventually) to papers. There are efforts to develop search engines to find author's contributions to scientific literature or publications. This implies the use of persistent identifiers (such as DOI), as is done in ORCID. However very few efforts are dedicated to link publications to the data cited or used or that can be of importance for the published studies. This is the objective of MAPS. Full-text technologies are often unsuccessful since they assume the presence of specific keywords in the text; in order to fix this problem, the MAPS project suggests to use different semantic technologies for retrieving the text and data and thus getting much more complying results. The main parts of our design of the search engine are: • Syntactic parser - This module is responsible for the extraction of "rich words" from the text

  4. Determining Fitness-For-Use of Ontologies Through Change Management, Versioning and Publication Best Practices

    NASA Astrophysics Data System (ADS)

    West, P.; Zednik, S.; Fu, L.; Ma, X.; Fox, P. A.

    2015-12-01

    There is a large and growing number of domain ontologies available for researchers to leverage in their applications. When evaluating the use of an ontology it is important to not only consider whether the concepts and relationships defined in the ontology meet the requirements for purpose of use, but also how the change management, versioning and publication practices followed by the ontology publishers affect the maturity, stability, and long-term fitness-for-use of the ontology. In this presentation we share our experiences and a list of best practices we have developed when determining fitness for use of existing ontologies, and the process we follow when developing of our own ontologies and extensions to existing ontologies. Our experience covers domains such as solar terrestrial physics, geophysics and oceanography; and the use of general purpose ontologies such as those with representations of people, organizations, data catalogs, observations and measurements and provenance. We will cover how we determine ontology scope, manage ontology change, specify ontology version, and what best practices we follow for ontology publication and use. The implications of following these best practices is that the ontologies we use and develop are mature, stable, have a well-defined scope, and are published in accordance with linked data principles.

  5. GFVO: the Genomic Feature and Variation Ontology.

    PubMed

    Baran, Joachim; Durgahee, Bibi Sehnaaz Begum; Eilbeck, Karen; Antezana, Erick; Hoehndorf, Robert; Dumontier, Michel

    2015-01-01

    Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology's GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use.

  6. GFVO: the Genomic Feature and Variation Ontology.

    PubMed

    Baran, Joachim; Durgahee, Bibi Sehnaaz Begum; Eilbeck, Karen; Antezana, Erick; Hoehndorf, Robert; Dumontier, Michel

    2015-01-01

    Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology's GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use. PMID:26019997

  7. Ontological Modeling for Integrated Spacecraft Analysis

    NASA Technical Reports Server (NTRS)

    Wicks, Erica

    2011-01-01

    Current spacecraft work as a cooperative group of a number of subsystems. Each of these requiresmodeling software for development, testing, and prediction. It is the goal of my team to create anoverarching software architecture called the Integrated Spacecraft Analysis (ISCA) to aid in deploying the discrete subsystems' models. Such a plan has been attempted in the past, and has failed due to the excessive scope of the project. Our goal in this version of ISCA is to use new resources to reduce the scope of the project, including using ontological models to help link the internal interfaces of subsystems' models with the ISCA architecture.I have created an ontology of functions specific to the modeling system of the navigation system of a spacecraft. The resulting ontology not only links, at an architectural level, language specificinstantiations of the modeling system's code, but also is web-viewable and can act as a documentation standard. This ontology is proof of the concept that ontological modeling can aid in the integration necessary for ISCA to work, and can act as the prototype for future ISCA ontologies.

  8. AmiGO: online access to ontology and annotation data

    SciTech Connect

    Carbon, Seth; Ireland, Amelia; Mungall, Christopher J.; Shu, ShengQiang; Marshall, Brad; Lewis, Suzanna

    2009-01-15

    AmiGO is a web application that allows users to query, browse, and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium; it can also be downloaded and installed to browse local ontologies and annotations. AmiGO is free open source software developed and maintained by the GO Consortium.

  9. Towards a core ontology for integrating ecological and environmental ontologies to enable improved data interoperability

    NASA Astrophysics Data System (ADS)

    Bowers, S.; Madin, J.; Jones, M.; Schildhauer, M.; Ludaescher, B.

    2007-12-01

    Research in the ecological and environmental sciences increasingly relies on the integration of traditionally small, focused studies to form larger datasets for synthetic analyses. However, a broad range of data types, structures, and semantic subtleties occur in ecological data, making data discovery and integration a difficult and time-consuming task. Our work focuses on capturing the subtleties of scientific data through semantic annotations, which involve linking ecological data to concepts and relationships in domain-specific ontologies, thereby enabling more advanced forms of data discovery and integration. A variety of ontologies related to ecological data are actively being developed, ranging from low-level and highly focused vocabularies to high-level models and classifications. However, as the number of ontologies and their included terms increase, organizing these into a coherent framework useful for data annotation becomes increasingly complex (we note that similar issues have been recognized within the molecular biology and bioinformatics communities). We describe a core ontology model for semantic annotation that provides a structured approach for integrating the growing number of ecology-relevant ontologies. The ontology defines the notion of "scientific observation" as a unifying concept for capturing the basic semantics of ecological data. Observations are distinguished at the level of the entity (e.g., location, time, thing, concept), and characteristics of an entity (e.g., height, name, color) are measured (named or classified) as data. The ontology permits observations to be related via context (such as spatial or temporal containment), further supporting the discovery and automated comparison and alignment (e.g., merging) of heterogeneous data. The core ontology also defines a set of extension points that can be used to either directly build new domain ontologies (as extension ontologies), or to provide a common basis to which existing

  10. Environmental behaviour of stabilised foundry sludge.

    PubMed

    Coz, Alberto; Andrés, Ana; Soriano, Sonia; Irabien, Angel

    2004-06-18

    Environmental characterisation of foundry sludge (FS) and the stabilised/solidified (S/S) derived products has been performed according to the leaching behaviour. Portland cement and lime have been used as binders and foundry sand fines, activated carbon and black carbon have been used as additives in the S/S processes. The results of the characterisation show that the behaviour of the waste in acid media is mainly influenced by the inorganic components of the waste, while the organic matter only has an influence in the redox potential of the leachates. Due to the complexity of the waste, a computer modelling of equilibrium (MINTEQ) has been used in order to compare the experimental extractability with the simulated curves of the metallic species. The zinc content in the leachate is close related to the theoretical curves in the waste and all S/S products, while the rest of the metals do not show a coherent behaviour with the hydroxides evolution. The results of compliance testing allow to obtain the best S/S formulations using activated and black carbon as sorbents. The comparison between different leaching procedures leads to equivalent results depending only on the pH. PMID:15177750

  11. New EUROPRACTICE microsystem design and foundry services

    NASA Astrophysics Data System (ADS)

    Salomon, Patric R.; Beernaert, Dirk; Turner, Rob

    2000-08-01

    The microsystems market for MST is predicted to grow to 38 billion dollars by the year 2002, with systems containing these components generating even higher revenues and growth. One of the barriers to successful exploitation of this technology has been the lack of access to industrial foundries capable of producing certified microsystems devices in commercial quantities. To overcome this problem, the European Commission has started the EUROPRACTICE program in 1996 with the installation of manufacturing clusters and demonstration activities to provide access to microsystems foundry services for European small and medium sized companies (SMEs). Since 1996, there has been a shift form providing 'broad technology offers' and 'raising awareness fro microsystem capabilities' to 'direct support of design needs' and 'focused services' which allow SMEs to use even complex microsystems technologies to implement their products, The third phase of EUROPRACTICE has just been launched, and contains 5 Manufacturing Clusters, 12 Designs Houses, and 7 Competence Centers, each working in different application/technology areas. The EUROPRACTICE program will be presented together with a detail description of the capabilities of the participants and information on how to access their services.

  12. A framework for lipoprotein ontology.

    PubMed

    Chen, Meifania; Hadzic, Maja

    2011-01-01

    Clinical and epidemiological studies have established a significant correlation between abnormal plasma lipoprotein levels and cardiovascular disease, which remains the leading cause of mortality in the world today. In addition, lipoprotein dysregulation, known as dyslipidemia, is a central feature in disease states, such as diabetes and hypertension, which increases the risk of cardiovascular disease. While a corpus of literature exists on different areas of lipoprotein research, one of the major challenges that researchers face is the difficulties in accessing and integrating relevant information amidst massive quantities of heterogeneous data. Semantic web technologies, specifically ontologies, target these problems by providing an organizational framework of the concepts involved in a system of related instances to support systematic querying of information. In this paper, we identify issues within the lipoprotein research domain and present a preliminary framework for Lipoprotein Ontology, which consists of five specific areas of lipoprotein research: Classification, Metabolism, Pathophysiology, Etiology, and Treatment. By integrating specific aspects of lipoprotein research, Lipoprotein Ontology will provide the basis for the design of various applications to enable interoperability between research groups or software agents, as well as the development of tools for the diagnosis and treatment of dyslipidemia.

  13. The cognitive paradigm ontology: design and application.

    PubMed

    Turner, Jessica A; Laird, Angela R

    2012-01-01

    We present the basic structure of the Cognitive Paradigm Ontology (CogPO) for human behavioral experiments. While the experimental psychology and cognitive neuroscience literature may refer to certain behavioral tasks by name (e.g., the Stroop paradigm or the Sternberg paradigm) or by function (a working memory task, a visual attention task), these paradigms can vary tremendously in the stimuli that are presented to the subject, the response expected from the subject, and the instructions given to the subject. Drawing from the taxonomy developed and used by the BrainMap project ( www.brainmap.org ) for almost two decades to describe key components of published functional imaging results, we have developed an ontology capable of representing certain characteristics of the cognitive paradigms used in the fMRI and PET literature. The Cognitive Paradigm Ontology is being developed to be compliant with the Basic Formal Ontology (BFO), and to harmonize where possible with larger ontologies such as RadLex, NeuroLex, or the Ontology of Biomedical Investigations (OBI). The key components of CogPO include the representation of experimental conditions focused on the stimuli presented, the instructions given, and the responses requested. The use of alternate and even competitive terminologies can often impede scientific discoveries. Categorization of paradigms according to stimulus, response, and instruction has been shown to allow advanced data retrieval techniques by searching for similarities and contrasts across multiple paradigm levels. The goal of CogPO is to develop, evaluate, and distribute a domain ontology of cognitive paradigms for application and use in the functional neuroimaging community.

  14. Mappings of MDA-Based Languages and Ontologies

    NASA Astrophysics Data System (ADS)

    Gaševic, Dragan; Djuric, Dragan; Devedžic, Vladan

    The MOF-based ontology metamodels of ontology languages presented in this book, namely the ODM and the Ontology UML Profile (OUP), are defined in the context of the MDA’s metamodeling architecture. However, such a definition is not sufficient; they need to interact with real-word ontologies, for example with OWL ontologies. It is obvious that we need to develop transformations to support conversions between MDA ontology languages and OWL. The current ODM specification itself provides a solution to this problem by defining the QVT transformations among the defined metamodels in the specification. In this chapter, we analyze the problem of transformations in terms of the modeling and technical spaces that we described earlier in the book (see Chap. 5).

  15. Enabling Ontology Based Semantic Queries in Biomedical Database Systems.

    PubMed

    Zheng, Shuai; Wang, Fusheng; Lu, James; Saltz, Joel

    2012-01-01

    While current biomedical ontology repositories offer primitive query capabilities, it is difficult or cumbersome to support ontology based semantic queries directly in semantically annotated biomedical databases. The problem may be largely attributed to the mismatch between the models of the ontologies and the databases, and the mismatch between the query interfaces of the two systems. To fully realize semantic query capabilities based on ontologies, we develop a system DBOntoLink to provide unified semantic query interfaces by extending database query languages. With DBOntoLink, semantic queries can be directly and naturally specified as extended functions of the database query languages without any programming needed. DBOntoLink is adaptable to different ontologies through customizations and supports major biomedical ontologies hosted at the NCBO BioPortal. We demonstrate the use of DBOntoLink in a real world biomedical database with semantically annotated medical image annotations. PMID:23404054

  16. A 2013 workshop: vaccine and drug ontology studies (VDOS 2013)

    PubMed Central

    2014-01-01

    The 2013 “Vaccine and Drug Ontology Studies” (VDOS 2013) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have contributed to dramatic improvements in public health worldwide. Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugs – extending existing clinical terminology systems such as SNOMED, RxNorm, NDF-RT, and MedDRA, as well as developing new models such as Vaccine Ontology. The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs and vaccines, their administration, host immune responses, adverse events, and other related topics. The six full-length papers included in this thematic issue focuses on three main areas: (i) ontology development and representation, (ii) ontology mapping, maintaining and auditing, and (iii) ontology applications. PMID:24650607

  17. Toward a general ontology for digital forensic disciplines.

    PubMed

    Karie, Nickson M; Venter, Hein S

    2014-09-01

    Ontologies are widely used in different disciplines as a technique for representing and reasoning about domain knowledge. However, despite the widespread ontology-related research activities and applications in different disciplines, the development of ontologies and ontology research activities is still wanting in digital forensics. This paper therefore presents the case for establishing an ontology for digital forensic disciplines. Such an ontology would enable better categorization of the digital forensic disciplines, as well as assist in the development of methodologies and specifications that can offer direction in different areas of digital forensics. This includes such areas as professional specialization, certifications, development of digital forensic tools, curricula, and educational materials. In addition, the ontology presented in this paper can be used, for example, to better organize the digital forensic domain knowledge and explicitly describe the discipline's semantics in a common way. Finally, this paper is meant to spark discussions and further research on an internationally agreed ontological distinction of the digital forensic disciplines. Digital forensic disciplines ontology is a novel approach toward organizing the digital forensic domain knowledge and constitutes the main contribution of this paper.

  18. Design process optimization, virtual prototyping of manufacturing, and foundry-portable DFM (Invited Paper)

    NASA Astrophysics Data System (ADS)

    Hogan, James; Progler, Christopher; Chatila, Ahmad; Bruggeman, Bert; Heins, Mitchell; Pack, Robert; Boksha, Victor

    2005-05-01

    We consider modern design for manufacturing (DFM) as a manifestation of IC industry re-integration and intensive cost management dynamics. In that regard DFM is somewhat different from so-called design for yield (DFY) which essentially focuses on productivity (yield) management (that is not to say that DFM and DFY do not have significant overlaps and interactions). We clearly see the shaping of a new "full-chip DFM" infrastructure on the background of the "back to basics" design-manufacturing re-integration dynamics. In the presented work we are focusing on required DFM-efficiencies in a "foundry-fabless" link. Concepts of "virtual prototyping of manufacturing", "design process optimization", and "foundry-portable DFM" models are explored. Both senior management of the industry and leading design groups finally realize the need for a radical change of design styles. Some of the DFM super-goals are to isolate designers from process details and to make designs foundry portable. It requires qualification of designs at different foundries. In their turn, foundries specified and are implementing a set of DFM rules: "action-required", "recommended", and "guidelines" while asking designers to provide netlist and testing information. Also, we observe strong signs of innovation coming back to the mask industry. Powerful solutions are emerging and shaping up toward mask-centered IP as a business. While it seems that pure-play foundries have found their place for now in the "IDM+" model (supporting manufacturing capacity of IDMs) it is not obvious how sustainable the model is. Wafer as a production unit is not sufficient anymore; foundries are being asked by large customers to price products in terms of good die. It brings back the notion of the old ASIC business model where the foundry is responsible for dealing with both random and systematic yield issues for a given design. One scenario of future development would be that some of the leading foundries might eventually

  19. Application of Ontologies for Big Earth Data

    NASA Astrophysics Data System (ADS)

    Huang, T.; Chang, G.; Armstrong, E. M.; Boening, C.

    2014-12-01

    Connected data is smarter data! Earth Science research infrastructure must do more than just being able to support temporal, geospatial discovery of satellite data. As the Earth Science data archives continue to expand across NASA data centers, the research communities are demanding smarter data services. A successful research infrastructure must be able to present researchers the complete picture, that is, datasets with linked citations, related interdisciplinary data, imageries, current events, social media discussions, and scientific data tools that are relevant to the particular dataset. The popular Semantic Web for Earth and Environmental Terminology (SWEET) ontologies is a collection of ontologies and concepts designed to improve discovery and application of Earth Science data. The SWEET ontologies collection was initially developed to capture the relationships between keywords in the NASA Global Change Master Directory (GCMD). Over the years this popular ontologies collection has expanded to cover over 200 ontologies and 6000 concepts to enable scalable classification of Earth system science concepts and Space science. This presentation discusses the semantic web technologies as the enabling technology for data-intensive science. We will discuss the application of the SWEET ontologies as a critical component in knowledge-driven research infrastructure for some of the recent projects, which include the DARPA Ontological System for Context Artifact and Resources (OSCAR), 2013 NASA ACCESS Virtual Quality Screening Service (VQSS), and the 2013 NASA Sea Level Change Portal (SLCP) projects. The presentation will also discuss the benefits in using semantic web technologies in developing research infrastructure for Big Earth Science Data in an attempt to "accommodate all domains and provide the necessary glue for information to be cross-linked, correlated, and discovered in a semantically rich manner." [1] [1] Savas Parastatidis: A platform for all that we know

  20. Mechanisms in biomedical ontology

    PubMed Central

    2012-01-01

    The concept of a mechanism has become a standard proposal for explanations in biology. It has been claimed that mechanistic explanations are appropriate for systems biology, because they occupy a middle ground between strict reductionism and holism. Because of their importance in the field a formal ontological description of mechanisms is desirable. The standard philosophical accounts of mechanisms are often ambiguous and lack the clarity that can be provided by a formal-ontological framework. The goal of this paper is to clarify some of these ambiguities and suggest such a framework for mechanisms. Taking some hints from an "ontology of devices" I suggest as a general approach for this task the introduction of functional kinds and functional parts by which the particular relations between a mechanism and its components can be captured. PMID:23046727

  1. Ontology-Driven Information Integration

    NASA Technical Reports Server (NTRS)

    Tissot, Florence; Menzel, Chris

    2005-01-01

    Ontology-driven information integration (ODII) is a method of computerized, automated sharing of information among specialists who have expertise in different domains and who are members of subdivisions of a large, complex enterprise (e.g., an engineering project, a government agency, or a business). In ODII, one uses rigorous mathematical techniques to develop computational models of engineering and/or business information and processes. These models are then used to develop software tools that support the reliable processing and exchange of information among the subdivisions of this enterprise or between this enterprise and other enterprises.

  2. An Approach to Folksonomy-Based Ontology Maintenance for Learning Environments

    ERIC Educational Resources Information Center

    Gasevic, D.; Zouaq, Amal; Torniai, Carlo; Jovanovic, J.; Hatala, Marek

    2011-01-01

    Recent research in learning technologies has demonstrated many promising contributions from the use of ontologies and semantic web technologies for the development of advanced learning environments. In spite of those benefits, ontology development and maintenance remain the key research challenges to be solved before ontology-enhanced learning…

  3. IMGT-ONTOLOGY 2012.

    PubMed

    Giudicelli, Véronique; Lefranc, Marie-Paule

    2012-01-01

    Immunogenetics is the science that studies the genetics of the immune system and immune responses. Owing to the complexity and diversity of the immune repertoire, immunogenetics represents one of the greatest challenges for data interpretation: a large biological expertise, a considerable effort of standardization and the elaboration of an efficient system for the management of the related knowledge were required. IMGT®, the international ImMunoGeneTics information system® (http://www.imgt.org) has reached that goal through the building of a unique ontology, IMGT-ONTOLOGY, which represents the first ontology for the formal representation of knowledge in immunogenetics and immunoinformatics. IMGT-ONTOLOGY manages the immunogenetics knowledge through diverse facets that rely on the seven axioms of the Formal IMGT-ONTOLOGY or IMGT-Kaleidoscope: "IDENTIFICATION," "DESCRIPTION," "CLASSIFICATION," "NUMEROTATION," "LOCALIZATION," "ORIENTATION," and "OBTENTION." The concepts of identification, description, classification, and numerotation generated from the axioms led to the elaboration of the IMGT(®) standards that constitute the IMGT Scientific chart: IMGT®standardized keywords (concepts of identification), IMGT® standardized labels (concepts of description), IMGT® standardized gene and allele nomenclature (concepts of classification) and IMGT unique numbering and IMGT Collier de Perles (concepts of numerotation). IMGT-ONTOLOGY has become the global reference in immunogenetics and immunoinformatics for the knowledge representation of immunoglobulins (IG) or antibodies, T cell receptors (TR), and major histocompatibility (MH) proteins of humans and other vertebrates, proteins of the immunoglobulin superfamily (IgSF) and MH superfamily (MhSF), related proteins of the immune system (RPI) of vertebrates and invertebrates, therapeutic monoclonal antibodies (mAbs), fusion proteins for immune applications (FPIA), and composite proteins for clinical applications (CPCA).

  4. Ontology and medical diagnosis.

    PubMed

    Bertaud-Gounot, Valérie; Duvauferrier, Régis; Burgun, Anita

    2012-03-01

    Ontology and associated generic tools are appropriate for knowledge modeling and reasoning, but most of the time, disease definitions in existing description logic (DL) ontology are not sufficient to classify patient's characteristics under a particular disease because they do not formalize operational definitions of diseases (association of signs and symptoms=diagnostic criteria). The main objective of this study is to propose an ontological representation which takes into account the diagnostic criteria on which specific patient conditions may be classified under a specific disease. This method needs as a prerequisite a clear list of necessary and sufficient diagnostic criteria as defined for lots of diseases by learned societies. It does not include probability/uncertainty which Web Ontology Language (OWL 2.0) cannot handle. We illustrate it with spondyloarthritis (SpA). Ontology has been designed in Protégé 4.1 OWL-DL2.0. Several kinds of criteria were formalized: (1) mandatory criteria, (2) picking two criteria among several diagnostic criteria, (3) numeric criteria. Thirty real patient cases were successfully classified with the reasoner. This study shows that it is possible to represent operational definitions of diseases with OWL and successfully classify real patient cases. Representing diagnostic criteria as descriptive knowledge (instead of rules in Semantic Web Rule Language or Prolog) allows us to take advantage of tools already available for OWL. While we focused on Assessment of SpondyloArthritis international Society SpA criteria, we believe that many of the representation issues addressed here are relevant to using OWL-DL for operational definition of other diseases in ontology.

  5. On the Ontology Based Representation of Cell Lines

    PubMed Central

    Ganzinger, Matthias; He, Shan; Breuhahn, Kai; Knaup, Petra

    2012-01-01

    Cell lines are frequently used as highly standardized and reproducible in vitro models for biomedical analyses and assays. Cell lines are distributed by cell banks that operate databases describing their products. However, the description of the cell lines' properties are not standardized across different cell banks. Existing cell line-related ontologies mostly focus on the description of the cell lines' names, but do not cover aspects like the origin or optimal growth conditions. The objective of this work is to develop an ontology that allows for a more comprehensive description of cell lines and their metadata, which should cover the data elements provided by cell banks. This will provide the basis for the standardized annotation of cell lines and corresponding assays in biomedical research. In addition, the ontology will be the foundation for automated evaluation of such assays and their respective protocols in the future. To accomplish this, a broad range of cell bank databases as well as existing ontologies were analyzed in a comprehensive manner. We identified existing ontologies capable of covering different aspects of the cell line domain. However, not all data fields derived from the cell banks' databases could be mapped to existing ontologies. As a result, we created a new ontology called cell culture ontology (CCONT) integrating existing ontologies where possible. CCONT provides classes from the areas of cell line identification, origin, cell line properties, propagation and tests performed. PMID:23144907

  6. A tuberculosis ontology for host systems biology.

    PubMed

    Levine, David M; Dutta, Noton K; Eckels, Josh; Scanga, Charles; Stein, Catherine; Mehra, Smriti; Kaushal, Deepak; Karakousis, Petros C; Salamon, Hugh

    2015-09-01

    A major hurdle facing tuberculosis (TB) investigators who want to utilize a rapidly growing body of data from both systems biology approaches and omics technologies is the lack of a standard vocabulary for data annotation and reporting. Lacking a means to readily compare samples from different research groups, a significant quantity of potentially informative data is largely ignored by researchers. To facilitate standardizing data across studies, a simple ontology of TB terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address animal models and experimental systems, and existing clinically focused terminology was modified and adapted. This ontology can be used to annotate host TB data in public databases and collaborations, thereby standardizing database searches and allowing researchers to more easily compare results. To demonstrate the utility of a standard TB ontology for host systems biology, a web application was developed to annotate and compare human and animal model gene expression data sets.

  7. A Tuberculosis Ontology for Host Systems Biology

    PubMed Central

    Levine, David M.; Dutta, Noton K.; Eckels, Josh; Scanga, Charles; Stein, Catherine; Mehra, Smriti; Kaushal, Deepak; Karakousis, Petros C.; Salamon, Hugh

    2015-01-01

    Summary A major hurdle facing tuberculosis (TB) investigators who want to utilize a rapidly growing body of data from both systems biology approaches and omics technologies is the lack of a standard vocabulary for data annotation and reporting. Lacking a means to readily compare samples from different research groups, a significant quantity of potentially informative data is largely ignored by researchers. To facilitate standardizing data across studies, a simple ontology of TB terms was developed to provide a common vocabulary for annotating data sets. New terminology was developed to address animal models and experimental systems, and existing clinically focused terminology was modified and adapted. This ontology can be used to annotate host TB data in public databases and collaborations, thereby standardizing database searches and allowing researchers to more easily compare results. To demonstrate the utility of a standard TB ontology for host systems biology, a web application was developed to annotate and compare human and animal model gene expression data sets. PMID:26190839

  8. Ion traps fabricated in a CMOS foundry

    SciTech Connect

    Mehta, K. K.; Ram, R. J.; Eltony, A. M.; Chuang, I. L.; Bruzewicz, C. D.; Sage, J. M. Chiaverini, J.

    2014-07-28

    We demonstrate trapping in a surface-electrode ion trap fabricated in a 90-nm CMOS (complementary metal-oxide-semiconductor) foundry process utilizing the top metal layer of the process for the trap electrodes. The process includes doped active regions and metal interconnect layers, allowing for co-fabrication of standard CMOS circuitry as well as devices for optical control and measurement. With one of the interconnect layers defining a ground plane between the trap electrode layer and the p-type doped silicon substrate, ion loading is robust and trapping is stable. We measure a motional heating rate comparable to those seen in surface-electrode traps of similar size. This demonstration of scalable quantum computing hardware utilizing a commercial CMOS process opens the door to integration and co-fabrication of electronics and photonics for large-scale quantum processing in trapped-ion arrays.

  9. 13. TOOL ROOM SHOWING W. ROBERTSON MACHINE & FOUNDRY CO. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    13. TOOL ROOM SHOWING W. ROBERTSON MACHINE & FOUNDRY CO. NO. 5 POWER HACKSAW (FOREGROUND) AND WELLS METAL BAND SAW (BACKGROUND). VIEW SOUTHEAST - Oldman Boiler Works, Office/Machine Shop, 32 Illinois Street, Buffalo, Erie County, NY

  10. 7. BUILDING 40. MUSEUM, LIBRARY, PRINTING SHOP, FOUNDRY, VACUUM HEATING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    7. BUILDING 40. MUSEUM, LIBRARY, PRINTING SHOP, FOUNDRY, VACUUM HEATING SYSTEM. July 31, 1916. - Frankford Arsenal, Building No. 40, South of Tacony Street between Bridge Street & tracks of former Pennsylvania Railroad, Philadelphia, Philadelphia County, PA

  11. 28. VIEW OF FOUNDRY SAND BLASTING AND CLEANING BUILDING UNDER ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    28. VIEW OF FOUNDRY SAND BLASTING AND CLEANING BUILDING UNDER DEMOLITION. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  12. 29. DETAIL VIEW OF FOUNDRY SAND BLASTING AND CLEANING BUILDING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    29. DETAIL VIEW OF FOUNDRY SAND BLASTING AND CLEANING BUILDING UNDER DEMOLITION. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  13. 32. VIEW OF DEMOLISHED FOUNDRY SAND BLASTING AND CLEANING BUILDING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    32. VIEW OF DEMOLISHED FOUNDRY SAND BLASTING AND CLEANING BUILDING AFTER DUST HAS SETTLED. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  14. 65. VIEW OF IRON FOUNDRY FROM CORNER OF CAREY AND ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    65. VIEW OF IRON FOUNDRY FROM CORNER OF CAREY AND PRATT STREETS LOOKING SOUTHEAST - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  15. FOUNDRY LANDSCAPE LOOKING WESTNORTHWEST FROM MALLEABLE STOCK YARD CRANE, SHOWING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    FOUNDRY LANDSCAPE LOOKING WEST-NORTHWEST FROM MALLEABLE STOCK YARD CRANE, SHOWING CRANE MOTOR AND MALLEABLE CUPOLAS WITH OPEN TOPS AND EMISSION RECOVERY DUCTS. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  16. FOUNDRY LANDSCAPE LOOKING WESTSOUTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    FOUNDRY LANDSCAPE LOOKING WEST-SOUTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING SHED ROOF OF OLD MALLEABLE CUPOLA CHARGER. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  17. FOUNDRY LANDSCAPE LOOKING SOUTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    FOUNDRY LANDSCAPE LOOKING SOUTHWEST FROM MALLEABLE STOCK YARD CRANE SHOWING CRANE RAILS, GREY IRON CUPOLA AND EMISSION RECOVERY SYSTEM. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  18. SCRAP STEEL AND FOUNDRY SCRAP IRON, USED AS THE PRIMARY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    SCRAP STEEL AND FOUNDRY SCRAP IRON, USED AS THE PRIMARY METAL SOURCES, ARE STORED IN THESE BINS AND LIFTED TO SCALES BY AN ELECTRIC MAGNET. - Southern Ductile Casting Company, Melting, 2217 Carolina Avenue, Bessemer, Jefferson County, AL

  19. 10. VIEW OF DEPLETED URANIUM INGOT AND MOLD IN FOUNDRY. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    10. VIEW OF DEPLETED URANIUM INGOT AND MOLD IN FOUNDRY. (11/11/56) - Rocky Flats Plant, Non-Nuclear Production Facility, South of Cottonwood Avenue, west of Seventh Avenue & east of Building 460, Golden, Jefferson County, CO

  20. Evaluation of occupational exposure to free silica in Alberta foundries.

    PubMed

    Ayalp, A; Myroniuk, D

    1982-11-01

    The Occupational Hygiene Branch of Alberta Workers' Health, Safety and Compensation conducted a comprehensive study of the foundry industry in Alberta. The surveys assessed both the degree of health hazards present and the effectiveness of existing control systems for airborne contaminants. All nine of Alberta's ferrous foundries were surveyed in the course of the project. The foundries varied from those which were small with limited mechanization to those which were large and highly automated. The concentrations of free silica in the work environment are correlated to the different attempts to control silica using substitution and various ventilation systems. The particular foundry processes evaluated for airborne free silica were sand preparation, shakeout, dry sand transport and sand molding. Workers' exposure to free airborne silica was evaluated by personal and area samples. The free silica content of the samples was determined by infra-red spectrophotometry. The results indicated most control systems were inadequate. Effective control methods are described to reduce the health hazard.

  1. Process attributes in bio-ontologies

    PubMed Central

    2012-01-01

    Background Biomedical processes can provide essential information about the (mal-) functioning of an organism and are thus frequently represented in biomedical terminologies and ontologies, including the GO Biological Process branch. These processes often need to be described and categorised in terms of their attributes, such as rates or regularities. The adequate representation of such process attributes has been a contentious issue in bio-ontologies recently; and domain ontologies have correspondingly developed ad hoc workarounds that compromise interoperability and logical consistency. Results We present a design pattern for the representation of process attributes that is compatible with upper ontology frameworks such as BFO and BioTop. Our solution rests on two key tenets: firstly, that many of the sorts of process attributes which are biomedically interesting can be characterised by the ways that repeated parts of such processes constitute, in combination, an overall process; secondly, that entities for which a full logical definition can be assigned do not need to be treated as primitive within a formal ontology framework. We apply this approach to the challenge of modelling and automatically classifying examples of normal and abnormal rates and patterns of heart beating processes, and discuss the expressivity required in the underlying ontology representation language. We provide full definitions for process attributes at increasing levels of domain complexity. Conclusions We show that a logical definition of process attributes is feasible, though limited by the expressivity of DL languages so that the creation of primitives is still necessary. This finding may endorse current formal upper-ontology frameworks as a way of ensuring consistency, interoperability and clarity. PMID:22928880

  2. GFVO: the Genomic Feature and Variation Ontology

    PubMed Central

    Durgahee, Bibi Sehnaaz Begum; Eilbeck, Karen; Antezana, Erick; Hoehndorf, Robert; Dumontier, Michel

    2015-01-01

    Falling costs in genomic laboratory experiments have led to a steady increase of genomic feature and variation data. Multiple genomic data formats exist for sharing these data, and whilst they are similar, they are addressing slightly different data viewpoints and are consequently not fully compatible with each other. The fragmentation of data format specifications makes it hard to integrate and interpret data for further analysis with information from multiple data providers. As a solution, a new ontology is presented here for annotating and representing genomic feature and variation dataset contents. The Genomic Feature and Variation Ontology (GFVO) specifically addresses genomic data as it is regularly shared using the GFF3 (incl. FASTA), GTF, GVF and VCF file formats. GFVO simplifies data integration and enables linking of genomic annotations across datasets through common semantics of genomic types and relations. Availability and implementation. The latest stable release of the ontology is available via its base URI; previous and development versions are available at the ontology’s GitHub repository: https://github.com/BioInterchange/Ontologies; versions of the ontology are indexed through BioPortal (without external class-/property-equivalences due to BioPortal release 4.10 limitations); examples and reference documentation is provided on a separate web-page: http://www.biointerchange.org/ontologies.html. GFVO version 1.0.2 is licensed under the CC0 1.0 Universal license (https://creativecommons.org/publicdomain/zero/1.0) and therefore de facto within the public domain; the ontology can be appropriated without attribution for commercial and non-commercial use. PMID:26019997

  3. 29. DEPENDABLE FORDATHSHELL CORE MACHINES IN THE GREY IRON FOUNDRY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    29. DEPENDABLE FORDATH-SHELL CORE MACHINES IN THE GREY IRON FOUNDRY INJECTS SAND INTO A CLOSED CORE BOX. SOME OF THE UNITS HEAT THE CORE BOX TO FIX THE RESINS AS THE CORE REMAINS IN THE BOX, OTHERS MERELY SHAPED THE CORE SAND REQUIRING BAKING OF THE CORES TO HARDEN THEM. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  4. Measuring Hydraulic Properties of Soil-Foundry Sand Mixtures

    NASA Astrophysics Data System (ADS)

    Shouse, P. J.; Dungan, R. S.; Dees, N.; Fargerlund, J.

    2005-12-01

    The foundry industry produces clay coated sand particles that have potential to affect soil water retention and conductivity if mixed with soils at the proper ratio. The purpose of our study was to determine the effects of mixing foundry sand on increasing the saturated hydraulic conductivity of slowly permeable soils. Our methods included mixing Walla-Walla silt loam soil with increasing volumes of foundry sand from 0% to 100%. We then used several packing methods to determine the optimum bulk density for our automated retention and outflow experiments. To increase the range of the retention function, we also measured soil water retention using pressure plates at pressures between 1000 and 15000 cm pressure head. We measured saturated hydraulic conductivity using the constant head method and a single blind approach (the Ksat was measured in two labs, one had knowledge of the mixtures and one had no knowledge of the mixtures). The single blind approach was used to reduce the chance of bias in measuring Ksat and water retention. Our results for the saturated hydraulic conductivity did indicate that additions of foundry sand had a limited effect on Ksat until a critical level of sand was added to the mixture. The retention function was similarly affected by increasing volumes of foundry sand. The rankings of the Ksat measurements between the labs was constant, but the values obtained did differ (some significantly). For the Walla-Walla soil, additions of foundry sands exceeding 40% were needed to affect the measured Ksat and retention function. At these large volumes of foundry sands, it may be more appropriate to use the sands for new installations of turf grass such as athletic fields, and/or golf greens. We are continuing to study the characteristics of different foundry sands and quantifying their effects on the hydraulic properties of clay soils.

  5. Interior of rail mill, now an iron foundry; The submarine ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Interior of rail mill, now an iron foundry; The submarine car in the distance is filled with molten iron that will be poured into a ladle which will, in turn, be poured into the molds lining the center of the building - Bethlehem Steel Corporation, South Bethlehem Works, Iron Foundry, Along Lehigh River, North of Fourth Street, West of Minsi Trail Bridge, Bethlehem, Northampton County, PA

  6. A RESTful way to Manage Ontologies

    NASA Astrophysics Data System (ADS)

    Lowry, R. K.; Lawrence, B. N.

    2009-04-01

    In 2005 BODC implemented the first version of a vocabulary server developed as a contribution to the NERC DataGrid project. Vocabularies were managed within an RDBMS environment and accessed through a SOAP Web Service API. This was designed as a database query interface with operations targeted at designated database fields and results returned as strings. At the end of 2007 a new version of the server was released capable of serving thesauri and ontologies as well as vocabularies. The SOAP API functionality was enhanced and the output format changed to XML. In addition, a pseudo-RESTful query interface was developed directly addressing terms and lists by URLs. This is in full operational use by projects such as SeaDataNet and will run for the foreseeable future. However, operational experience has exposed shortcomings in both the API and its document payload. Other ontology servers, notably at MMI and CSIRO, are coming on-line making now the time to unify ontology management. This paper presents a RESTful API and payload document schema. It is based on the lessons learned in four years of operational vocabulary serving, provides full ontology management functionality and has the potential to form the basis for an interoperable network of distributed ontologies.

  7. Using a Foundational Ontology for Reengineering a Software Enterprise Ontology

    NASA Astrophysics Data System (ADS)

    Perini Barcellos, Monalessa; de Almeida Falbo, Ricardo

    The knowledge about software organizations is considerably relevant to software engineers. The use of a common vocabulary for representing the useful knowledge about software organizations involved in software projects is important for several reasons, such as to support knowledge reuse and to allow communication and interoperability between tools. Domain ontologies can be used to define a common vocabulary for sharing and reuse of knowledge about some domain. Foundational ontologies can be used for evaluating and re-designing domain ontologies, giving to these real-world semantics. This paper presents an evaluating of a Software Enterprise Ontology that was reengineered using the Unified Foundation Ontology (UFO) as basis.

  8. Evaluating the Good Ontology Design Guideline (GoodOD) with the Ontology Quality Requirements and Evaluation Method and Metrics (OQuaRE)

    PubMed Central

    Duque-Ramos, Astrid; Boeker, Martin; Jansen, Ludger; Schulz, Stefan; Iniesta, Miguela; Fernández-Breis, Jesualdo Tomás

    2014-01-01

    Objective To (1) evaluate the GoodOD guideline for ontology development by applying the OQuaRE evaluation method and metrics to the ontology artefacts that were produced by students in a randomized controlled trial, and (2) informally compare the OQuaRE evaluation method with gold standard and competency questions based evaluation methods, respectively. Background In the last decades many methods for ontology construction and ontology evaluation have been proposed. However, none of them has become a standard and there is no empirical evidence of comparative evaluation of such methods. This paper brings together GoodOD and OQuaRE. GoodOD is a guideline for developing robust ontologies. It was previously evaluated in a randomized controlled trial employing metrics based on gold standard ontologies and competency questions as outcome parameters. OQuaRE is a method for ontology quality evaluation which adapts the SQuaRE standard for software product quality to ontologies and has been successfully used for evaluating the quality of ontologies. Methods In this paper, we evaluate the effect of training in ontology construction based on the GoodOD guideline within the OQuaRE quality evaluation framework and compare the results with those obtained for the previous studies based on the same data. Results Our results show a significant effect of the GoodOD training over developed ontologies by topics: (a) a highly significant effect was detected in three topics from the analysis of the ontologies of untrained and trained students; (b) both positive and negative training effects with respect to the gold standard were found for five topics. Conclusion The GoodOD guideline had a significant effect over the quality of the ontologies developed. Our results show that GoodOD ontologies can be effectively evaluated using OQuaRE and that OQuaRE is able to provide additional useful information about the quality of the GoodOD ontologies. PMID:25148262

  9. Two Cases of Lung Cancer in Foundry Workers

    PubMed Central

    2013-01-01

    Background Iron and steel foundry workers are exposed to various toxic and carcinogenic substances including crystalline silica, polycyclic aromatic hydrocarbons, and arsenic. Studies have been conducted on lung cancer in iron and steel founding workers and the concentration of crystalline silica in foundries; however, the concentration of crystalline silica and cases of lung cancer in a single foundry has never been reported in Korea. Therefore, the authors report two cases of lung cancer and concentration of crystalline silica by the X-ray diffraction method. Case presentation A 55-year-old blasting and grinding worker who worked in a foundry for 33 years was diagnosed with lung cancer. Another 64-year-old forklift driver who worked in foundries for 39 years was also diagnosed with lung cancer. Shot blast operatives were exposed to the highest level of respirable quartz (0.412 mg/m3), and a forklift driver was exposed to 0.223 mg/m3. Conclusions The lung cancer of the two workers is very likely due to occupationally related exposure given their occupational history, the level of exposure to crystalline silica, and epidemiologic evidence. Further studies on the concentration of crystalline silica in foundries and techniques to reduce the crystalline silica concentration are required. PMID:24472520

  10. Methodology of decreasing software complexity using ontology

    NASA Astrophysics Data System (ADS)

    DÄ browska-Kubik, Katarzyna

    2015-09-01

    In this paper a model of web application`s source code, based on the OSD ontology (Ontology for Software Development), is proposed. This model is applied to implementation and maintenance phase of software development process through the DevOntoCreator tool [5]. The aim of this solution is decreasing software complexity of that source code, using many different maintenance techniques, like creation of documentation, elimination dead code, cloned code or bugs, which were known before [1][2]. Due to this approach saving on software maintenance costs of web applications will be possible.

  11. DeMO: An Ontology for Discrete-event Modeling and Simulation

    PubMed Central

    Silver, Gregory A; Miller, John A; Hybinette, Maria; Baramidze, Gregory; York, William S

    2011-01-01

    Several fields have created ontologies for their subdomains. For example, the biological sciences have developed extensive ontologies such as the Gene Ontology, which is considered a great success. Ontologies could provide similar advantages to the Modeling and Simulation community. They provide a way to establish common vocabularies and capture knowledge about a particular domain with community-wide agreement. Ontologies can support significantly improved (semantic) search and browsing, integration of heterogeneous information sources, and improved knowledge discovery capabilities. This paper discusses the design and development of an ontology for Modeling and Simulation called the Discrete-event Modeling Ontology (DeMO), and it presents prototype applications that demonstrate various uses and benefits that such an ontology may provide to the Modeling and Simulation community. PMID:22919114

  12. POSet Ontology Categorizer

    2005-03-01

    POSet Ontology Categorizer (POSOC) V1.0 The POSet Ontology Categorizer (POSOC) software package provides tools for creating and mining of poset-structured ontologies, such as the Gene Ontology (GO). Given a list of weighted query items (ex.genes,proteins, and/or phrases) and one or more focus nodes, POSOC determines the ordered set of GO nodes that summarize the query, based on selections of a scoring function, pseudo-distance measure, specificity level, and cluster determination. Pseudo-distance measures provided are minimum chainmore » length, maximum chain length, average of extreme chain lengths, and average of all chain lengths. A low specificity level, such as -1 or 0, results in a general set of clusters. Increasing the specificity results in more specific results in more specific and lighter clusters. POSOC cluster results can be compared agaist known results by calculations of precision, recall, and f-score for graph neighborhood relationships. This tool has been used in understanding the function of a set of genes, finding similar genes, and annotating new proteins. The POSOC software consists of a set of Java interfaces, classes, and programs that run on Linux or Windows platforms. It incorporates graph classes from OpenJGraph (openjgraph.sourceforge.net).« less

  13. Dahlbeck and Pure Ontology

    ERIC Educational Resources Information Center

    Mackenzie, Jim

    2016-01-01

    This article responds to Johan Dahlbeck's "Towards a pure ontology: Children's bodies and morality" ["Educational Philosophy and Theory," vol. 46 (1), 2014, pp. 8-23 (EJ1026561)]. His arguments from Nietzsche and Spinoza do not carry the weight he supposes, and the conclusions he draws from them about pedagogy would be…

  14. POSet Ontology Categorizer

    SciTech Connect

    Miniszewski, Sue M.

    2005-03-01

    POSet Ontology Categorizer (POSOC) V1.0 The POSet Ontology Categorizer (POSOC) software package provides tools for creating and mining of poset-structured ontologies, such as the Gene Ontology (GO). Given a list of weighted query items (ex.genes,proteins, and/or phrases) and one or more focus nodes, POSOC determines the ordered set of GO nodes that summarize the query, based on selections of a scoring function, pseudo-distance measure, specificity level, and cluster determination. Pseudo-distance measures provided are minimum chain length, maximum chain length, average of extreme chain lengths, and average of all chain lengths. A low specificity level, such as -1 or 0, results in a general set of clusters. Increasing the specificity results in more specific results in more specific and lighter clusters. POSOC cluster results can be compared agaist known results by calculations of precision, recall, and f-score for graph neighborhood relationships. This tool has been used in understanding the function of a set of genes, finding similar genes, and annotating new proteins. The POSOC software consists of a set of Java interfaces, classes, and programs that run on Linux or Windows platforms. It incorporates graph classes from OpenJGraph (openjgraph.sourceforge.net).

  15. Benchmarking Ontologies: Bigger or Better?

    PubMed Central

    Yao, Lixia; Divoli, Anna; Mayzus, Ilya; Evans, James A.; Rzhetsky, Andrey

    2011-01-01

    A scientific ontology is a formal representation of knowledge within a domain, typically including central concepts, their properties, and relations. With the rise of computers and high-throughput data collection, ontologies have become essential to data mining and sharing across communities in the biomedical sciences. Powerful approaches exist for testing the internal consistency of an ontology, but not for assessing the fidelity of its domain representation. We introduce a family of metrics that describe the breadth and depth with which an ontology represents its knowledge domain. We then test these metrics using (1) four of the most common medical ontologies with respect to a corpus of medical documents and (2) seven of the most popular English thesauri with respect to three corpora that sample language from medicine, news, and novels. Here we show that our approach captures the quality of ontological representation and guides efforts to narrow the breach between ontology and collective discourse within a domain. Our results also demonstrate key features of medical ontologies, English thesauri, and discourse from different domains. Medical ontologies have a small intersection, as do English thesauri. Moreover, dialects characteristic of distinct domains vary strikingly as many of the same words are used quite differently in medicine, news, and novels. As ontologies are intended to mirror the state of knowledge, our methods to tighten the fit between ontology and domain will increase their relevance for new areas of biomedical science and improve the accuracy and power of inferences computed across them. PMID:21249231

  16. An ontology for description of drug discovery investigations.

    PubMed

    Qi, Da; King, Ross D; Hopkins, Andrew L; Bickerton, G Richard J; Soldatova, Larisa N

    2010-01-01

    The paper presents an ontology for the description of Drug Discovery Investigation (DDI).This has been developed through the use of a Robot Scientist "Eve", and in consultation with industry. DDI aims to define the principle entities and the relations in the research and development phase of the drug discovery pipeline. DDI is highly transferable and extendable due to its adherence to accepted standards, and compliance with existing ontology resources. This enables DDI to be integrated with such related ontologies as the Vaccine Ontology, the Advancing Clinico-Genomic Trials on Cancer Master Ontology, etc. DDI is available at http://purl.org/ddi/wikipedia or http://purl.org/ddi/home. PMID:20375446

  17. Toward the design of a nursing ontology system.

    PubMed

    Benedik, Peter; Rajkovič, Uroš; Šušteršič, Olga

    2014-12-01

    The unambiguous and consistent representation of the healthcare domain is the foundation of modernized healthcare (eg, electronic medical records). However, the nursing domain often fails to meet this requirement. In this article, we address this challenge by presenting a three-stage methodological approach that can be used to (1) capture knowledge in a nursing domain; (2) design a nursing ontology, composed of data models linked with terminology concepts in a multirelational property graph; and (3) implement and (4) evaluate the ontology. Through the feasibility, development, and evaluation phases of our methodological approach, we modeled a nursing domain (ontology) and the indices that partition the domain into an efficient, searchable space, where the solution to a nursing problem is seen as abstractly defined traversals through its graph vertices and edges. Thus, the use of the three-phase ontology development process and multirelational property graph was sufficiently comprehensive for achieving the representation of a nursing domain ontology and its instantiation.

  18. OWL 2 learn profile: an ontology sublanguage for the learning domain.

    PubMed

    Heiyanthuduwage, Sudath R; Schwitter, Rolf; Orgun, Mehmet A

    2016-01-01

    Many experimental ontologies have been developed for the learning domain for use at different institutions. These ontologies include different OWL/OWL 2 (Web Ontology Language) constructors. However, it is not clear which OWL 2 constructors are the most appropriate ones for designing ontologies for the learning domain. It is possible that the constructors used in these learning domain ontologies match one of the three standard OWL 2 profiles (sublanguages). To investigate whether this is the case, we have analysed a corpus of 14 ontologies designed for the learning domain. We have also compared the constructors used in these ontologies with those of the OWL 2 RL profile, one of the OWL 2 standard profiles. The results of our analysis suggest that the OWL 2 constructors used in these ontologies do not exactly match the standard OWL 2 RL profile, but form a subset of that profile which we call OWL 2 Learn.

  19. OWL 2 learn profile: an ontology sublanguage for the learning domain.

    PubMed

    Heiyanthuduwage, Sudath R; Schwitter, Rolf; Orgun, Mehmet A

    2016-01-01

    Many experimental ontologies have been developed for the learning domain for use at different institutions. These ontologies include different OWL/OWL 2 (Web Ontology Language) constructors. However, it is not clear which OWL 2 constructors are the most appropriate ones for designing ontologies for the learning domain. It is possible that the constructors used in these learning domain ontologies match one of the three standard OWL 2 profiles (sublanguages). To investigate whether this is the case, we have analysed a corpus of 14 ontologies designed for the learning domain. We have also compared the constructors used in these ontologies with those of the OWL 2 RL profile, one of the OWL 2 standard profiles. The results of our analysis suggest that the OWL 2 constructors used in these ontologies do not exactly match the standard OWL 2 RL profile, but form a subset of that profile which we call OWL 2 Learn. PMID:27066328

  20. A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.

    PubMed

    Ochs, Christopher; Geller, James; Perl, Yehoshua; Musen, Mark A

    2016-08-01

    Software tools play a critical role in the development and maintenance of biomedical ontologies. One important task that is difficult without software tools is ontology quality assurance. In previous work, we have introduced different kinds of abstraction networks to provide a theoretical foundation for ontology quality assurance tools. Abstraction networks summarize the structure and content of ontologies. One kind of abstraction network that we have used repeatedly to support ontology quality assurance is the partial-area taxonomy. It summarizes structurally and semantically similar concepts within an ontology. However, the use of partial-area taxonomies was ad hoc and not generalizable. In this paper, we describe the Ontology Abstraction Framework (OAF), a unified framework and software system for deriving, visualizing, and exploring partial-area taxonomy abstraction networks. The OAF includes support for various ontology representations (e.g., OWL and SNOMED CT's relational format). A Protégé plugin for deriving "live partial-area taxonomies" is demonstrated.

  1. An ontology design pattern for surface water features

    USGS Publications Warehouse

    Sinha, Gaurav; Mark, David; Kolas, Dave; Varanka, Dalia; Romero, Boleslo E.; Feng, Chen-Chieh; Usery, E. Lynn; Liebermann, Joshua; Sorokine, Alexandre

    2014-01-01

    Surface water is a primary concept of human experience but concepts are captured in cultures and languages in many different ways. Still, many commonalities exist due to the physical basis of many of the properties and categories. An abstract ontology of surface water features based only on those physical properties of landscape features has the best potential for serving as a foundational domain ontology for other more context-dependent ontologies. The Surface Water ontology design pattern was developed both for domain knowledge distillation and to serve as a conceptual building-block for more complex or specialized surface water ontologies. A fundamental distinction is made in this ontology between landscape features that act as containers (e.g., stream channels, basins) and the bodies of water (e.g., rivers, lakes) that occupy those containers. Concave (container) landforms semantics are specified in a Dry module and the semantics of contained bodies of water in a Wet module. The pattern is implemented in OWL, but Description Logic axioms and a detailed explanation is provided in this paper. The OWL ontology will be an important contribution to Semantic Web vocabulary for annotating surface water feature datasets. Also provided is a discussion of why there is a need to complement the pattern with other ontologies, especially the previously developed Surface Network pattern. Finally, the practical value of the pattern in semantic querying of surface water datasets is illustrated through an annotated geospatial dataset and sample queries using the classes of the Surface Water pattern.

  2. Ontology-Based Model Of Firm Competitiveness

    NASA Astrophysics Data System (ADS)

    Deliyska, Boryana; Stoenchev, Nikolay

    2010-10-01

    Competitiveness is important characteristics of each business organization (firm, company, corporation etc). It is of great significance for the organization existence and defines evaluation criteria of business success at microeconomical level. Each criterium comprises set of indicators with specific weight coefficients. In the work an ontology-based model of firm competitiveness is presented as a set of several mutually connected ontologies. It would be useful for knowledge structuring, standardization and sharing among experts and software engineers who develop application in the domain. Then the assessment of the competitiveness of various business organizations could be generated more effectively.

  3. Asbestos-related x-ray changes in foundry workers.

    PubMed

    Rosenman, K D; Reilly, M J

    1998-08-01

    Michigan has a statewide mandatory occupational disease reporting system. As part of that system, reports are received from hospital, physicians, death certificates, the worker's compensation bureau, and company medical departments. Based on this reporting, the State of Michigan has a special emphasis program for the surveillance of silicosis, a known disease outcome among foundry workers. From 1985-1996, 115 cases reported to the State Surveillance System as silicosis, pneumoconiosis not specified, or pulmonary fibrosis were reclassified as having asbestos related x-ray changes after a B-reader interpretation of each case's chest x-ray. During this same period there were an additional 697 reports confirmed as silicosis and 6,724 cases reported to the surveillance system as asbestosis. Among the 115 reports reclassified as having asbestos-related x-ray changes without evidence of silicosis-related x-ray changes, 54 had worked in foundries. Only 7 (14.8%) of these individuals had their primary work in maintenance in the foundry; 40 (85.1%) had their primary foundry work in a production job; and for 10 individuals the occupation was not known. Asbestos has been used in foundries on pipe laggings, boiler coverings, as insulation in fan housings, in gloves, aprons and curtains, as insulation in cupolas, and in ladles and insulation in sand molds. Clinicians caring for foundry workers need to be aware that asbestos-related x-ray changes are not uncommon in this population and asbestos exposure should be considered as one of the carcinogens contributing to the known increased risk of lung cancer among foundry workers. PMID:9651631

  4. View from west sharp perspective, foundry/propeller shop. Naval Base ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View from west sharp perspective, foundry/propeller shop. - Naval Base Philadelphia-Philadelphia Naval Shipyard, Foundry-Propeller Shop, North of Porter Avenue, west of Third Street West, Philadelphia, Philadelphia County, PA

  5. View of foundry/propeller shop (building no. 20) looking northeast. ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View of foundry/propeller shop (building no. 20) looking northeast. - Naval Base Philadelphia-Philadelphia Naval Shipyard, Foundry-Propeller Shop, North of Porter Avenue, west of Third Street West, Philadelphia, Philadelphia County, PA

  6. Silicosis among foundry workers. Implication for the need to revise the OSHA standard.

    PubMed

    Rosenman, K D; Reilly, M J; Rice, C; Hertzberg, V; Tseng, C Y; Anderson, H A

    1996-11-01

    To evaluate the risk of pneumoconiosis among workers in a Midwestern automotive foundry, medical records and silica sand exposure data were analyzed for 1,072 current and retired employees with at least 5 years of employment as of June 1991. Approximately half of these employees had worked at the foundry for 20 or more years. Sixty workers were found to have radiographic evidence of pneumoconiosis. Twenty-eight workers had radiographs consistent with silicosis, of which 25 were consistent with simple silicosis and three with progressive massive fibrosis. The prevalence of radiographic changes consistent with silicosis increased with: number of years worked at the foundry (6% for 20-29 years and 12% for 30 or more years); cigarette smoking (12.2% among smokers with high silica exposure vs. 4.4% among never smokers with high silica exposure); work area within the foundry (cleaning room, core room, mold area, core knockout); and quantitative silica exposure (0.3-2.7% of workers at the current Occupational Safety and Health Administration (OSHA) standard and 4.9-9.9% of workers above the OSHA standard). In addition, the odds of developing radiographic changes consistent with silicosis were increased for African Americans (odds ratio = 2.14, 95% confidence interval 0.85-5.60) in comparison with whites. (The risk was similar when silica exposure was equal, but African-American workers on average had greater exposure to silica, despite having a similar duration of work as white workers.) Another eight workers had radiographic evidence of asbestosis, and 24 had pleural plaques. These asbestos-related changes were not associated with increasing exposure to silica but rather were associated with being in the maintenance department and performing repair work. After controlling for cigarette smoking, race, and exposure to silica at another job besides the foundry, the authors found a 1.45 increased risk of developing a radiograph consistent with silicosis after 20 years of

  7. IDEF5 Ontology Description Capture Method: Concept Paper

    NASA Technical Reports Server (NTRS)

    Menzel, Christopher P.; Mayer, Richard J.

    1990-01-01

    The results of research towards an ontology capture method referred to as IDEF5 are presented. Viewed simply as the study of what exists in a domain, ontology is an activity that can be understood to be at work across the full range of human inquiry prompted by the persistent effort to understand the world in which it has found itself - and which it has helped to shape. In the contest of information management, ontology is the task of extracting the structure of a given engineering, manufacturing, business, or logistical domain and storing it in an usable representational medium. A key to effective integration is a system ontology that can be accessed and modified across domains and which captures common features of the overall system relevant to the goals of the disparate domains. If the focus is on information integration, then the strongest motivation for ontology comes from the need to support data sharing and function interoperability. In the correct architecture, an enterprise ontology base would allow th e construction of an integrated environment in which legacy systems appear to be open architecture integrated resources. If the focus is on system/software development, then support for the rapid acquisition of reliable systems is perhaps the strongest motivation for ontology. Finally, ontological analysis was demonstrated to be an effective first step in the construction of robust knowledge based systems.

  8. An evaluation of ontology exchange languages for bioinformatics.

    PubMed

    McEntire, R; Karp, P; Abernethy, N; Benton, D; Helt, G; DeJongh, M; Kent, R; Kosky, A; Lewis, S; Hodnett, D; Neumann, E; Olken, F; Pathak, D; Tarczy-Hornoch, P; Toldo, L; Topaloglou, T

    2000-01-01

    Ontologies are specifications of the concepts in a given field, and of the relationships among those concepts. The development of ontologies for molecular-biology information and the sharing of those ontologies within the bioinformatics community are central problems in bioinformatics. If the bioinformatics community is to share ontologies effectively, ontologies must be exchanged in a form that uses standardized syntax and semantics. This paper reports on an effort among the authors to evaluate alternative ontology-exchange languages, and to recommend one or more languages for use within the larger bioinformatics community. The study selected a set of candidate languages, and defined a set of capabilities that the ideal ontology-exchange language should satisfy. The study scored the languages according to the degree to which they satisfied each capability. In addition, the authors performed several ontology-exchange experiments with the two languages that received the highest scores: OML and Ontolingua. The result of those experiments, and the main conclusion of this study, was that the frame-based semantic model of Ontolingua is preferable to the conceptual graph model of OML, but that the XML-based syntax of OML is preferable to the Lisp-based syntax of Ontolingua. PMID:10977085

  9. 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.

  10. An Internet-based ontology editor for medical appropriateness criteria.

    PubMed

    Kahn, C E

    1998-04-01

    Appropriateness criteria and practice guidelines seek to promote the cost-effectiveness use of medical interventions, and can be most useful when integrated with computer-based patient records and order-entry systems. Building an abstract model (ontology) of appropriateness criteria can require considerable effort among investigators at geographically dispersed institutions. To facilitate the construction and maintenance of ontologies for clinical appropriateness criteria, the author developed an Internet-based system for viewing and editing the knowledge model. The system, called NEON (Network-based Editor for ONtologies), uses the World Wide Web as a platform-independent user interface. NEON allows users to edit the indexing terms and the semantic network that form the ontology for a set of appropriateness criteria. Ontologies built using the system can be imported and exported using an open, internationally standardized format based on the Standard Generalized Markup Language (SGML).

  11. In Defense of Chi's Ontological Incompatibility Hypothesis

    ERIC Educational Resources Information Center

    Slotta, James D.

    2011-01-01

    This article responds to an article by A. Gupta, D. Hammer, and E. F. Redish (2010) that asserts that M. T. H. Chi's (1992, 2005) hypothesis of an "ontological commitment" in conceptual development is fundamentally flawed. In this article, I argue that Chi's theoretical perspective is still very much intact and that the critique offered by Gupta…

  12. Epidemiological adaptation of quartz exposure modeling in Swedish aluminum foundries: nested case-control study on lung cancer.

    PubMed

    Westberg, Håkan B; Bellander, Tom

    2003-12-01

    In a recent cohort study in aluminum foundries and remelting plants an unexpectedly high risk of lung cancer was found in workers in sand foundries. On the basis of present and historical measurement data, we developed a statistical model for exposure to total dust and crystalline quartz for different jobs and time periods. Cumulative dose estimates of total dust and crystalline quartz were calculated and used in a nested case-control study in the cohort. From the cohort of foundry workers (n = 5016), 46 cases of lung cancer were identified. The final analysis was performed on 31 cases and 233 controls with one year or more of employment. Historical measurement data from the 1960s and onward were collected, totaling 203 total dust and 103 crystalline quartz exposure observations. Regression models, using the determinants of job title, time period, type of foundry, and size of production, were developed for assessing historical total dust and crystalline quartz air concentrations. These estimates were used to calculate individual cumulative exposure in the case-control study. In the multiple linear regression analysis, the determinants explained much of the variations in dust level (r(2) = 0.58). The explained variation in crystalline quartz was much lower (r(2) = 0.13). The regression coefficients for the type of foundry, time period, and size of production were statistically significant for total dust. On the basis of the regression analysis, the final models were used to calculate individual cumulative exposures. The calculated cumulative dust and quartz exposures averaged 33 mg/m(3) * year and 0.42 mg/m(3) * year, respectively. The odds ratios (ORs) were not significant, but showed dose-response trends for both dust and crystalline quartz. PMID:14612297

  13. Exposure to mutagenic chemicals in foundry and urban environments.

    PubMed

    Barański, B; Palus, J; Janik-Spiechowicz, E

    1989-01-01

    The study was aimed at the estimation of occupational exposure to mutagenic substances in a piston-ring foundry. The following samples were examined: solid phase of aerosol from the foundry and from different places of urban environment together with the foundry workers' urine collected during the 8-hour shift. The mutagenic substances were extracted from the collected material with acetone or concentrated with XAD-2 resin. The mutagenic property was estimated with the Ames' test using S. typhimurium strain TA98 without and with S9 fraction. The highest mutagenic activity was found at the following work-posts: caster, moulder, steerer of an induction furnace, and smelter and in the office rooms and in the flat occupied by heavy smokers. The mutagenic activity of aerosol at some other productive workposts in the foundry was similar to the mutagenic activity of aerosol in the office and flat rooms occupied by nonsmokers or in the street in Lodz. The mutagenic activity of urine from foundry workers was not correlated with the level of the occupational inhalation exposure to the mutagenic substances, however, the mutagenic activity of urine from smoking workers was about 10-20 times higher than from nonsmokers. PMID:2489412

  14. An Ontology for Software Engineering Education

    ERIC Educational Resources Information Center

    Ling, Thong Chee; Jusoh, Yusmadi Yah; Adbullah, Rusli; Alwi, Nor Hayati

    2013-01-01

    Software agents communicate using ontology. It is important to build an ontology for specific domain such as Software Engineering Education. Building an ontology from scratch is not only hard, but also incur much time and cost. This study aims to propose an ontology through adaptation of the existing ontology which is originally built based on a…

  15. Ontology Mappings to Improve Learning Resource Search

    ERIC Educational Resources Information Center

    Gasevic, Dragan; Hatala, Marek

    2006-01-01

    This paper proposes an ontology mapping-based framework that allows searching for learning resources using multiple ontologies. The present applications of ontologies in e-learning use various ontologies (eg, domain, curriculum, context), but they do not give a solution on how to interoperate e-learning systems based on different ontologies. The…

  16. Understanding and using the meaning of statements in a bio-ontology: recasting the Gene Ontology in OWL.

    PubMed

    Aranguren, Mikel Egaña; Bechhofer, Sean; Lord, Phillip; Sattler, Ulrike; Stevens, Robert

    2007-01-01

    The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge about techniques and best practice on ontology development. In the bio-ontology domain, these two camps have often come into conflict, especially where pragmatism comes into conflict with perceived best practice. One of these areas is the insistence of computer scientists on a well-defined semantic basis for the Knowledge Representation language being used. In this article, we will first describe why this community is so insistent. Second, we will illustrate this by examining the semantics of the Web Ontology Language and the semantics placed on the Directed Acyclic Graph as used by the Gene Ontology. Finally we will reconcile the two representations, including the broader Open Biomedical Ontologies format. The ability to exchange between the two representations means that we can capitalise on the features of both languages. Such utility can only arise by the understanding of the semantics of the languages being used. By this illustration of the usefulness of a clear, well-defined language semantics, we wish to promote a wider understanding of the computer science perspective amongst potential users within the biological community.

  17. 40 CFR 63.7682 - What parts of my foundry does this subpart cover?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... 40 Protection of Environment 13 2010-07-01 2010-07-01 false What parts of my foundry does this... CATEGORIES (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Iron and Steel Foundries What This Subpart Covers § 63.7682 What parts of my foundry does this subpart cover? (a) The...

  18. The ontology of biological taxa

    PubMed Central

    Schulz, Stefan; Stenzhorn, Holger; Boeker, Martin

    2008-01-01

    Motivation: The classification of biological entities in terms of species and taxa is an important endeavor in biology. Although a large amount of statements encoded in current biomedical ontologies is taxon-dependent there is no obvious or standard way for introducing taxon information into an integrative ontology architecture, supposedly because of ongoing controversies about the ontological nature of species and taxa. Results: In this article, we discuss different approaches on how to represent biological taxa using existing standards for biomedical ontologies such as the description logic OWL DL and the Open Biomedical Ontologies Relation Ontology. We demonstrate how hidden ambiguities of the species concept can be dealt with and existing controversies can be overcome. A novel approach is to envisage taxon information as qualities that inhere in biological organisms, organism parts and populations. Availability: The presented methodology has been implemented in the domain top-level ontology BioTop, openly accessible at http://purl.org/biotop. BioTop may help to improve the logical and ontological rigor of biomedical ontologies and further provides a clear architectural principle to deal with biological taxa information. Contact: stschulz@uni-freiburg.de PMID:18586729

  19. Selected papers from the 16th Annual Bio-Ontologies Special Interest Group Meeting

    PubMed Central

    2014-01-01

    Over the 16 years, the Bio-Ontologies SIG at ISMB has provided a forum for vibrant discussions of the latest and most innovative advances in the research area of bio-ontologies, its applications to biomedicine and more generally in the organisation, sharing and re-use of knowledge in biomedicine and the life sciences. The six papers selected for this supplement span a wide range of topics including: ontology-based data integration, ontology-based annotation of scientific literature, ontology and data model development, representation of scientific results and gene candidate prediction.

  20. Towards a Pattern-Driven Topical Ontology Modeling Methodology in Elderly Care Homes

    NASA Astrophysics Data System (ADS)

    Tang, Yan; de Baer, Peter; Zhao, Gang; Meersman, Robert; Pudkey, Kevin

    This paper presents a pattern-driven ontology modeling methodology, which is used to create topical ontologies in the human resource management (HRM) domain. An ontology topic is used to group concepts from different contexts (or even from different domain ontologies). We use the Organization for Economic Co-operation and Development (OECD) and the National Vocational Qualification (NVQ) as the resource to create the topical ontologies in this paper. The methodology is implemented in a tool called PAD-ON suit. The paper approach is illustrated with a use case from elderly care homes in UK.

  1. VIEW OF INTERIOR OF SOUTHERN DUCTILE CASTING COMPANY, CENTERVILLE FOUNDRY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW OF INTERIOR OF SOUTHERN DUCTILE CASTING COMPANY, CENTERVILLE FOUNDRY SHOWING MOLD MAKING WITH PNEWMATIC JOLT SQUEEZE COPE AND DRAG MOLDING MACHINES THAT INDIVIDUALLY MADE EITHER A COPE OR DRAG AND A SMALL WHEELED MATCHPLATE JOLT-SQUEEZE MACHINE THAT COMPRESSED AN ENTIRE MOLD AT A SINGLE TIME USING A DOUBLE-SIDED PATTERN (MATCHPLATE). ALSO SHOWN ARE RAILED PALLET CAR CONVEYORS THAT CARRIED COMPLETED MOLDS FROM MOLDING MACHINES TO POURING AREAS WHERE WORKERS USED SMALL OVERHEAD CRANE TO LIFT JACKETS AND WEIGHTS ONTO THE MOLDS TO HOLD THEM TOGETHER WHILE POURING. - Southern Ductile Casting Company, Centerville Foundry, 101 Airport Road, Centreville, Bibb County, AL

  2. Molecular Foundry Workshop draws overflow crowd to BerkeleyLab

    SciTech Connect

    Robinson, Art

    2002-11-27

    Nanoscale science and technology is now one of the top research priorities in the United States. With this background, it is no surprise that an overflow crowd or more than 350 registrants filled two auditoriums to hear about and contribute ideas for the new Molecular Foundry during a two-day workshop at the Lawrence Berkeley National Laboratory (Berkeley Lab). Scheduled to open for business at Berkeley Labin early 2006, the Molecular Foundry is one of three Nanoscale Science Research Centers (NSRCs) put forward for funding by the DOE's Office of Basic Energy Sciences (BES).

  3. The Ontology for Biomedical Investigations.

    PubMed

    Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H; Bug, Bill; Chibucos, Marcus C; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Soldatova, Larisa N; Stoeckert, Christian J; Taylor, Chris F; Torniai, Carlo; Turner, Jessica A; Vita, Randi; Whetzel, Patricia L; Zheng, Jie

    2016-01-01

    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed

  4. The Ontology for Biomedical Investigations

    PubMed Central

    Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H.; Chibucos, Marcus C.; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A.; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L.; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A.; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H.; Schober, Daniel; Smith, Barry; Soldatova, Larisa N.; Stoeckert, Christian J.; Taylor, Chris F.; Torniai, Carlo; Turner, Jessica A.; Vita, Randi; Whetzel, Patricia L.; Zheng, Jie

    2016-01-01

    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed

  5. The Ontology for Biomedical Investigations.

    PubMed

    Bandrowski, Anita; Brinkman, Ryan; Brochhausen, Mathias; Brush, Matthew H; Bug, Bill; Chibucos, Marcus C; Clancy, Kevin; Courtot, Mélanie; Derom, Dirk; Dumontier, Michel; Fan, Liju; Fostel, Jennifer; Fragoso, Gilberto; Gibson, Frank; Gonzalez-Beltran, Alejandra; Haendel, Melissa A; He, Yongqun; Heiskanen, Mervi; Hernandez-Boussard, Tina; Jensen, Mark; Lin, Yu; Lister, Allyson L; Lord, Phillip; Malone, James; Manduchi, Elisabetta; McGee, Monnie; Morrison, Norman; Overton, James A; Parkinson, Helen; Peters, Bjoern; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Schober, Daniel; Smith, Barry; Soldatova, Larisa N; Stoeckert, Christian J; Taylor, Chris F; Torniai, Carlo; Turner, Jessica A; Vita, Randi; Whetzel, Patricia L; Zheng, Jie

    2016-01-01

    The Ontology for Biomedical Investigations (OBI) is an ontology that provides terms with precisely defined meanings to describe all aspects of how investigations in the biological and medical domains are conducted. OBI re-uses ontologies that provide a representation of biomedical knowledge from the Open Biological and Biomedical Ontologies (OBO) project and adds the ability to describe how this knowledge was derived. We here describe the state of OBI and several applications that are using it, such as adding semantic expressivity to existing databases, building data entry forms, and enabling interoperability between knowledge resources. OBI covers all phases of the investigation process, such as planning, execution and reporting. It represents information and material entities that participate in these processes, as well as roles and functions. Prior to OBI, it was not possible to use a single internally consistent resource that could be applied to multiple types of experiments for these applications. OBI has made this possible by creating terms for entities involved in biological and medical investigations and by importing parts of other biomedical ontologies such as GO, Chemical Entities of Biological Interest (ChEBI) and Phenotype Attribute and Trait Ontology (PATO) without altering their meaning. OBI is being used in a wide range of projects covering genomics, multi-omics, immunology, and catalogs of services. OBI has also spawned other ontologies (Information Artifact Ontology) and methods for importing parts of ontologies (Minimum information to reference an external ontology term (MIREOT)). The OBI project is an open cross-disciplinary collaborative effort, encompassing multiple research communities from around the globe. To date, OBI has created 2366 classes and 40 relations along with textual and formal definitions. The OBI Consortium maintains a web resource (http://obi-ontology.org) providing details on the people, policies, and issues being addressed

  6. A unified anatomy ontology of the vertebrate skeletal system.

    PubMed

    Dahdul, Wasila M; Balhoff, James P; Blackburn, David C; Diehl, Alexander D; Haendel, Melissa A; Hall, Brian K; Lapp, Hilmar; Lundberg, John G; Mungall, Christopher J; Ringwald, Martin; Segerdell, Erik; Van Slyke, Ceri E; Vickaryous, Matthew K; Westerfield, Monte; Mabee, Paula M

    2012-01-01

    The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity.

  7. Standardized description of scientific evidence using the Evidence Ontology (ECO).

    PubMed

    Chibucos, Marcus C; Mungall, Christopher J; Balakrishnan, Rama; Christie, Karen R; Huntley, Rachael P; White, Owen; Blake, Judith A; Lewis, Suzanna E; Giglio, Michelle

    2014-01-01

    The Evidence Ontology (ECO) is a structured, controlled vocabulary for capturing evidence in biological research. ECO includes diverse terms for categorizing evidence that supports annotation assertions including experimental types, computational methods, author statements and curator inferences. Using ECO, annotation assertions can be distinguished according to the evidence they are based on such as those made by curators versus those automatically computed or those made via high-throughput data review versus single test experiments. Originally created for capturing evidence associated with Gene Ontology annotations, ECO is now used in other capacities by many additional annotation resources including UniProt, Mouse Genome Informatics, Saccharomyces Genome Database, PomBase, the Protein Information Resource and others. Information on the development and use of ECO can be found at http://evidenceontology.org. The ontology is freely available under Creative Commons license (CC BY-SA 3.0), and can be downloaded in both Open Biological Ontologies and Web Ontology Language formats at http://code.google.com/p/evidenceontology. Also at this site is a tracker for user submission of term requests and questions. ECO remains under active development in response to user-requested terms and in collaborations with other ontologies and database resources. Database URL: Evidence Ontology Web site: http://evidenceontology.org.

  8. Application of Alignment Methodologies to Spatial Ontologies in the Hydro Domain

    NASA Astrophysics Data System (ADS)

    Lieberman, J. E.; Cheatham, M.; Varanka, D.

    2015-12-01

    Ontologies are playing an increasing role in facilitating mediation and translation between datasets representing diverse schemas, vocabularies, or knowledge communities. This role is relatively straightforward when there is one ontology comprising all relevant common concepts that can be mapped to entities in each dataset. Frequently, one common ontology has not been agreed to. Either each dataset is represented by a distinct ontology, or there are multiple candidates for commonality. Either the one most appropriate (expressive, relevant, correct) ontology must be chosen, or else concepts and relationships matched across multiple ontologies through an alignment process so that they may be used in concert to carry out mediation or other semantic operations. A resulting alignment can be effective to the extent that entities in in the ontologies represent differing terminology for comparable conceptual knowledge. In cases such as spatial ontologies, though, ontological entities may also represent disparate conceptualizations of space according to the discernment methods and application domains on which they are based. One ontology's wetland concept may overlap in space with another ontology's recharge zone or wildlife range or water feature. In order to evaluate alignment with respect to spatial ontologies, alignment has been applied to a series of ontologies pertaining to surface water that are used variously in hydrography (characterization of water features), hydrology (study of water cycling), and water quality (nutrient and contaminant transport) application domains. There is frequently a need to mediate between datasets in each domain in order to develop broader understanding of surface water systems, so there is a practical as well theoretical value in the alignment. From a domain expertise standpoint, the ontologies under consideration clearly contain some concepts that are spatially as well as conceptually identical and then others with less clear

  9. ICEPO: the ion channel electrophysiology ontology

    PubMed Central

    Hinard, V.; Britan, A.; Rougier, J.S.; Bairoch, A.; Abriel, H.; Gaudet, P.

    2016-01-01

    Ion channels are transmembrane proteins that selectively allow ions to flow across the plasma membrane and play key roles in diverse biological processes. A multitude of diseases, called channelopathies, such as epilepsies, muscle paralysis, pain syndromes, cardiac arrhythmias or hypoglycemia are due to ion channel mutations. A wide corpus of literature is available on ion channels, covering both their functions and their roles in disease. The research community needs to access this data in a user-friendly, yet systematic manner. However, extraction and integration of this increasing amount of data have been proven to be difficult because of the lack of a standardized vocabulary that describes the properties of ion channels at the molecular level. To address this, we have developed Ion Channel ElectroPhysiology Ontology (ICEPO), an ontology that allows one to annotate the electrophysiological parameters of the voltage-gated class of ion channels. This ontology is based on a three-state model of ion channel gating describing the three conformations/states that an ion channel can adopt: closed, open and inactivated. This ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. Here, we present ICEPO (ICEPO ftp site: ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/), as well as examples of its use. PMID:27055825

  10. ICEPO: the ion channel electrophysiology ontology.

    PubMed

    Hinard, V; Britan, A; Rougier, J S; Bairoch, A; Abriel, H; Gaudet, P

    2016-01-01

    Ion channels are transmembrane proteins that selectively allow ions to flow across the plasma membrane and play key roles in diverse biological processes. A multitude of diseases, called channelopathies, such as epilepsies, muscle paralysis, pain syndromes, cardiac arrhythmias or hypoglycemia are due to ion channel mutations. A wide corpus of literature is available on ion channels, covering both their functions and their roles in disease. The research community needs to access this data in a user-friendly, yet systematic manner. However, extraction and integration of this increasing amount of data have been proven to be difficult because of the lack of a standardized vocabulary that describes the properties of ion channels at the molecular level. To address this, we have developed Ion Channel ElectroPhysiology Ontology (ICEPO), an ontology that allows one to annotate the electrophysiological parameters of the voltage-gated class of ion channels. This ontology is based on a three-state model of ion channel gating describing the three conformations/states that an ion channel can adopt: closed, open and inactivated. This ontology supports the capture of voltage-gated ion channel electrophysiological data from the literature in a structured manner and thus enables other applications such as querying and reasoning tools. Here, we present ICEPO (ICEPO ftp site:ftp://ftp.nextprot.org/pub/current_release/controlled_vocabularies/), as well as examples of its use.

  11. Ontology-Based Administration of Web Directories

    NASA Astrophysics Data System (ADS)

    Horvat, Marko; Gledec, Gordan; Bogunović, Nikola

    Administration of a Web directory and maintenance of its content and the associated structure is a delicate and labor intensive task performed exclusively by human domain experts. Subsequently there is an imminent risk of a directory structures becoming unbalanced, uneven and difficult to use to all except for a few users proficient with the particular Web directory and its domain. These problems emphasize the need to establish two important issues: i) generic and objective measures of Web directories structure quality, and ii) mechanism for fully automated development of a Web directory's structure. In this paper we demonstrate how to formally and fully integrate Web directories with the Semantic Web vision. We propose a set of criteria for evaluation of a Web directory's structure quality. Some criterion functions are based on heuristics while others require the application of ontologies. We also suggest an ontology-based algorithm for construction of Web directories. By using ontologies to describe the semantics of Web resources and Web directories' categories it is possible to define algorithms that can build or rearrange the structure of a Web directory. Assessment procedures can provide feedback and help steer the ontology-based construction process. The issues raised in the article can be equally applied to new and existing Web directories.

  12. An Ontology Representation for Water Bodies

    NASA Astrophysics Data System (ADS)

    Brodaric, B.; Hahmann, T.; Gruninger, M.

    2015-12-01

    The interoperability of hydrological data has been a major concern in recent years, as evident by the maturation of international standards as well as the development of national and international data systems. Notwithstanding the related significant efforts at modeling hydrological entities, there remain unresolved questions about some core entities that impact the design of hydro schemas, ontologies, and similar knowledge models. One such central entity is the water body, which is represented quite heterogeneously in such models, potentially challenging their interoperability. To meet this challenge, we carry out an ontological analysis of the water body entity and propose a new ontological representation for it, as part of a wider initiative into foundational hydro ontology. The representation exhibits the surprising result that a water body is a mereological entity that is essentially grounded in two types of whole-part relations. The nuanced nature of this result has the potential to inform the design of other hydro knowledge models, as well as to foster interoperability between them.

  13. Ontology for cell-based geographic information

    NASA Astrophysics Data System (ADS)

    Zheng, Bin; Huang, Lina; Lu, Xinhai

    2009-10-01

    Inter-operability is a key notion in geographic information science (GIS) for the sharing of geographic information (GI). That requires a seamless translation among different information sources. Ontology is enrolled in GI discovery to settle the semantic conflicts for its natural language appearance and logical hierarchy structure, which are considered to be able to provide better context for both human understanding and machine cognition in describing the location and relationships in the geographic world. However, for the current, most studies on field ontology are deduced from philosophical theme and not applicable for the raster expression in GIS-which is a kind of field-like phenomenon but does not physically coincide to the general concept of philosophical field (mostly comes from the physics concepts). That's why we specifically discuss the cell-based GI ontology in this paper. The discussion starts at the investigation of the physical characteristics of cell-based raster GI. Then, a unified cell-based GI ontology framework for the recognition of the raster objects is introduced, from which a conceptual interface for the connection of the human epistemology and the computer world so called "endurant-occurrant window" is developed for the better raster GI discovery and sharing.

  14. Constructing a Geology Ontology Using a Relational Database

    NASA Astrophysics Data System (ADS)

    Hou, W.; Yang, L.; Yin, S.; Ye, J.; Clarke, K.

    2013-12-01

    In geology community, the creation of a common geology ontology has become a useful means to solve problems of data integration, knowledge transformation and the interoperation of multi-source, heterogeneous and multiple scale geological data. Currently, human-computer interaction methods and relational database-based methods are the primary ontology construction methods. Some human-computer interaction methods such as the Geo-rule based method, the ontology life cycle method and the module design method have been proposed for applied geological ontologies. Essentially, the relational database-based method is a reverse engineering of abstracted semantic information from an existing database. The key is to construct rules for the transformation of database entities into the ontology. Relative to the human-computer interaction method, relational database-based methods can use existing resources and the stated semantic relationships among geological entities. However, two problems challenge the development and application. One is the transformation of multiple inheritances and nested relationships and their representation in an ontology. The other is that most of these methods do not measure the semantic retention of the transformation process. In this study, we focused on constructing a rule set to convert the semantics in a geological database into a geological ontology. According to the relational schema of a geological database, a conversion approach is presented to convert a geological spatial database to an OWL-based geological ontology, which is based on identifying semantics such as entities, relationships, inheritance relationships, nested relationships and cluster relationships. The semantic integrity of the transformation was verified using an inverse mapping process. In a geological ontology, an inheritance and union operations between superclass and subclass were used to present the nested relationship in a geochronology and the multiple inheritances

  15. Ontology through a Mindfulness Process

    ERIC Educational Resources Information Center

    Bearance, Deborah; Holmes, Kimberley

    2015-01-01

    Traditionally, when ontology is taught in a graduate studies course on social research, there is a tendency for this concept to be examined through the process of lectures and readings. Such an approach often leaves graduate students to grapple with a personal embodiment of this concept and to comprehend how ontology can ground their research.…

  16. Ontology Performance Profiling and Model Examination: First Steps

    NASA Astrophysics Data System (ADS)

    Wang, Taowei David; Parsia, Bijan

    "[Reasoner] performance can be scary, so much so, that we cannot deploy the technology in our products." - Michael Shepard. What are typical OWL users to do when their favorite reasoner never seems to return? In this paper, we present our first steps considering this problem. We describe the challenges and our approach, and present a prototype tool to help users identify reasoner performance bottlenecks with respect to their ontologies. We then describe 4 case studies on synthetic and real-world ontologies. While the anecdotal evidence suggests that the service can be useful for both ontology developers and reasoner implementors, much more is desired.

  17. Inexact Matching of Ontology Graphs Using Expectation-Maximization

    PubMed Central

    Doshi, Prashant; Kolli, Ravikanth; Thomas, Christopher

    2009-01-01

    We present a new method for mapping ontology schemas that address similar domains. The problem of ontology matching is crucial since we are witnessing a decentralized development and publication of ontological data. We formulate the problem of inferring a match between two ontologies as a maximum likelihood problem, and solve it using the technique of expectation-maximization (EM). Specifically, we adopt directed graphs as our model for ontology schemas and use a generalized version of EM to arrive at a map between the nodes of the graphs. We exploit the structural, lexical and instance similarity between the graphs, and differ from the previous approaches in the way we utilize them to arrive at, a possibly inexact, match. Inexact matching is the process of finding a best possible match between the two graphs when exact matching is not possible or is computationally difficult. In order to scale the method to large ontologies, we identify the computational bottlenecks and adapt the generalized EM by using a memory bounded partitioning scheme. We provide comparative experimental results in support of our method on two well-known ontology alignment benchmarks and discuss their implications. PMID:20160892

  18. An ontology for PACS integration.

    PubMed

    Kahn, Charles E; Channin, David S; Rubin, Daniel L

    2006-12-01

    An ontology describes a set of classes and the relationships among them. We explored the use of an ontology to integrate picture archiving and communication systems (PACS) with other information systems in the clinical enterprise. We created an ontological model of thoracic radiology that contained knowledge of anatomy, imaging procedures, and performed procedure steps. We explored the use of the model in two use cases: (1) to determine examination completeness and (2) to identify reference (comparison) images obtained in the same imaging projection. The model incorporated a total of 138 classes, including radiology orderables, procedures, procedure steps, imaging modalities, patient positions, and imaging planes. Radiological knowledge was encoded as relationships among these classes. The ontology successfully met the information requirements of the two use-case scenarios. Ontologies can represent radiological and clinical knowledge to integrate PACS with the clinical enterprise and to support the radiology interpretation process.

  19. BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

    PubMed

    Whetzel, Patricia L; Noy, Natalya F; Shah, Nigam H; Alexander, Paul R; Nyulas, Csongor; Tudorache, Tania; Musen, Mark A

    2011-07-01

    The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection.

  20. Alterations in immune parameters in foundry and pottery workers.

    PubMed

    Başaran, Nurşen; Shubair, Mohammed; Undeğer, Ulkü; Canpinar, Hande; Kars, Ayşe

    2002-09-01

    To assess the immune competence of workers occupationally exposed to mainly silica, peripheral blood lymphocytes, serum immunoglobulins (IgG, IgA and IgM), C3 and C4 complement protein concentrations of foundry and pottery workers were evaluated and compared to healthy controls with no history of silica and other chemical exposure. The absolute number and percentage of functionally different subsets of peripheral blood mononuclear lymphocytes, i.e. T, T-suppressor and natural killer cells were unchanged. However, T-helper lymphocytes in pottery (P<0.05) and B cells in foundry (P<0.01) workers were significantly lower when compared to their controls. In addition, silica-exposed foundry workers had a significant reduction in the IgG, IgA and IgM levels. No significant differences were observed in the serum complement C3 and C4 levels of the workers. These results suggest that human chronic exposure to mainly silica and other chemicals originating from foundry and pottery settings may be detrimental to the immune system. PMID:12160616

  1. Geoenvironmental behavior of foundry sand amended mixtures for highway subbases.

    PubMed

    Guney, Yucel; Aydilek, Ahmet H; Demirkan, M Melih

    2006-01-01

    The high cost of landfilling and the potential uses of waste foundry sands have prompted research into their beneficial reuse. Roadways have a high potential for large volume usage of the foundry sands. A laboratory testing program was conducted on soil-foundry sand mixtures amended with cement and lime to assess their applicability as highway subbase materials. The mixtures were compacted in the laboratory at a variety of moisture contents and compactive efforts and subjected to unconfined compression, California bearing ratio, and hydraulic conductivity tests. The environmental suitability of the prepared mixtures was evaluated by analyzing the effluent collected during hydraulic conductivity tests. Finally, required subbase thicknesses were calculated using the laboratory-based strength parameters. The results of the study show that the strength of a mixture is highly dependent on the curing period, compactive energy, lime or cement presence, and water content at compaction. The resistance of foundry sand-based specimens to winter conditions is generally better than that of a typical subbase reference material. Laboratory leaching tests indicated that if these mixtures later come in contact with water that has been discharged directly to the environment (e.g., drainage through asphalt pavement), the quality of water will not be affected. PMID:16111882

  2. Ecotoxicity assessment of stabilized/solidified foundry sludge.

    PubMed

    Coz, Alberto; Andrés, Ana; Irabien, Angel

    2004-03-15

    The aim of this study is to evaluate the toxicity of the leachates from a foundry sludge and the derived products based on the stabilization/solidification (S/S) processes. Foundry sludge is an industrial hazardous waste containing inorganic and organic pollutants. The immobilization of the foundry waste has been performed using different S/S procedures based on cement or lime as binder agents and foundry sand fines, calcium-magnesium lignosulfonate, silica fume, activated carbon and black carbon as additives. The waste and stabilized/solidified derived products have been evaluated according to environmental considerations. The relation between the chemical composition and the ecotoxicity of the leachates has been studied in this paper. The ecotoxicity of the leachates has been related to the heavy metals and the organic pollutants by an empirical logarithmic linear expression. Different parameters of the logarithmic fitting have been obtained for the studied binder agents and additives allowing the establishment of a relationship between the S/S process and the ecotoxicity of the derived products. Results of this study have wide-ranging implications for immediate management strategies of waste with organic and inorganic pollutants in addition to application in long-term remediation efforts. PMID:15074704

  3. GRINDING ROOM AT SOUTHERN DUCTILE CASTING COMPANY, BESSEMER FOUNDRY SHOWING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    GRINDING ROOM AT SOUTHERN DUCTILE CASTING COMPANY, BESSEMER FOUNDRY SHOWING WHEELABORATOR THAT IMPALE SHOT AT TUMBLING CASTINGS TO REMOVE EXCESS SURFACE METALS AND SAND; ANNEALING OVENS TO HEAT CERTAIN CASTINGS TO ACHIEVE A DESIRED CHARACTERISTIC; AND GRINDING WHEELS USED TO REMOVE GATES. - Southern Ductile Casting Company, Grinding & Shipping, 2217 Carolina Avenue, Bessemer, Jefferson County, AL

  4. 52. SLABBING AND BLOOMING MILLS AND FOUNDRY (IN FOREGROUND), AS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    52. SLABBING AND BLOOMING MILLS AND FOUNDRY (IN FOREGROUND), AS SEEN FROM THE CLARK AVENUE BRIDGE. AT RIGHT, REAR, IS THE BASIC OXYGEN FURNACE. VIEW LOOKING NORTH. - Corrigan, McKinney Steel Company, 3100 East Forty-fifth Street, Cleveland, Cuyahoga County, OH

  5. 54. STEEL COMPLEX FROM CLARK AVENUE BRIDGE, LOOKING NORTHEAST. FOUNDRY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    54. STEEL COMPLEX FROM CLARK AVENUE BRIDGE, LOOKING NORTHEAST. FOUNDRY IN FOREGROUND, INGOT MOLDS ON TRACK AT RIGHT, BASIC OXYGEN FURNACE ON TRACK AT RIGHT. - Corrigan, McKinney Steel Company, 3100 East Forty-fifth Street, Cleveland, Cuyahoga County, OH

  6. View east to west, from tunnel between Foundry (right) and ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View east to west, from tunnel between Foundry (right) and Coal Bin (left) toward Machine Shop and Tool Room behind Wheelsets - East Broad Top Railroad & Coal Company, State Route 994, West of U.S. Route 522, Rockhill Furnace, Huntingdon County, PA

  7. COKE STORAGE HOPPER LOCATED OUTSIDE THE MALLEABLE FOUNDRY SHOWING LOADING ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    COKE STORAGE HOPPER LOCATED OUTSIDE THE MALLEABLE FOUNDRY SHOWING LOADING DEVICE THAT USED A SKIP CAR TO FILL THE HOPPER FROM UNDERGROUND GRAVITY-FED STORAGE AREAS FROM INCOMING RAILROAD CARS. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  8. Geoenvironmental behavior of foundry sand amended mixtures for highway subbases.

    PubMed

    Guney, Yucel; Aydilek, Ahmet H; Demirkan, M Melih

    2006-01-01

    The high cost of landfilling and the potential uses of waste foundry sands have prompted research into their beneficial reuse. Roadways have a high potential for large volume usage of the foundry sands. A laboratory testing program was conducted on soil-foundry sand mixtures amended with cement and lime to assess their applicability as highway subbase materials. The mixtures were compacted in the laboratory at a variety of moisture contents and compactive efforts and subjected to unconfined compression, California bearing ratio, and hydraulic conductivity tests. The environmental suitability of the prepared mixtures was evaluated by analyzing the effluent collected during hydraulic conductivity tests. Finally, required subbase thicknesses were calculated using the laboratory-based strength parameters. The results of the study show that the strength of a mixture is highly dependent on the curing period, compactive energy, lime or cement presence, and water content at compaction. The resistance of foundry sand-based specimens to winter conditions is generally better than that of a typical subbase reference material. Laboratory leaching tests indicated that if these mixtures later come in contact with water that has been discharged directly to the environment (e.g., drainage through asphalt pavement), the quality of water will not be affected.

  9. 26. SOME CORES, SUCH AS THESE IN THE BRASS FOUNDRY ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    26. SOME CORES, SUCH AS THESE IN THE BRASS FOUNDRY CA.1950, ARE DIPPED INTO A SOLUTION PRIOR TO BEING BAKED IN THE CORE OVEN BEHIND, TO SET THE RESIN AND CREATE A STRUCTURE STRONG ENOUGH TO HOLD UP AGAINST MOLTEN METAL. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  10. 13. THESE STOCKHAM WORKERS FROM THE MALLEABLE FOUNDRY TYPIFIED THE ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    13. THESE STOCKHAM WORKERS FROM THE MALLEABLE FOUNDRY TYPIFIED THE RACIAL SEPARATIONS WITHIN THE COMPANY WHERE AFRICAN-AMERICANS FILLED THE VAST MAJORITY OF LABOR-INTENSIVE POSITIONS WITHOUT BEING REPRESENTED IN WHITE COLLAR JOBS CA. 1950. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

  11. Alterations in immune parameters in foundry and pottery workers.

    PubMed

    Başaran, Nurşen; Shubair, Mohammed; Undeğer, Ulkü; Canpinar, Hande; Kars, Ayşe

    2002-09-01

    To assess the immune competence of workers occupationally exposed to mainly silica, peripheral blood lymphocytes, serum immunoglobulins (IgG, IgA and IgM), C3 and C4 complement protein concentrations of foundry and pottery workers were evaluated and compared to healthy controls with no history of silica and other chemical exposure. The absolute number and percentage of functionally different subsets of peripheral blood mononuclear lymphocytes, i.e. T, T-suppressor and natural killer cells were unchanged. However, T-helper lymphocytes in pottery (P<0.05) and B cells in foundry (P<0.01) workers were significantly lower when compared to their controls. In addition, silica-exposed foundry workers had a significant reduction in the IgG, IgA and IgM levels. No significant differences were observed in the serum complement C3 and C4 levels of the workers. These results suggest that human chronic exposure to mainly silica and other chemicals originating from foundry and pottery settings may be detrimental to the immune system.

  12. Pyrolysis of Carbonaceous Foundry Sand Additives: Seacoal and Gilsonite

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Seacoal and gilsonite are used by the foundry industry as carbonaceous additives in green molding sands. In this study, pyrolysis was used to simulate the heating conditions that the carbonaceous additives would experience during metal casting. Gas chromatography-mass spectrometry was used to tent...

  13. VIEW LOOKING WEST TOWARD BIRMINGHAM CITY CENTER, HARDIETYNES FOUNDRY IN ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    VIEW LOOKING WEST TOWARD BIRMINGHAM CITY CENTER, HARDIE-TYNES FOUNDRY IN FOREGROUND, RED MOUNTAIN IN FAR LEFT HORIZON, US 280 RUNNING HORIZONTAL, I20-59 RUNNING VERTICAL. - Hardie-Tynes Manufacturing Company, 800 Twenty-eighth Street, North, Birmingham, Jefferson County, AL

  14. Mechanical engineering note - safety analysis of molten uranium/water interaction in the uranium foundry furnace

    SciTech Connect

    Gourdin, W H; Sze, J

    1999-08-19

    This Engineering Note describes the development of the accident criteria used the basis for the design of the uranium foundry vacuum vessel. The results of this analysis provide input into other safety notes that investigate how well the uranium containment boundary will maintain its integrity during the design basis accident. The preventative measures that have been designed into the system to minimize the potential to produce a flammable gas mixture are described. The system response is designed for consistency with applicable sections of the LLNL Health and Safety Manual, as well as the Mechanical engineering Safety Design Standards.

  15. Open foundry platform for high-performance electronic-photonic integration.

    PubMed

    Orcutt, Jason S; Moss, Benjamin; Sun, Chen; Leu, Jonathan; Georgas, Michael; Shainline, Jeffrey; Zgraggen, Eugen; Li, Hanqing; Sun, Jie; Weaver, Matthew; Urošević, Stevan; Popović, Miloš; Ram, Rajeev J; Stojanović, Vladimir

    2012-05-21

    This paper presents photonic devices with 3 dB/cm waveguide loss fabricated in an existing commercial electronic 45 nm SOI-CMOS foundry process. By utilizing existing front-end fabrication processes the photonic devices are monolithically integrated with electronics in the same physical device layer as transistors achieving 4 ps logic stage delay, without degradation in transistor performance. We demonstrate an 8-channel optical microring-resonator filter bank and optical modulators, both controlled by integrated digital circuits. By developing a device design methodology that requires zero process infrastructure changes, a widely available platform for high-performance photonic-electronic integrated circuits is enabled.

  16. Occupational eosinophilic bronchitis in a foundry worker exposed to isocyanate and a baker exposed to flour

    PubMed Central

    Stefano, Fabio Di; Giampaolo, Luca Di; Verna, Nicola; Gioacchino, Mario Di

    2007-01-01

    Eosinophilic bronchitis without asthma may occur as a consequence of occupational exposure. The cases of a foundry worker and a baker who developed symptoms, respectively, due to exposure to isocyanate and flour, are reported. Cough was not associated with variable airflow obstruction or with airway hyper‐responsiveness and was responsive to inhaled corticosteroids. The eosinophilia detectable in their sputum was causally related to the occupational exposure in the workplace. The examination of induced sputum should be used in addition to the objective monitoring of lung function for workers who have asthma‐like symptoms in an occupational setting. PMID:16055615

  17. The Application of Ontological Methods toward Coastal Restoration

    NASA Astrophysics Data System (ADS)

    Ramachandran, R.; Movva, S.; Hardin, D.

    2007-12-01

    At the fall 2006 AGU meeting the Information Technology and Systems Center at the University of Alabama in Huntsville debuted a tool for ontology based search and resource aggregation called Noesis. Since that time Noesis, with a new ontology for seagrass habitats in the Gulf of Mexico, has been utilized to support evaluations of potential seagrass restoration sites. The seagrass ontology was generated from a standard stressor conceptual model description for five species of seagrass common to the Northern Gulf of Mexico. Coupling the seagrass ontology with the existing atmospheric science ontology allowed scientists to locate and retrieve substantial information about the seagrass habitat as well as stressors that impact the habitat induced by climate change and short term atmospheric phenomena. A domain specific catalog of seagrass resources was constructed and an application ontology developed that mapped the keywords of the catalog to the combined (atmospheric and seagrass) ontologies of Noesis. Noesis uses domain ontologies to help the user scope the search queries to ensure that the search results are both accurate and complete. The domain ontologies guide the user to refine their search query and thereby reduce the user's burden of experimenting with different search strings. Semantics are captured by refining the query terms to cover synonyms, specializations, generalizations and related concepts. As a resource aggregator Noesis categorizes search results from different online resources such as education materials, publications, datasets, web search engines that might be of interest to the user. This presentation will give an overview of Noesis and describe how it has been applied to coastal restoration investigations.

  18. An Ontological Solution to Support Interoperability in the Textile Industry

    NASA Astrophysics Data System (ADS)

    Duque, Arantxa; Campos, Cristina; Jiménez-Ruiz, Ernesto; Chalmeta, Ricardo

    Significant developments in information and communication technologies and challenging market conditions have forced enterprises to adapt their way of doing business. In this context, providing mechanisms to guarantee interoperability among heterogeneous organisations has become a critical issue. Even though prolific research has already been conducted in the area of enterprise interoperability, we have found that enterprises still struggle to introduce fully interoperable solutions, especially, in terms of the development and application of ontologies. Thus, the aim of this paper is to introduce basic ontology concepts in a simple manner and to explain the advantages of the use of ontologies to improve interoperability. We will also present a case study showing the implementation of an application ontology for an enterprise in the textile/clothing sector.

  19. An ontology of scientific experiments.

    PubMed

    Soldatova, Larisa N; King, Ross D

    2006-12-22

    The formal description of experiments for efficient analysis, annotation and sharing of results is a fundamental part of the practice of science. Ontologies are required to achieve this objective. A few subject-specific ontologies of experiments currently exist. However, despite the unity of scientific experimentation, no general ontology of experiments exists. We propose the ontology EXPO to meet this need. EXPO links the SUMO (the Suggested Upper Merged Ontology) with subject-specific ontologies of experiments by formalizing the generic concepts of experimental design, methodology and results representation. EXPO is expressed in the W3C standard ontology language OWL-DL. We demonstrate the utility of EXPO and its ability to describe different experimental domains, by applying it to two experiments: one in high-energy physics and the other in phylogenetics. The use of EXPO made the goals and structure of these experiments more explicit, revealed ambiguities, and highlighted an unexpected similarity. We conclude that, EXPO is of general value in describing experiments and a step towards the formalization of science. PMID:17015305

  20. An ontology of scientific experiments

    PubMed Central

    Soldatova, Larisa N; King, Ross D

    2006-01-01

    The formal description of experiments for efficient analysis, annotation and sharing of results is a fundamental part of the practice of science. Ontologies are required to achieve this objective. A few subject-specific ontologies of experiments currently exist. However, despite the unity of scientific experimentation, no general ontology of experiments exists. We propose the ontology EXPO to meet this need. EXPO links the SUMO (the Suggested Upper Merged Ontology) with subject-specific ontologies of experiments by formalizing the generic concepts of experimental design, methodology and results representation. EXPO is expressed in the W3C standard ontology language OWL-DL. We demonstrate the utility of EXPO and its ability to describe different experimental domains, by applying it to two experiments: one in high-energy physics and the other in phylogenetics. The use of EXPO made the goals and structure of these experiments more explicit, revealed ambiguities, and highlighted an unexpected similarity. We conclude that, EXPO is of general value in describing experiments and a step towards the formalization of science. PMID:17015305

  1. Ontological System for Context Artifacts and Resources

    NASA Astrophysics Data System (ADS)

    Huang, T.; Chung, N. T.; Mukherjee, R. M.

    2012-12-01

    The Adaptive Vehicle Make (AVM) program is a portfolio of programs, managed by the Defense Advanced Research Projects Agency (DARPA). It was established to revolutionize how DoD designs, verifies, and manufactures complex defense systems and vehicles. The Component, Context, and Manufacturing Model Library (C2M2L; pronounced "camel") seeks to develop domain-specific models needed to enable design, verification, and fabrication of the Fast Adaptable Next-Generation (FANG) infantry fighting vehicle using in its overall infrastructure. Terrain models are being developed to represent the surface/fluid that an amphibious infantry fighting vehicle would traverse, ranging from paved road surfaces to rocky, mountainous terrain, slope, discrete obstacles, mud, sand snow, and water fording. Context models are being developed to provide additional data for environmental factors, such as: humidity, wind speed, particulate presence and character, solar radiation, cloud cover, precipitation, and more. The Ontological System for Context Artifacts and Resources (OSCAR) designed and developed at the Jet Propulsion Laboratory is semantic web data system that enables context artifacts to be registered and searched according to their meaning, rather than indexed according to their syntactic structure alone (as in the case for traditional search engines). The system leverages heavily on the Semantic Web for Earth and Environmental Terminology (SWEET) ontologies to model physical terrain environment and context model characteristics. In this talk, we focus on the application of the SWEET ontologies and the design of the OSCAR system architecture.

  2. Ontology for FMRI as a biomedical informatics method.

    PubMed

    Nakai, Toshiharu; Bagarinao, Epifanio; Tanaka, Yoshio; Matsuo, Kayako; Racoceanu, Daniel

    2008-01-01

    Ontological engineering is one of the most challenging topics in biomedical informatics because of its key role in integrating the heterogeneous database used by biomedical information services. Ontology can translate concepts and their real-world relationships into expressions that can be processed by computer programs or web services, providing a unique taxonomic frame to describe a pathway for extracting, processing, storing, and retrieving information. In developing clinical functional neuroimaging, which requires the integration of heterogeneous information derived from multimodal measurement of the brain, these features will be indispensable. Neuroimaging ontology is remarkable in that it requires detailed description of the hypothesis, the paradigm employed, and a scheme for data generation. Neuroimaging modalities, such as functional magnetic resonance imaging (fMRI), magnetoencephalography (MEG), electroencephalography (EEG), and near infrared spectroscopy (NIRS), share similar application purposes, imaging protocol, analyzing methods, and data structure; semantic gaps that remain among the modalities will be bridged as ontology develops. High-performance, global resource information database (GRID) computing and the applications organized as service-oriented computing (SOC) will support the heavy processing to integrate the heterogeneous neuroimaging system. We have been developing such a distributed intelligent neuroimaging system for real-time fMRI analysis, called BAXGRID, and a neuroimaging database. The fMRI ontology of this system will be integrated with established medical ontologies, such as the Unified Medical Language System (UMLS).

  3. Adverse Drug Event Ontology: Gap Analysis for Clinical Surveillance Application.

    PubMed

    Adam, Terrence J; Wang, Jin

    2015-01-01

    Adverse drug event identification and management are an important patient safety problem given the potential for event prevention. Previous efforts to provide structured data methods for population level identification of adverse drug events have been established, but important gaps in coverage remain. ADE identification gaps contribute to suboptimal and inefficient event identification. To address the ADE identification problem, a gap assessment was completed with the creation of a proposed comprehensive ontology using a Minimal Clinical Data Set framework incorporating existing identification approaches, clinical literature and a large set of inpatient clinical data. The new ontology was developed and tested using the National Inpatient Sample database with the validation results demonstrating expanded ADE identification capacity. In addition, the newly proposed ontology elements are noted to have significant inpatient mortality, above median inpatient costs and a longer length of stay when compared to existing ADE ontology elements and patients without ADE exposure.

  4. Adverse Drug Event Ontology: Gap Analysis for Clinical Surveillance Application

    PubMed Central

    Adam, Terrence J.; Wang, Jin

    2015-01-01

    Adverse drug event identification and management are an important patient safety problem given the potential for event prevention. Previous efforts to provide structured data methods for population level identification of adverse drug events have been established, but important gaps in coverage remain. ADE identification gaps contribute to suboptimal and inefficient event identification. To address the ADE identification problem, a gap assessment was completed with the creation of a proposed comprehensive ontology using a Minimal Clinical Data Set framework incorporating existing identification approaches, clinical literature and a large set of inpatient clinical data. The new ontology was developed and tested using the National Inpatient Sample database with the validation results demonstrating expanded ADE identification capacity. In addition, the newly proposed ontology elements are noted to have significant inpatient mortality, above median inpatient costs and a longer length of stay when compared to existing ADE ontology elements and patients without ADE exposure. PMID:26306223

  5. Enhancing Terminological Knowledge With Upper Level Ontologies

    PubMed Central

    Seppälä, Selja; Hicks, Amanda

    2016-01-01

    In this communication, we advocate the use of upper level ontologies such as the Basic Formal Ontology (BFO) to enhance terminological resources and research. First, we present common issues in ontologized terminological work. Then, we review two projects that illustrate the potential advantages of integrating rigorous formal upper level ontologies. Finally, we discuss possible challenges and conclude with a summary of the benefits that such ontologies can bring to both terminological theory and practice. PMID:27011763

  6. Suggesting Missing Relations in Biomedical Ontologies Based on Lexical Regularities.

    PubMed

    Quesada-Martínez, Manuel; Fernández-Breis, Jesualdo Tomás; Karlsson, Daniel

    2016-01-01

    The number of biomedical ontologies has increased significantly in recent years. Many of such ontologies are the result of efforts of communities of domain experts and ontology engineers. The development and application of quality assurance (QA) methods should help these communities to develop useful ontologies for both humans and machines. According to previous studies, biomedical ontologies are rich in natural language content, but most of them are not so rich in axiomatic terms. Here, we are interested in studying the relation between content in natural language and content in axiomatic form. The analysis of the labels of the classes permits to identify lexical regularities (LRs), which are sets of words that are shared by labels of different classes. Our assumption is that the classes exhibiting an LR should be logically related through axioms, which is used to propose an algorithm to detect missing relations in the ontology. Here, we analyse a lexical regularity of SNOMED CT, congenital stenosis, which is reported as problematic by the SNOMED CT maintenance team. PMID:27577409

  7. The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge

    SciTech Connect

    Rubin, Daniel L.; Lewis, Suzanna E.; Mungall, Chris J.; Misra,Sima; Westerfield, Monte; Ashburner, Michael; Sim, Ida; Chute,Christopher G.; Solbrig, Harold; Storey, Margaret-Anne; Smith, Barry; Day-Richter, John; Noy, Natalya F.; Musen, Mark A.

    2006-01-23

    The National Center for Biomedical Ontology (http://bioontology.org) is a consortium that comprises leading informaticians, biologists, clinicians, and ontologists funded by the NIH Roadmap to develop innovative technology and methods that allow scientists to record, manage, and disseminate biomedical information and knowledge in machine-processable form. The goals of the Center are: (1) to help unify the divergent and isolated efforts in ontology development by promoting high quality open-source, standards-based tools to create, manage, and use ontologies, (2) to create new software tools so that scientists can use ontologies to annotate and analyze biomedical data, (3) to provide a national resource for the ongoing evaluation, integration, and evolution of biomedical ontologies and associated tools and theories in the context of driving biomedical projects (DBPs), and (4) to disseminate the tools and resources of the Center and to identify, evaluate, and communicate best practices of ontology development to the biomedical community. The Center is working toward these objectives by providing tools to develop ontologies and to annotate experimental data, and by developing resources to integrate and relate existing ontologies as well as by creating repositories of biomedical data that are annotated using those ontologies. The Center is providing training workshops in ontology design, development, and usage, and is also pursuing research in ontology evaluation, quality, and use of ontologies to promote scientific discovery. Through the research activities within the Center, collaborations with the DBPs, and interactions with the biomedical community, our goal is to help scientists to work more effectively in the e-science paradigm, enhancing experiment design, experiment execution, data analysis, information synthesis, hypothesis generation and testing, and understand human disease.

  8. Experience in Aligning Anatomical Ontologies.

    PubMed

    Zhang, Songmao; Bodenreider, Olivier

    2007-01-01

    An ontology is a formal representation of a domain modeling the entities in the domain and their relations. When a domain is represented by multiple ontologies, there is need for creating mappings among these ontologies in order to facilitate the integration of data annotated with these ontologies and reasoning across ontologies. The objective of this paper is to recapitulate our experience in aligning large anatomical ontologies and to reflect on some of the issues and challenges encountered along the way. The four anatomical ontologies under investigation are the Foundational Model of Anatomy, GALEN, the Adult Mouse Anatomical Dictionary and the NCI Thesaurus. Their underlying representation formalisms are all different. Our approach to aligning concepts (directly) is automatic, rule-based, and operates at the schema level, generating mostly point-to-point mappings. It uses a combination of domain-specific lexical techniques and structural and semantic techniques (to validate the mappings suggested lexically). It also takes advantage of domain-specific knowledge (lexical knowledge from external resources such as the Unified Medical Language System, as well as knowledge augmentation and inference techniques). In addition to point-to-point mapping of concepts, we present the alignment of relationships and the mapping of concepts group-to-group. We have also successfully tested an indirect alignment through a domain-specific reference ontology. We present an evaluation of our techniques, both against a gold standard established manually and against a generic schema matching system. The advantages and limitations of our approach are analyzed and discussed throughout the paper.

  9. A set of ontologies to drive tools for the control of vector-borne diseases

    PubMed Central

    Topalis, Pantelis; Dialynas, Emmanuel; Mitraka, Elvira; Deliyanni, Elena; Siden-Kiamos, Inga; Louis, Christos

    2010-01-01

    We are developing a set of ontologies dealing with vector-borne diseases as well as the arthropod vectors that transmit them. After building ontologies for mosquito and tick anatomy we continued this project with an ontology of insecticide resistance followed by a series of ontologies that describe malaria as well as physiological processes of mosquitoes that are relevant to, and involved in, disease transmission. These will later be expanded to encompass other vector-borne diseases as well as non-mosquito vectors. The aim of the whole undertaking, which is worked out in the frame of the international IDO (Infectious Disease Ontology) project, is to provide the community with a set of ontological tools that can be used both in the development of specific databases and, most importantly, in the construction of decision support systems (DSS) to control these diseases. PMID:20363364

  10. Ontology integration: experience with medical terminologies.

    PubMed

    Lee, Yugyung; Supekar, Kaustubh; Geller, James

    2006-01-01

    To build a common controlled vocabulary is a formidable challenge in medical informatics. Due to vast scale and multiplicity in interpretation of medical data, it is natural to face overlapping terminologies in the process of practicing medical informatics [A. Rector, Clinical terminology: why is it so hard? Methods Inf. Med. 38 (1999) 239-252]. A major concern lies in the integration of seemingly overlapping terminologies in the medical domain and this issue has not been well addressed. In this paper, we describe a novel approach for medical ontology integration that relies on the theory of Algorithmic Semantic Refinement we previously developed. Our approach simplifies the task of matching pairs of corresponding concepts derived from a pair of ontologies, which is vital to terminology mapping. A formal theory and algorithm for our approach have been devised and the application of this method to two medical terminologies has been developed. The result of our work is an integrated medical terminology and a methodology and implementation ready to use for other ontology integration tasks.

  11. Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting.

    PubMed

    Soldatova, Larisa N; Sansone, Susanna-Assunta; Dumontier, Michel; Shah, Nigam H

    2013-04-15

    Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes. PMID:23735191

  12. Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting

    PubMed Central

    2013-01-01

    Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes. PMID:23735191

  13. Selected papers from the 15th Annual Bio-Ontologies Special Interest Group Meeting.

    PubMed

    Soldatova, Larisa N; Sansone, Susanna-Assunta; Dumontier, Michel; Shah, Nigam H

    2013-04-15

    Over the 15 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers and the commentary selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data, annotating patent records, NCBO Web services, ontology developments for probabilistic reasoning and for physiological processes, and analysis of the progress of annotation and structural GO changes.

  14. Formal ontology for natural language processing and the integration of biomedical databases.

    PubMed

    Simon, Jonathan; Dos Santos, Mariana; Fielding, James; Smith, Barry

    2006-01-01

    The central hypothesis underlying this communication is that the methodology and conceptual rigor of a philosophically inspired formal ontology can bring significant benefits in the development and maintenance of application ontologies [A. Flett, M. Dos Santos, W. Ceusters, Some Ontology Engineering Procedures and their Supporting Technologies, EKAW2002, 2003]. This hypothesis has been tested in the collaboration between Language and Computing (L&C), a company specializing in software for supporting natural language processing especially in the medical field, and the Institute for Formal Ontology and Medical Information Science (IFOMIS), an academic research institution concerned with the theoretical foundations of ontology. In the course of this collaboration L&C's ontology, LinKBase, which is designed to integrate and support reasoning across a plurality of external databases, has been subjected to a thorough auditing on the basis of the principles underlying IFOMIS's Basic Formal Ontology (BFO) [B. Smith, Basic Formal Ontology, 2002. http://ontology.buffalo.edu/bfo]. The goal is to transform a large terminology-based ontology into one with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase are standardized in the framework of first-order logic. In this paper we describe how this principles-based standardization has led to a greater degree of internal coherence of the LinKBase structure, and how it has facilitated the construction of mappings between external databases using LinKBase as translation hub. We argue that the collaboration here described represents a new phase in the quest to solve the so-called "Tower of Babel" problem of ontology integration [F. Montayne, J. Flanagan, Formal Ontology: The Foundation for Natural Language Processing, 2003. http://www.landcglobal.com/].

  15. Structuring an event ontology for disease outbreak detection

    PubMed Central

    Kawazoe, Ai; Chanlekha, Hutchatai; Shigematsu, Mika; Collier, Nigel

    2008-01-01

    Background This paper describes the design of an event ontology being developed for application in the machine understanding of infectious disease-related events reported in natural language text. This event ontology is designed to support timely detection of disease outbreaks and rapid judgment of their alerting status by 1) bridging a gap between layman's language used in disease outbreak reports and public health experts' deep knowledge, and 2) making multi-lingual information available. Construction and content This event ontology integrates a model of experts' knowledge for disease surveillance, and at the same time sets of linguistic expressions which denote disease-related events, and formal definitions of events. In this ontology, rather general event classes, which are suitable for application to language-oriented tasks such as recognition of event expressions, are placed on the upper-level, and more specific events of the experts' interest are in the lower level. Each class is related to other classes which represent participants of events, and linked with multi-lingual synonym sets and axioms. Conclusions We consider that the design of the event ontology and the methodology introduced in this paper are applicable to other domains which require integration of natural language information and machine support for experts to assess them. The first version of the ontology, with about 40 concepts, will be available in March 2008. PMID:18426553

  16. Biomedical imaging ontologies: A survey and proposal for future work

    PubMed Central

    Smith, Barry; Arabandi, Sivaram; Brochhausen, Mathias; Calhoun, Michael; Ciccarese, Paolo; Doyle, Scott; Gibaud, Bernard; Goldberg, Ilya; Kahn, Charles E.; Overton, James; Tomaszewski, John; Gurcan, Metin

    2015-01-01

    Background: Ontology is one strategy for promoting interoperability of heterogeneous data through consistent tagging. An ontology is a controlled structured vocabulary consisting of general terms (such as “cell” or “image” or “tissue” or “microscope”) that form the basis for such tagging. These terms are designed to represent the types of entities in the domain of reality that the ontology has been devised to capture; the terms are provided with logical definitions thereby also supporting reasoning over the tagged data. Aim: This paper provides a survey of the biomedical imaging ontologies that have been developed thus far. It outlines the challenges, particularly faced by ontologies in the fields of histopathological imaging and image analysis, and suggests a strategy for addressing these challenges in the example domain of quantitative histopathology imaging. Results and Conclusions: The ultimate goal is to support the multiscale understanding of disease that comes from using interoperable ontologies to integrate imaging data with clinical and genomics data. PMID:26167381

  17. Ontology-centric integration and navigation of the dengue literature.

    PubMed

    Rajapakse, Menaka; Kanagasabai, Rajaraman; Ang, Wee Tiong; Veeramani, Anitha; Schreiber, Mark J; Baker, Christopher J O

    2008-10-01

    Uninhibited access to the unstructured information distributed across the web and in scientific literature databases continues to be beyond the reach of scientists and health professionals. To address this challenge we have developed a literature driven, ontology-centric navigation infrastructure consisting of a content acquisition engine, a domain-specific ontology (in OWL-DL) and an ontology instantiation pipeline delivering sentences derived by domain-specific text mining. A visual query tool for reasoning over A-box instances in the populated ontology is presented and used to build conceptual queries that can be issued to the knowledgebase. We have deployed this generic infrastructure to facilitate data integration and knowledge sharing in the domain of dengue, which is one of the most prevalent viral diseases that continue to infect millions of people in the tropical and subtropical regions annually. Using our unique methodology we illustrate simplified search and discovery on dengue information derived from distributed resources and aggregated according to dengue ontology. Furthermore we apply data mining to the instantiated ontology to elucidate trends in the mentions of dengue serotypes in scientific abstracts since 1974.

  18. A Chronostratigraphic Relational Database Ontology

    NASA Astrophysics Data System (ADS)

    Platon, E.; Gary, A.; Sikora, P.

    2005-12-01

    A chronostratigraphic research database was donated by British Petroleum to the Stratigraphy Group at the Energy and Geoscience Institute (EGI), University of Utah. These data consists of over 2,000 measured sections representing over three decades of research into the application of the graphic correlation method. The data are global and includes both microfossil (foraminifera, calcareous nannoplankton, spores, pollen, dinoflagellate cysts, etc) and macrofossil data. The objective of the donation was to make the research data available to the public in order to encourage additional chronostratigraphy studies, specifically regarding graphic correlation. As part of the National Science Foundation's Cyberinfrastructure for the Geosciences (GEON) initiative these data have been made available to the public at http://css.egi.utah.edu. To encourage further research using the graphic correlation method, EGI has developed a software package, StrataPlot that will soon be publicly available from the GEON website as a standalone software download. The EGI chronostratigraphy research database, although relatively large, has many data holes relative to some paleontological disciplines and geographical areas, so the challenge becomes how do we expand the data available for chronostratigrahic studies using graphic correlation. There are several public or soon-to-be public databases available to chronostratigraphic research, but they have their own data structures and modes of presentation. The heterogeneous nature of these database schemas hinders their integration and makes it difficult for the user to retrieve and consolidate potentially valuable chronostratigraphic data. The integration of these data sources would facilitate rapid and comprehensive data searches, thus helping advance studies in chronostratigraphy. The GEON project will host a number of databases within the geology domain, some of which contain biostratigraphic data. Ontologies are being developed to provide

  19. Blending foundry sands with soil: Effect on dehydrogenase activity.

    PubMed

    Dungan, Robert S; Kukier, Urzsula; Lee, Brad

    2006-03-15

    Each year U.S. foundries landfill several million tons of sand that can no longer be used to make metalcasting molds and cores. A possible use for these materials is as an ingredient in manufactured soils; however, potentially harmful metals and resin binders (used to make cores) may adversely impact the soil microbial community. In this study, the dehydrogenase activity (DHA) of soil amended with molding sand (clay-coated sand known as "green sand") or core sands at 10%, 30%, and 50% (dry wt.) was determined. The green sands were obtained from iron, aluminum, and brass foundries; the core sands were made with phenol-formaldehyde or furfuryl alcohol based resins. Overall, incremental additions of these sands resulted in a decrease in the DHA which lasted throughout the 12-week experimental period. A brass green sand, which contained high concentrations of Cu, Pb, and Zn, severely impacted the DHA. By week 12 no DHA was detected in the 30% and 50% treatments. In contrast, the DHA in soil amended with an aluminum green sand was 2.1 times higher (all blending ratios), on average, at week 4 and 1.4 times greater (30% and 50% treatments only) than the controls by week 12. In core sand-amended soil, the DHA results were similar to soils amended with aluminum and iron green sands. Increased activity in some treatments may be a result of the soil microorganisms utilizing the core resins as a carbon source. The DHA assay is a sensitive indicator of environmental stress caused by foundry sand constituents and may be useful to assess which foundry sands are suitable for beneficial use in the environment. PMID:15975632

  20. Possibilities of energy recovery and integrated energy supply for foundries

    NASA Astrophysics Data System (ADS)

    Pautz, J.

    1980-08-01

    The energy utilization of foundries equipped with electric melting and arc furnaces was investigated. Systems were studied which optimize heat economy. Studies of the energy balance of arc furnaces with conventional refractory linings and with water cooled linings clearly demonstrate recovery possibilities as a function of the temperature of the waste heat. Domestic water heating, central heating, scrap drying and steam generator plant applications are proposed for the recovered heat. A considerable overall improvement in efficiency can be achieved.

  1. ``Force,'' ontology, and language

    NASA Astrophysics Data System (ADS)

    Brookes, David T.; Etkina, Eugenia

    2009-06-01

    We introduce a linguistic framework through which one can interpret systematically students’ understanding of and reasoning about force and motion. Some researchers have suggested that students have robust misconceptions or alternative frameworks grounded in everyday experience. Others have pointed out the inconsistency of students’ responses and presented a phenomenological explanation for what is observed, namely, knowledge in pieces. We wish to present a view that builds on and unifies aspects of this prior research. Our argument is that many students’ difficulties with force and motion are primarily due to a combination of linguistic and ontological difficulties. It is possible that students are primarily engaged in trying to define and categorize the meaning of the term “force” as spoken about by physicists. We found that this process of negotiation of meaning is remarkably similar to that engaged in by physicists in history. In this paper we will describe a study of the historical record that reveals an analogous process of meaning negotiation, spanning multiple centuries. Using methods from cognitive linguistics and systemic functional grammar, we will present an analysis of the force and motion literature, focusing on prior studies with interview data. We will then discuss the implications of our findings for physics instruction.

  2. The regeneration of waste foundry sand and residue stabilization using coal refuse.

    PubMed

    Park, Chong-Lyuck; Kim, Byoung-Gon; Yu, Youngchul

    2012-02-15

    The processes for recycling waste foundry sand are divided between regeneration and beneficial reuse, and the potential for regeneration is higher than that of reuse. In this study, two processes for the recycling and residue stabilization of waste foundry sands were considered. One is the dry mechanical process for recycling, and the other is the stabilization process for powdered residue. The dry mechanical process of regeneration consists of crushing, grinding, separation, and classification. To stabilize the residues that were generated through the regeneration process, powdered residues were pelletized by a high-shear pelletizer, and the surfaces of the pellets were subsequently coated with coal refuse powders that contained sodium silicate as a binder. Coated pellets were sintered by a self-propagating combustion method. The refractory index of the recycled sands, as measured by the Seger cone method, was over -34, and their SiO(2) contents of 94% was similar to that of green sand. The general conclusion that coal refuse and sodium silicate stabilize heavy metals better than other processes may lead to the development of a cost-effective solution for stabilizing heavy metals in residues. PMID:22197564

  3. Asthma caused by diphenylmethane diisocyanate in foundry workers. Clinical, bronchial provocation, and immunologic studies

    SciTech Connect

    Zammit-Tabona, M.; Sherkin, M.; Kijek, K.; Chan, H.; Chan-Yeung, M.

    1983-08-01

    Eleven foundry workers who developed asthmatic symptoms were studied with inhalation provocation tests with formaldehyde and diphenylmethane diisocyanate (MDI). These latter two chemicals are components of PepSet used for making molds for casting. Six subjects showed specific asthmatic reactions to MDI challenge (more than 20% fall in FEV1), 2 had a combined immediate and late reaction, and 4 had a predominantly late reaction. Four of the 6 subjects experienced recurrent nocturnal asthmatic reactions after a single challenge with MDI that lasted as long as 7 days, and this was associated with a significant increase in bronchial reactivity to methacholine. One subject had an immediate irritant reaction to both MDI and formaldehyde, which was spontaneously reversed in a few minutes. None of the remaining 10 subjects had a positive reaction to formaldehyde challenge. The reactors to MDI showed more evidence of air-flow obstruction in their lung function measurements and had a greater bronchial sensitivity to methacholine than the nonreactors but there was no difference in age, smoking habits, or atopic status. Specific IgE antibodies to MDI-human serum albumin conjugate were detected in 2 subjects, a reactor and a nonreactor. Specific IgG anti-MDI antibodies were detected in 4 subjects, 2 who reacted and 2 who did not. No difference in the pattern of response to MDI inhalation was observed in relation to the different immunologic findings. We conclude that MDI is a cause of asthma in foundry workers.

  4. The regeneration of waste foundry sand and residue stabilization using coal refuse.

    PubMed

    Park, Chong-Lyuck; Kim, Byoung-Gon; Yu, Youngchul

    2012-02-15

    The processes for recycling waste foundry sand are divided between regeneration and beneficial reuse, and the potential for regeneration is higher than that of reuse. In this study, two processes for the recycling and residue stabilization of waste foundry sands were considered. One is the dry mechanical process for recycling, and the other is the stabilization process for powdered residue. The dry mechanical process of regeneration consists of crushing, grinding, separation, and classification. To stabilize the residues that were generated through the regeneration process, powdered residues were pelletized by a high-shear pelletizer, and the surfaces of the pellets were subsequently coated with coal refuse powders that contained sodium silicate as a binder. Coated pellets were sintered by a self-propagating combustion method. The refractory index of the recycled sands, as measured by the Seger cone method, was over -34, and their SiO(2) contents of 94% was similar to that of green sand. The general conclusion that coal refuse and sodium silicate stabilize heavy metals better than other processes may lead to the development of a cost-effective solution for stabilizing heavy metals in residues.

  5. Cognitive ontologies for neuropsychiatric phenomics research.

    PubMed

    Bilder, Robert M; Sabb, Fred W; Parker, D Stott; Kalar, Donald; Chu, Wesley W; Fox, Jared; Freimer, Nelson B; Poldrack, Russell A

    2009-01-01

    Now that genome-wide association studies (GWAS) are dominating the landscape of genetic research on neuropsychiatric syndromes, investigators are being faced with complexity on an unprecedented scale. It is now clear that phenomics, the systematic study of phenotypes on a genome-wide scale, comprises a rate-limiting step on the road to genomic discovery. To gain traction on the myriad paths leading from genomic variation to syndromal manifestations, informatics strategies must be deployed to navigate increasingly broad domains of knowledge and help researchers find the most important signals. The success of the Gene Ontology project suggests the potential benefits of developing schemata to represent higher levels of phenotypic expression. Challenges in cognitive ontology development include the lack of formal definitions of key concepts and relations among entities, the inconsistent use of terminology across investigators and time, and the fact that relations among cognitive concepts are not likely to be well represented by simple hierarchical "tree" structures. Because cognitive concept labels are labile, there is a need to represent empirical findings at the cognitive test indicator level. This level of description has greater consistency, and benefits from operational definitions of its concepts and relations to quantitative data. Considering cognitive test indicators as the foundation of cognitive ontologies carries several implications, including the likely utility of cognitive task taxonomies. The concept of cognitive "test speciation" is introduced to mark the evolution of paradigms sufficiently unique that their results cannot be "mated" productively with others in meta-analysis. Several projects have been initiated to develop cognitive ontologies at the Consortium for Neuropsychiatric Phenomics (www.phenomics.ucla.edu), in the hope that these ultimately will enable more effective collaboration, and facilitate connections of information about cognitive

  6. Respiratory abnormalities among workers in an iron and steel foundry.

    PubMed Central

    Johnson, A; Moira, C Y; MacLean, L; Atkins, E; Dybuncio, A; Cheng, F; Enarson, D

    1985-01-01

    A study of the health of 78 workers in an iron and steel foundry in Vancouver, British Columbia, was carried out and the results compared with those found in 372 railway repair yard workers who were not significantly exposed to air contaminants at work. The foundry workers were exposed to PepSet, which consists of diphenyl methane diisocyanate (MDI) and phenol formaldehyde and their decomposition products as well as to silica containing particulates. A questionnaire was administered by trained interviewers, and chest radiography, allergy skin tests, pulmonary function tests, and methacholine inhalation tests were carried out as well as measurement levels of dust and MDI. Compared with the controls, the foundry workers had more respiratory symptoms and a significantly lower mean FEV1 and FEF25-75% after adjustments had been made for differences in age, height, and smoking habit. Three workers (4.8%) had radiographic evidence of pneumoconiosis and 12 (18.2%) had asthma defined as presence of bronchial hyperreactivity, cough, and additional respiratory symptoms such as wheeze, chest tightness, or breathlessness. Sensitisation to MDI is probably the cause of asthma in these workers. PMID:2982392

  7. A novel application of concentrated solar thermal energy in foundries.

    PubMed

    Selvaraj, J; Harikesavan, V; Eshwanth, A

    2016-05-01

    Scrap preheating in foundries is a technology that saves melting energy, leading to economic and environmental benefits. The proposed method in this paper utilizes solar thermal energy for preheating scrap, effected through a parabolic trough concentrator that focuses sunlight onto a receiver which carries the metallic scrap. Scraps of various thicknesses were placed on the receiver to study the heat absorption by them. Experimental results revealed the pattern with which heat is gained by the scrap, the efficiency of the process and how it is affected as the scrap gains heat. The inferences from them gave practical guidelines on handling scraps for best possible energy savings. Based on the experiments conducted, preheat of up to 160 °C and a maximum efficiency of 70 % and a minimum efficiency of 40 % could be achieved across the time elapsed and heat gained by the scrap. Calculations show that this technology has the potential to save around 8 % of the energy consumption in foundries. Cumulative benefits are very encouraging: 180.45 million kWh of energy savings and 203,905 t of carbon emissions cut per year across the globe. This research reveals immense scope for this technology to be adopted by foundries throughout the world.

  8. Cyber Forensics Ontology for Cyber Criminal Investigation

    NASA Astrophysics Data System (ADS)

    Park, Heum; Cho, Sunho; Kwon, Hyuk-Chul

    We developed Cyber Forensics Ontology for the criminal investigation in cyber space. Cyber crime is classified into cyber terror and general cyber crime, and those two classes are connected with each other. The investigation of cyber terror requires high technology, system environment and experts, and general cyber crime is connected with general crime by evidence from digital data and cyber space. Accordingly, it is difficult to determine relational crime types and collect evidence. Therefore, we considered the classifications of cyber crime, the collection of evidence in cyber space and the application of laws to cyber crime. In order to efficiently investigate cyber crime, it is necessary to integrate those concepts for each cyber crime-case. Thus, we constructed a cyber forensics domain ontology for criminal investigation in cyber space, according to the categories of cyber crime, laws, evidence and information of criminals. This ontology can be used in the process of investigating of cyber crime-cases, and for data mining of cyber crime; classification, clustering, association and detection of crime types, crime cases, evidences and criminals.

  9. Animal trait ontology: The importance and usefulness of a unified trait vocabulary for animal species.

    PubMed

    Hughes, L M; Bao, J; Hu, Z-L; Honavar, V; Reecy, J M

    2008-06-01

    Ontologies help to identify and formally define the entities and relationships in specific domains of interest. Bio-ontologies, in particular, play a central role in the annotation, integration, analysis, and interpretation of biological data. Missing from the number of bio-ontologies is one that includes phenotypic trait information found in livestock species. As a result, the Animal Trait Ontology (ATO) project being carried out under the auspices of the USDA-National Animal Genome Research Program is aimed at the development of a standardized trait ontology for farm animals and software tools to assist the research community in collaborative creation, editing, maintenance, and use of such an ontology. The ATO is currently inclusive of cattle, pig, and chicken species, and will include other livestock species in the future. The ATO will eventually be linked to other species (e.g., human, rat, mouse) so that comparative analysis can be efficiently performed between species. PMID:18272850

  10. CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives.

    PubMed

    Tao, Cui; Solbrig, Harold R; Chute, Christopher G

    2011-01-01

    The Clinical Narrative Temporal Relation Ontology (CNTRO) has been developed for the purpose of allowing temporal information of clinical data to be semantically annotated and queried, and using inference to expose new temporal features and relations based on the semantic assertions and definitions of the temporal aspects in the ontology. While CNTRO provides a formal semantic foundation to leverage the semantic-web techniques, it is still necessary to arrive at a shared set of semantics and operational rules with commonly used ontologies for the time domain. This paper introduces CNTRO 2.0, which tries to harmonize CNTRO 1.0 and a list of existing time ontologies or top-level ontologies into a unified model-an OWL based ontology of temporal relations for clinical research.

  11. Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease.

    PubMed

    Mulder, Nicola; Nembaware, Victoria; Adekile, Adekunle; Anie, Kofi A; Inusa, Baba; Brown, Biobele; Campbell, Andrew; Chinenere, Furahini; Chunda-Liyoka, Catherine; Derebail, Vimal K; Geard, Amy; Ghedira, Kais; Hamilton, Carol M; Hanchard, Neil A; Haendel, Melissa; Huggins, Wayne; Ibrahim, Muntaser; Jupp, Simon; Kamga, Karen Kengne; Knight-Madden, Jennifer; Lopez-Sall, Philomène; Mbiyavanga, Mamana; Munube, Deogratias; Nirenberg, Damian; Nnodu, Obiageli; Ofori-Acquah, Solomon Fiifi; Ohene-Frempong, Kwaku; Opap, Kenneth Babu; Panji, Sumir; Park, Miriam; Pule, Gift; Royal, Charmaine; Sangeda, Raphael; Tayo, Bamidele; Treadwell, Marsha; Tshilolo, Léon; Wonkam, Ambroise

    2016-06-01

    Sickle cell disease (SCD) is a debilitating single gene disorder caused by a single point mutation that results in physical deformation (i.e. sickling) of erythrocytes at reduced oxygen tensions. Up to 75% of SCD in newborns world-wide occurs in sub-Saharan Africa, where neonatal and childhood mortality from sickle cell related complications is high. While SCD research across the globe is tackling the disease on multiple fronts, advances have yet to significantly impact on the health and quality of life of SCD patients, due to lack of coordination of these disparate efforts. Ensuring data across studies is directly comparable through standardization is a necessary step towards realizing this goal. Such a standardization requires the development and implementation of a disease-specific ontology for SCD that is applicable globally. Ontology development is best achieved by bringing together experts in the domain to contribute their knowledge. The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology. PMID:27354937

  12. Dynamic sub-ontology evolution for traditional Chinese medicine web ontology.

    PubMed

    Mao, Yuxin; Wu, Zhaohui; Tian, Wenya; Jiang, Xiaohong; Cheung, William K

    2008-10-01

    As a form of important domain knowledge, large-scale ontologies play a critical role in building a large variety of knowledge-based systems. To overcome the problem of semantic heterogeneity and encode domain knowledge in reusable format, a large-scale and well-defined ontology is also required in the traditional Chinese medicine discipline. We argue that to meet the on-demand and scalability requirement ontology-based systems should go beyond the use of static ontology and be able to self-evolve and specialize for the domain knowledge they possess. In particular, we refer to the context-specific portions from large-scale ontologies like the traditional Chinese medicine ontology as sub-ontologies. Ontology-based systems are able to reuse sub-ontologies in local repository called ontology cache. In order to improve the overall performance of ontology cache, we propose to evolve sub-ontologies in ontology cache to optimize the knowledge structure of sub-ontologies. Moreover, we present the sub-ontology evolution approach based on a genetic algorithm for reusing large-scale ontologies. We evaluate the proposed evolution approach with the traditional Chinese medicine ontology and obtain promising results.

  13. Use of the CIM Ontology

    SciTech Connect

    Neumann, Scott; Britton, Jay; Devos, Arnold N.; Widergren, Steven E.

    2006-02-08

    There are many uses for the Common Information Model (CIM), an ontology that is being standardized through Technical Committee 57 of the International Electrotechnical Commission (IEC TC57). The most common uses to date have included application modeling, information exchanges, information management and systems integration. As one should expect, there are many issues that become apparent when the CIM ontology is applied to any one use. Some of these issues are shortcomings within the current draft of the CIM, and others are a consequence of the different ways in which the CIM can be applied using different technologies. As the CIM ontology will and should evolve, there are several dangers that need to be recognized. One is overall consistency and impact upon applications when extending the CIM for a specific need. Another is that a tight coupling of the CIM to specific technologies could limit the value of the CIM in the longer term as an ontology, which becomes a larger issue over time as new technologies emerge. The integration of systems is one specific area of interest for application of the CIM ontology. This is an area dominated by the use of XML for the definition of messages. While this is certainly true when using Enterprise Application Integration (EAI) products, it is even more true with the movement towards the use of Web Services (WS), Service-Oriented Architectures (SOA) and Enterprise Service Buses (ESB) for integration. This general IT industry trend is consistent with trends seen within the IEC TC57 scope of power system management and associated information exchange. The challenge for TC57 is how to best leverage the CIM ontology using the various XML technologies and standards for integration. This paper will provide examples of how the CIM ontology is used and describe some specific issues that should be addressed within the CIM in order to increase its usefulness as an ontology. It will also describe some of the issues and challenges that will

  14. Evaluating Health Information Systems Using Ontologies

    PubMed Central

    Anderberg, Peter; Larsson, Tobias C; Fricker, Samuel A; Berglund, Johan

    2016-01-01

    Background There are several frameworks that attempt to address the challenges of evaluation of health information systems by offering models, methods, and guidelines about what to evaluate, how to evaluate, and how to report the evaluation results. Model-based evaluation frameworks usually suggest universally applicable evaluation aspects but do not consider case-specific aspects. On the other hand, evaluation frameworks that are case specific, by eliciting user requirements, limit their output to the evaluation aspects suggested by the users in the early phases of system development. In addition, these case-specific approaches extract different sets of evaluation aspects from each case, making it challenging to collectively compare, unify, or aggregate the evaluation of a set of heterogeneous health information systems. Objectives The aim of this paper is to find a method capable of suggesting evaluation aspects for a set of one or more health information systems—whether similar or heterogeneous—by organizing, unifying, and aggregating the quality attributes extracted from those systems and from an external evaluation framework. Methods On the basis of the available literature in semantic networks and ontologies, a method (called Unified eValuation using Ontology; UVON) was developed that can organize, unify, and aggregate the quality attributes of several health information systems into a tree-style ontology structure. The method was extended to integrate its generated ontology with the evaluation aspects suggested by model-based evaluation frameworks. An approach was developed to extract evaluation aspects from the ontology that also considers evaluation case practicalities such as the maximum number of evaluation aspects to be measured or their required degree of specificity. The method was applied and tested in Future Internet Social and Technological Alignment Research (FI-STAR), a project of 7 cloud-based eHealth applications that were developed and

  15. Theory and ontology for sharing temporal knowledge

    NASA Technical Reports Server (NTRS)

    Loganantharaj, Rasiah

    1996-01-01

    Using current technology, the sharing or re-using of knowledge-bases is very difficult, if not impossible. ARPA has correctly recognized the problem and funded a knowledge sharing initiative. One of the outcomes of this project is a formal language called Knowledge Interchange Format (KIF) for representing knowledge that could be translated into other languages. Capturing and representing design knowledge and reasoning with them have become very important for NASA who is a pioneer of innovative design of unique products. For upgrading an existing design for changing technology, needs, or requirements, it is essential to understand the design rationale, design choices, options and other relevant information associated with the design. Capturing such information and presenting them in the appropriate form are part of the ongoing Design Knowledge Capture project of NASA. The behavior of an object and various other aspects related to time are captured by the appropriate temporal knowledge. The captured design knowledge will be represented in such a way that various groups of NASA who are interested in various aspects of the design cycle should be able to access and use the design knowledge effectively. To facilitate knowledge sharing among these groups, one has to develop a very well defined ontology. Ontology is a specification of conceptualization. In the literature several specific domains were studied and some well defined ontologies were developed for such domains. However, very little, or no work has been done in the area of representing temporal knowledge to facilitate sharing. During the ASEE summer program, I have investigated several temporal models and have proposed a theory for time that is flexible to accommodate the time elements, such as, points and intervals, and is capable of handling the qualitative and quantitative temporal constraints. I have also proposed a primitive temporal ontology using which other relevant temporal ontologies can be built. I

  16. BioPortal: ontologies and integrated data resources at the click of a mouse.

    PubMed

    Noy, Natalya F; Shah, Nigam H; Whetzel, Patricia L; Dai, Benjamin; Dorf, Michael; Griffith, Nicholas; Jonquet, Clement; Rubin, Daniel L; Storey, Margaret-Anne; Chute, Christopher G; Musen, Mark A

    2009-07-01

    Biomedical ontologies provide essential domain knowledge to drive data integration, information retrieval, data annotation, natural-language processing and decision support. BioPortal (http://bioportal.bioontology.org) is an open repository of biomedical ontologies that provides access via Web services and Web browsers to ontologies developed in OWL, RDF, OBO format and Protégé frames. BioPortal functionality includes the ability to browse, search and visualize ontologies. The Web interface also facilitates community-based participation in the evaluation and evolution of ontology content by providing features to add notes to ontology terms, mappings between terms and ontology reviews based on criteria such as usability, domain coverage, quality of content, and documentation and support. BioPortal also enables integrated search of biomedical data resources such as the Gene Expression Omnibus (GEO), ClinicalTrials.gov, and ArrayExpress, through the annotation and indexing of these resources with ontologies in BioPortal. Thus, BioPortal not only provides investigators, clinicians, and developers 'one-stop shopping' to programmatically access biomedical ontologies, but also provides support to integrate data from a variety of biomedical resources.

  17. Comparing categories among geographic ontologies

    NASA Astrophysics Data System (ADS)

    Kavouras, Marinos; Kokla, Margarita; Tomai, Eleni

    2005-03-01

    Numerous attempts have been made to generate semantic "mappings" between different ontologies, or create aligned/integrated ones. An essential step towards their success is the ability to compare the categories involved. This paper introduces a systematic methodology for comparing categories met in geographic ontologies. The methodology explores/extracts semantic information provided by categories' definitions. The first step towards this goal is the recognition of syntactic and lexical patterns in definitions, which help to identify (a) semantic properties such as purpose, location, cover, and (b) semantic relations such as hypernym, part of, has-parts, etc. At the second step, a similarity measure among categories is applied, in order to explore how (the) extracted properties and relations interrelate. This framework enables us to (a) better understand the impact of context in cross-ontology "mappings", (b) evaluate the "quality" of definitions as to whether they respect mere ontological aspects (such as unambiguous taxonomies), and (c) deal more effectively with the problem of semantic translation among geographic ontologies.

  18. An Ontology Design Pattern for Surface Water Features

    SciTech Connect

    Sinha, Gaurav; Mark, David; Kolas, Dave; Varanka, Dalia; Romero, Boleslo E; Feng, Chen-Chieh; Usery, Lynn; Liebermann, Joshua; Sorokine, Alexandre

    2014-01-01

    Surface water is a primary concept of human experience but concepts are captured in cultures and languages in many different ways. Still, many commonalities can be found due to the physical basis of many of the properties and categories. An abstract ontology of surface water features based only on those physical properties of landscape features has the best potential for serving as a foundational domain ontology. It can then be used to systematically incor-porate concepts that are specific to a culture, language, or scientific domain. The Surface Water ontology design pattern was developed both for domain knowledge distillation and to serve as a conceptual building-block for more complex surface water ontologies. A fundamental distinction is made in this on-tology between landscape features that act as containers (e.g., stream channels, basins) and the bodies of water (e.g., rivers, lakes) that occupy those containers. Concave (container) landforms semantics are specified in a Dry module and the semantics of contained bodies of water in a Wet module. The pattern is imple-mented in OWL, but Description Logic axioms and a detailed explanation is provided. The OWL ontology will be an important contribution to Semantic Web vocabulary for annotating surface water feature datasets. A discussion about why there is a need to complement the pattern with other ontologies, es-pecially the previously developed Surface Network pattern is also provided. Fi-nally, the practical value of the pattern in semantic querying of surface water datasets is illustrated through a few queries and annotated geospatial datasets.

  19. Complex Topographic Feature Ontology Patterns

    USGS Publications Warehouse

    Varanka, Dalia E.; Jerris, Thomas J.

    2015-01-01

    Semantic ontologies are examined as effective data models for the representation of complex topographic feature types. Complex feature types are viewed as integrated relations between basic features for a basic purpose. In the context of topographic science, such component assemblages are supported by resource systems and found on the local landscape. Ontologies are organized within six thematic modules of a domain ontology called Topography that includes within its sphere basic feature types, resource systems, and landscape types. Context is constructed not only as a spatial and temporal setting, but a setting also based on environmental processes. Types of spatial relations that exist between components include location, generative processes, and description. An example is offered in a complex feature type ‘mine.’ The identification and extraction of complex feature types are an area for future research.

  20. Ontology Matching with Semantic Verification

    PubMed Central

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

    2009-01-01

    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. PMID:20186256

  1. 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.

  2. Ontologies Come of Age Revisited (Invited)

    NASA Astrophysics Data System (ADS)

    McGuinness, D. L.

    2010-12-01

    Many (e.g. [1,2]) have recognized the acceptance of and reliance on ontologies in a wide variety of real world applications, including many earth science applications. Benefits include improved interoperability, reuse, consistency checking, and enhanced search. As ontologies become more integral in applications, ontology ecosystem issues arise. In this presentation, we will acknowledge some benefits of ontology-enhanced applications, identify related infrastructure issues such as ontology evolution and maintenance, provenance representation and management, and ontology modularity and evaluation. We will describe some emerging trends in ontology- and provenance-aware environments and discuss opportunities and challenges. [1] http://www-ksl.stanford.edu/people/dlm/papers/ontologies-come-of-age-mit-press-%28with-citation%29.htm [2] http://www.ksl.stanford.edu/KSL_Abstracts/KSL-07-01.html

  3. Standards and Ontologies in Computational Systems Biology

    PubMed Central

    Sauro, Herbert M.; Bergmann, Frank

    2009-01-01

    With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In this chapter two chief model exchange standards, SBML and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced together with a discussion on the future of modeling languages and visualization tools in systems biology. PMID:18793134

  4. COBrA: a bio-ontology editor.

    PubMed

    Aitken, Stuart; Korf, Roman; Webber, Bonnie; Bard, Jonathan

    2005-03-01

    COBrA is a Java-based ontology editor for bio-ontologies that distinguishes itself from other editors by supporting the linking of concepts between two ontologies, and providing sophisticated analysis and verification functions. In addition to the Gene Ontology and Open Biology Ontologies formats, COBrA can import and export ontologies in the Semantic Web formats RDF, RDFS and OWL.

  5. The semantic metadatabase (SEMEDA): ontology based integration of federated molecular biological data sources.

    PubMed

    Köhler, Jacob; Schulze-Kremer, Steffen

    2002-01-01

    A system for "intelligent" semantic integration and querying of federated databases is being implemented by using three main components: A component which enables SQL access to integrated databases by database federation (MARGBench), an ontology based semantic metadatabase (SEMEDA) and an ontology based query interface (SEMEDA-query). In this publication we explain and demonstrate the principles, architecture and the use of SEMEDA. Since SEMEDA is implemented as 3 tiered web application database providers can enter all relevant semantic and technical information about their databases by themselves via a web browser. SEMEDA' s collaborative ontology editing feature is not restricted to database integration, and might also be useful for ongoing ontology developments, such as the "Gene Ontology" [2]. SEMEDA can be found at http://www-bm.cs.uni-magdeburg.de/semeda/. We explain how this ontologically structured information can be used for semantic database integration. In addition, requirements to ontologies for molecular biological database integration are discussed and relevant existing ontologies are evaluated. We further discuss how ontologies and structured knowledge sources can be used in SEMEDA and whether they can be merged supplemented or updated to meet the requirements for semantic database integration.

  6. Querying non-materialized ontology views.

    PubMed

    Detwiler, Landon T; Brinkley, James F

    2007-01-01

    One approach to simplifying ontologies, for inclusion in a more tractable semantic web, is through the use of non-materialized view queries. View queries define how a simplified "view" or "application" ontology is derived from larger more complex ontologies. In this work we look at a language for specifying view queries over OWL/RDFS sources, and we illustrate some initial ideas for how to execute user queries over our view ontology, without materializing it first.

  7. Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

    PubMed

    Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A; Noy, Natalya F

    2014-10-01

    Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

  8. Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains

    PubMed Central

    Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A.; Noy, Natalya F.

    2014-01-01

    Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50, 000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

  9. Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

    PubMed

    Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A; Noy, Natalya F

    2014-10-01

    Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

  10. 77 FR 15123 - Foundry Coke From China; Scheduling of an Expedited Five-Year Review

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-14

    ... its notice of institution (76 FR 74810, December 1, 2011) of the subject five-year review was adequate... COMMISSION Foundry Coke From China; Scheduling of an Expedited Five-Year Review AGENCY: United States...)) (the Act) to determine whether revocation of the antidumping duty order on foundry coke from...

  11. Compressed Air System Retrofitting Project Improves Productivity at a Foundry (Cast Masters, Bowling Green, OH)

    SciTech Connect

    2002-06-01

    This case study highlights International Truck and Engine Corporation's optimization project on the compressed air system that serves its foundry, Indianapolis Casting Corporation. Due to the project's implementation, the system's efficiency was greatly improved, allowing the foundry to operate with less compressor capacity, which resulted in reduced energy consumption, significant maintenance savings, and more reliable production.

  12. Amelioration of physical strength in waste foundry green sands for reuse as a soil amendment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As available landfill space and profit margins steadily decrease, it becomes more important for U.S. foundries to find ways of diverting 8-12 million tons of waste foundry sand (WFS) away from landfills each year. A major drawback to the reuse of some WFSs as a soil amendment is their high soil str...

  13. 40 CFR 63.10900 - What parts of the General Provisions apply to my large foundry?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... requirements of the General Provisions (40 CFR part 63, subpart A) according to Table 3 of this subpart. (b) If... apply to my large foundry? 63.10900 Section 63.10900 Protection of Environment ENVIRONMENTAL PROTECTION... Foundries Area Sources Requirements for New and Existing Affected Sources Classified As Large Iron and...

  14. Use of standardized procedures to evaluate metal leaching from waste foundry sands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As part of the casting process, foundries create sand molds and cores to produce ferrous and non-ferrous metal castings. After the process, a portion of the sand is discarded and becomes waste foundry sand (WFS). The aim of this study was to quantify metals (i.e. Ag, Ba, Cd, Cr, Cu, Ni, Pb, and Zn)...

  15. Evolving BioAssay Ontology (BAO): modularization, integration and applications

    PubMed Central

    2014-01-01

    The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and

  16. Evolving BioAssay Ontology (BAO): modularization, integration and applications.

    PubMed

    Abeyruwan, Saminda; Vempati, Uma D; Küçük-McGinty, Hande; Visser, Ubbo; Koleti, Amar; Mir, Ahsan; Sakurai, Kunie; Chung, Caty; Bittker, Joshua A; Clemons, Paul A; Brudz, Steve; Siripala, Anosha; Morales, Arturo J; Romacker, Martin; Twomey, David; Bureeva, Svetlana; Lemmon, Vance; Schürer, Stephan C

    2014-01-01

    The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and

  17. Evolving BioAssay Ontology (BAO): modularization, integration and applications.

    PubMed

    Abeyruwan, Saminda; Vempati, Uma D; Küçük-McGinty, Hande; Visser, Ubbo; Koleti, Amar; Mir, Ahsan; Sakurai, Kunie; Chung, Caty; Bittker, Joshua A; Clemons, Paul A; Brudz, Steve; Siripala, Anosha; Morales, Arturo J; Romacker, Martin; Twomey, David; Bureeva, Svetlana; Lemmon, Vance; Schürer, Stephan C

    2014-01-01

    The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and

  18. Design of schistosomiasis ontology (IDOSCHISTO) extending the infectious disease ontology.

    PubMed

    Camara, Gaoussou; Despres, Sylvie; Djedidi, Rim; Lo, Moussa

    2013-01-01

    Epidemiological monitoring of the schistosomiasis' spreading brings together many practitioners working at different levels of granularity (biology, host individual, host population), who have different perspectives (biology, clinic and epidemiology) on the same phenomenon. Biological perspective deals with pathogens (e.g. life cycle) or physiopathology while clinical perspective deals with hosts (e.g. healthy or infected host, diagnosis, treatment, etc.). In an epidemiological perspective corresponding to the host population level of granularity, the schistosomiasis disease is characterized according to the way (causes, risk factors, etc.) it spreads in this population over space and time. In this paper we provide an ontological analysis and design for the Schistosomiasis domain knowledge and spreading dynamics. IDOSCHISTO - the schistosomiasis ontology - is designed as an extension of the Infectious Disease Ontology (IDO). This ontology aims at supporting the schistosomiasis monitoring process during a spreading crisis by enabling data integration, semantic interoperability, for collaborative work on one hand and for risk analysis and decision making on the other hand. PMID:23920598

  19. The Plant Ontology: A Tool for Plant Genomics.

    PubMed

    Cooper, Laurel; Jaiswal, Pankaj

    2016-01-01

    The use of controlled, structured vocabularies (ontologies) has become a critical tool for scientists in the post-genomic era of massive datasets. Adoption and integration of common vocabularies and annotation practices enables cross-species comparative analyses and increases data sharing and reusability. The Plant Ontology (PO; http://www.plantontology.org/ ) describes plant anatomy, morphology, and the stages of plant development, and offers a database of plant genomics annotations associated to the PO terms. The scope of the PO has grown from its original design covering only rice, maize, and Arabidopsis, and now includes terms to describe all green plants from angiosperms to green algae.This chapter introduces how the PO and other related ontologies are constructed and organized, including languages and software used for ontology development, and provides an overview of the key features. Detailed instructions illustrate how to search and browse the PO database and access the associated annotation data. Users are encouraged to provide input on the ontology through the online term request form and contribute datasets for integration in the PO database.

  20. Re-usage of waste foundry sand in high-strength concrete.

    PubMed

    Guney, Yucel; Sari, Yasin Dursun; Yalcin, Muhsin; Tuncan, Ahmet; Donmez, Senayi

    2010-01-01

    In this study, the potential re-use of waste foundry sand in high-strength concrete production was investigated. The natural fine sand is replaced with waste foundry sand (0%, 5%, 10%, and 15%). The findings from a series of test program has shown reduction in compressive and tensile strengths, and the elasticity modulus which is directly related to waste foundry inclusion in concrete. Nevertheless the concrete with 10% waste foundry sand exhibits almost similar results to that of the control one. The slump and the workability of the fresh concrete decreases with the increase of the waste foundry sand ratio. Although the freezing and thawing significantly reduces the mechanical and physical properties of the concrete. The obtained results satisfies the acceptable limits set by the American Concrete Institute (ACI). PMID:20219339

  1. Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ontology engineering and knowledge modeling for the plant sciences is expected to contribute to the understanding of the basis of plant traits that determine phenotypic expression in a given environment. Several crop- or clade-specific plant trait ontologies have been developed to describe plant tr...

  2. An Ontology-Based Framework for Bridging Learning Design and Learning Content

    ERIC Educational Resources Information Center

    Knight, Colin, Gasevic, Dragan; Richards, Griff

    2006-01-01

    The paper describes an ontology-based framework for bridging learning design and learning object content. In present solutions, researchers have proposed conceptual models and developed tools for both of those subjects, but without detailed discussions of how they can be used together. In this paper we advocate the use of ontologies to explicitly…

  3. Grinder Variant System Design and Implementation Based on Ontology

    NASA Astrophysics Data System (ADS)

    Yang, G. H.; Zhang, T. P.

    In order to improve the efficiency of product design and reuse in heterogeneous system of knowledge sharing, this paper introduced the concept of ontology into product variant design, and grinding machine design was as an example. A lot of experience and accumulated knowledge in product design was shared and reused. It is precisely to formulate ontology knowledge such as variant design features and parameter, and applied the software protégé4.3 to construct ontology model, as well as runed resoning on model data information. It developed a set of complete product intelligent system of variant design, which can effectively solve the problem of the repeated design and greatly shorten product development cycle.

  4. OntoSoft: An Ontology for Capturing Scientific Software Metadata

    NASA Astrophysics Data System (ADS)

    Gil, Y.

    2015-12-01

    We have developed OntoSoft, an ontology to describe metadata for scientific software. The ontology is designed considering how scientists would approach the reuse and sharing of software. This includes supporting a scientist to: 1) identify software, 2) understand and assess software, 3) execute software, 4) get support for the software, 5) do research with the software, and 6) update the software. The ontology is available in OWL and contains more than fifty terms. We have used OntoSoft to structure the OntoSoft software registry for geosciences, and to develop user interfaces to capture its metadata. OntoSoft is part of the NSF EarthCube initiative and contributes to its vision of scientific knowledge sharing, in this case about scientific software.

  5. The construction and practice of GIS ontology service mechanism

    NASA Astrophysics Data System (ADS)

    Yang, Kun; Wang, Jun; Peng, Shuang-yun; Cheng, Hong-ping

    2005-10-01

    With the development of Semantic Web technology, the spatial information service based on ontology is an effective way for sharing and interoperation of heterogeneous information resources in the distributed network environment. Based on the deep analysis for the spatial information service mechanism of geo-ontology, the system construction strategy and service workflow and combined with the present mainstream commercial GIS software packages, three solutions of system construction for spatial information sharing and interoperation have been proposed here in this paper. The different geographic information application systems distributed on the internet may be integrated dynamically and openly by using one of the three solutions for realizing the sharing and interoperation of heterogeneous spatial information resources in the distributing environment. In order to realize the practical applications of spatial information sharing and interoperation in different brunches of police system, a prototype system for crime case information sharing based on geo-ontology has also been developed by using the methods described above.

  6. Gaseous and adsorbed PAH in an iron foundry.

    PubMed Central

    Knecht, U; Elliehausen, H J; Woitowitz, H J

    1986-01-01

    The increased risk of lung cancer among foundry workers is assumed to be associated with the inhalation of gaseous and particle bound polycyclic aromatic hydrocarbons (PAH). These compounds are produced during pyrolysis of carbon containing loading material in the moulding sand. The concentrations of 20 PAH, some of which are carcinogenic, have been determined in the dusty casting area of an iron foundry by means of gas chromatography and mass spectrometry. The total dust was fractionated by means of a precision cascade impactor. It was possible to differentiate the PAH load in microgram/mg dust in seven particle size fractions ranging from 0.36- greater than or equal to 24.95 microns. Initially, there was an increase of the adsorbed PAH mass concentration with increasing particle diameter up to a maximum of 1.1 microgram/mg in the dust of the 1.57 micron fraction. Thereafter there was a continuous decrease of PAH mass concentration with increasing particle size. When the differing weights of the seven fractions are taken into account, however, the total PAH load of the individual fractions increases steadily with increasing particle size. The inhalable fine dust, 31.4% of the total dust, contains 49.9% of the total adsorbed PAH. The gas phase contained on average three times more carcinogenic PAH with four and five rings than was adsorbed on the dust. Thus the percentage of the gaseous substances amounts to 77% of the total PAH load at the place of work in an iron foundry. PMID:3801335

  7. Mortality at an automotive engine foundry and machining complex.

    PubMed

    Park, R M

    2001-05-01

    Mortality was analyzed for an automotive engine foundry and machining complex, with process exposures derived from department assignments. Logistic regression models of mortality odds ratios (ORs) were calculated for 2546 deaths, and numbers of work-related deaths were estimated. Lung cancer mortality in the foundry was increased where cleaning and finishing of castings was performed (OR, 1.7; 95% CI, 1.15 to 2.4 [at mean exposure duration of exposed cases]) and in care-making after 1967 (OR, 1.5; 95% CI, 1.11 to 2.0). Black workers had excess lung cancer mortality in machining heat-treat operations (OR, 2.5, 95% CI, 1.4 to 4.3) and excess nonmalignant respiratory disease mortality in molding (OR, 2.5; 95% CI, 1.16 to 5.5) and core-making (OR, 2.7; 95% CI, 1.25 to 5.8). Stomach cancer mortality was elevated among workers with metalworking fluid exposures in precision grinding (OR, 2.4; 95% CI, 1.14 to 5.1). Heart disease mortality was increased among all workers in molding (OR, 1.6; 95% CI, 1.09 to 2.3), as was stroke mortality among workers exposed to metalworking fluids (OR, 1.8; 95% CI, 1.22 to 2.7). Malignant and nonmalignant liver disease mortality was elevated in assembly/testing and precision grinding. In this modern foundry, 11% of deaths were estimated to be work-related despite it's being largely in regulatory compliance over its 40-year existence. Machining plant exposures accounted for 3% or more of deaths there.

  8. A novel paradigm for cell and molecule interaction ontology: from the CMM model to IMGT-ONTOLOGY

    PubMed Central

    2010-01-01

    Background Biology is moving fast toward the virtuous circle of other disciplines: from data to quantitative modeling and back to data. Models are usually developed by mathematicians, physicists, and computer scientists to translate qualitative or semi-quantitative biological knowledge into a quantitative approach. To eliminate semantic confusion between biology and other disciplines, it is necessary to have a list of the most important and frequently used concepts coherently defined. Results We propose a novel paradigm for generating new concepts for an ontology, starting from model rather than developing a database. We apply that approach to generate concepts for cell and molecule interaction starting from an agent based model. This effort provides a solid infrastructure that is useful to overcome the semantic ambiguities that arise between biologists and mathematicians, physicists, and computer scientists, when they interact in a multidisciplinary field. Conclusions This effort represents the first attempt at linking molecule ontology with cell ontology, in IMGT-ONTOLOGY, the well established ontology in immunogenetics and immunoinformatics, and a paradigm for life science biology. With the increasing use of models in biology and medicine, the need to link different levels, from molecules to cells to tissues and organs, is increasingly important. PMID:20167082

  9. Ontological Knowledge and Sentence Anomaly.

    ERIC Educational Resources Information Center

    Gerard, Anthony B.; Mandler, Jean M.

    1983-01-01

    Discusses attempt to replicate and extend Keil's study of effects of ontological knowledge on judgments of sentence acceptability (indicating there is hierarchical one-to-one mapping of predicate-term relations of language onto the basic structure of knowledge). New data does not support Keil but suggests that range of sentence interpretation…

  10. Quartz and dust exposure in Swedish iron foundries.

    PubMed

    Andersson, Lena; Bryngelsson, Ing-Liss; Ohlson, Carl-Göran; Nayström, Peter; Lilja, Bengt-Gunnar; Westberg, Håkan

    2009-01-01

    Exposure to respirable quartz continues to be a major concern in the Swedish iron foundry industry. Recommendations for reducing the European occupational exposure limit (EU-OEL) to 0.05 mg/m3 and the corresponding ACGIH(R) threshold limit value (ACGIH-TLV) to 0.025 mg/m3 prompted this exposure survey. Occupational exposure to respirable dust and respirable quartz were determined in 11 Swedish iron foundries, representing different sizes of industrial operation and different manufacturing techniques. In total, 436 respirable dust and 435 respirable quartz exposure measurements associated with all job titles were carried out and are presented as time-weighted averages. Our sampling strategy enabled us to evaluate the use of respirators in certain jobs, thus determining actual exposure. In addition, measurements using real-time dust monitors were made for high exposure jobs. For respirable quartz, 23% of all the measurements exceeded the EU-OEL, and 56% exceeded the ACGIH-TLV. The overall geometric mean (GM) for the quartz levels was 0.028 mg/m3, ranging from 0.003 to 2.1 mg/m3. Fettler and furnace and ladle repair operatives were exposed to the highest levels of both respirable dust (GM = 0.69 and 1.2 mg/m3; range 0.076-31 and 0.25-9.3 mg/m3 and respirable quartz (GM = 0.041 and 0.052 mg/m3; range 0.004-2.1 and 0.0098-0.83 mg/m3. Fettlers often used respirators and their actual quartz exposure was lower (range 0.003-0.21 mg/m3, but in some cases it still exceeded the Swedish OEL (0.1 mg/m3. For furnace and ladle repair operatives, the actual quartz exposure did not exceed the OEL (range 0.003-0.08 mg/m3, but most respirators provided insufficient protection, i.e., factors less than 200. In summary, measurements in Swedish iron foundries revealed high exposures to respirable quartz, in particular for fettlers and furnace and ladle repair workers. The suggested EU-OEL and the ACGIH-TLV were exceeded in, respectively, 23% and 56% of all measurements regardless of the

  11. Gradient Learning Algorithms for Ontology Computing

    PubMed Central

    Gao, Wei; Zhu, Linli

    2014-01-01

    The gradient learning model has been raising great attention in view of its promising perspectives for applications in statistics, data dimensionality reducing, and other specific fields. In this paper, we raise a new gradient learning model for ontology similarity measuring and ontology mapping in multidividing setting. The sample error in this setting is given by virtue of the hypothesis space and the trick of ontology dividing operator. Finally, two experiments presented on plant and humanoid robotics field verify the efficiency of the new computation model for ontology similarity measure and ontology mapping applications in multidividing setting. PMID:25530752

  12. Describing the Breakbone Fever: IDODEN, an Ontology for Dengue Fever

    PubMed Central

    Mitraka, Elvira; Topalis, Pantelis; Dritsou, Vicky; Dialynas, Emmanuel; Louis, Christos

    2015-01-01

    Background Ontologies represent powerful tools in information technology because they enhance interoperability and facilitate, among other things, the construction of optimized search engines. To address the need to expand the toolbox available for the control and prevention of vector-borne diseases we embarked on the construction of specific ontologies. We present here IDODEN, an ontology that describes dengue fever, one of the globally most important diseases that are transmitted by mosquitoes. Methodology/Principal Findings We constructed IDODEN using open source software, and modeled it on IDOMAL, the malaria ontology developed previously. IDODEN covers all aspects of dengue fever, such as disease biology, epidemiology and clinical features. Moreover, it covers all facets of dengue entomology. IDODEN, which is freely available, can now be used for the annotation of dengue-related data and, in addition to its use for modeling, it can be utilized for the construction of other dedicated IT tools such as decision support systems. Conclusions/Significance The availability of the dengue ontology will enable databases hosting dengue-associated data and decision-support systems for that disease to perform most efficiently and to link their own data to those stored in other independent repositories, in an architecture- and software-independent manner. PMID:25646954

  13. The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.

    PubMed

    Bug, William J; Ascoli, Giorgio A; Grethe, Jeffrey S; Gupta, Amarnath; Fennema-Notestine, Christine; Laird, Angela R; Larson, Stephen D; Rubin, Daniel; Shepherd, Gordon M; Turner, Jessica A; Martone, Maryann E

    2008-09-01

    A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF. PMID:18975148

  14. SWEET 2.0: Moving Toward Community-Based Ontologies

    NASA Astrophysics Data System (ADS)

    Raskin, R.

    2008-12-01

    The Semantic Web for Earth and Environmental Terminology (SWEET) project has produced an upper-level ontology set for Earth system science. These ontologies have been under development for several years and include concepts of science, data, and services. SWEET includes mappings to other controlled vocabulary lists such as the GCMD science keyword and CF standard names. The initial design (SWEET 1.0) defined about 1700 concepts organized by facet, such as: physical property, small-scale process, large-scale phenomena, living and non-living substance, Earth realm, space, time, units, etc. For Version 2.0, the number of concepts has doubled to 3500 and the facet structure is similar. However, there no longer remains a one-to-one mapping of a facet to an ontology file. The original 12 ontology files have been reorganized into nearly 100 files, organized by subject. This new design is much more scalable, as it is easy for domain specialists to add content for their specialization by adding an additional file. SWEET enables representations of all aspects of the Earth system (from core to heliosphere) and more general aspects of planetary and solar science. It is anticipated that the ESIP Federation Semantic Web Cluster will maintain this ontology set over the long-term.

  15. Quality assurance of the gene ontology using abstraction networks.

    PubMed

    Ochs, Christopher; Perl, Yehoshua; Halper, Michael; Geller, James; Lomax, Jane

    2016-06-01

    The gene ontology (GO) is used extensively in the field of genomics. Like other large and complex ontologies, quality assurance (QA) efforts for GO's content can be laborious and time consuming. Abstraction networks (AbNs) are summarization networks that reveal and highlight high-level structural and hierarchical aggregation patterns in an ontology. They have been shown to successfully support QA work in the context of various ontologies. Two kinds of AbNs, called the area taxonomy and the partial-area taxonomy, are developed for GO hierarchies and derived specifically for the biological process (BP) hierarchy. Within this framework, several QA heuristics, based on the identification of groups of anomalous terms which exhibit certain taxonomy-defined characteristics, are introduced. Such groups are expected to have higher error rates when compared to other terms. Thus, by focusing QA efforts on anomalous terms one would expect to find relatively more erroneous content. By automatically identifying these potential problem areas within an ontology, time and effort will be saved during manual reviews of GO's content. BP is used as a testbed, with samples of three kinds of anomalous BP terms chosen for a taxonomy-based QA review. Additional heuristics for QA are demonstrated. From the results of this QA effort, it is observed that different kinds of inconsistencies in the modeling of GO can be exposed with the use of the proposed heuristics. For comparison, the results of QA work on a sample of terms chosen from GO's general population are presented. PMID:27301779

  16. An integrated pharmacokinetics ontology and corpus for text mining

    PubMed Central

    2013-01-01

    Background Drug pharmacokinetics parameters, drug interaction parameters, and pharmacogenetics data have been unevenly collected in different databases and published extensively in the literature. Without appropriate pharmacokinetics ontology and a well annotated pharmacokinetics corpus, it will be difficult to develop text mining tools for pharmacokinetics data collection from the literature and pharmacokinetics data integration from multiple databases. Description A comprehensive pharmacokinetics ontology was constructed. It can annotate all aspects of in vitro pharmacokinetics experiments and in vivo pharmacokinetics studies. It covers all drug metabolism and transportation enzymes. Using our pharmacokinetics ontology, a PK-corpus was constructed to present four classes of pharmacokinetics abstracts: in vivo pharmacokinetics studies, in vivo pharmacogenetic studies, in vivo drug interaction studies, and in vitro drug interaction studies. A novel hierarchical three level annotation scheme was proposed and implemented to tag key terms, drug interaction sentences, and drug interaction pairs. The utility of the pharmacokinetics ontology was demonstrated by annotating three pharmacokinetics studies; and the utility of the PK-corpus was demonstrated by a drug interaction extraction text mining analysis. Conclusions The pharmacokinetics ontology annotates both in vitro pharmacokinetics experiments and in vivo pharmacokinetics studies. The PK-corpus is a highly valuable resource for the text mining of pharmacokinetics parameters and drug interactions. PMID:23374886

  17. Domain ontologies in software engineering: use of Protégé with the EON architecture.

    PubMed

    Musen, M A

    1998-11-01

    Domain ontologies are formal descriptions of the classes of concepts and the relationships among those concepts that describe an application area. The Protégé software-engineering methodology provides a clear division between domain ontologies and domain-independent problem-solvers that, when mapped to domain ontologies, can solve application tasks. The Protégé approach allows domain ontologies to inform the total software-engineering process, and for ontologies to be shared among a variety of problem-solving components. We illustrate the approach by describing the development of EON, a set of middleware components that automate various aspects of protocol-directed therapy. Our work illustrates the organizing effect that domain ontologies can have on the software-development process. Ontologies, like all formal representations, have limitations in their ability to capture the semantics of application areas. Nevertheless, the capability of ontologies to encode clinical distinctions not usually captured by controlled medical terminologies provides significant advantages for developers and maintainers of clinical software applications.

  18. INSOLUBILIZATION METHOD OF THE FLUORINE IN WASTE FOUNDRY SAND AND THE PRODUCTION METHOD OF THE ROADBED MATERIAL

    NASA Astrophysics Data System (ADS)

    Fukayama, Masamitu; Terazono, Katsuhiro; Koga, Yasuyuki

    We have studied how the fluorine-insoluble in the waste foundry sand (chromite sand) and production method of the roadbed material with insolubilized waste foundry sand. And we got following knowledges. (1) We found a minimum mixing rate to insolubilize of fluorine in the waste foundry sand by the ingenuity of mixing procedure. (2) Now we can insolubilize the waste foundry sand including comparatively high concentration fluorine (elution concentration: 20-70mg/l) by the mixing time difference of MgO and blast furnace cement. (3) In the verification test the roadbed material made from the insolubilized waste foundry sand satisfied reference value of environment safety.

  19. Laboratory Testing of Foundry Sands as Bulking Agents for Porous Media Filters Used to Treat Agricultural Drainage Waters

    NASA Astrophysics Data System (ADS)

    Allred, B. J.

    2008-12-01

    Foundry sands are industrial byproducts that may have potential application as bulking agents that when mixed with small amounts of more chemically reactive materials (i.e. sulfur modified iron, fly ash, etc.) can be used to produce porous media filters capable of removing contaminants from agricultural drainage waters. Foundry sand bulking agents are attractive primarily as a low cost means to maintain the hydraulic efficiency of a filter. Secondarily, the foundry sands themselves may have some capacity for removal of agricultural nutrients and pesticides from water. Consequently, a laboratory study was initiated to quantify hydraulic efficiency and agricultural contaminant removal abilities of six foundry sands. Of the six foundry sands tested, all were obtained in central Ohio, three from iron casting foundries, two from steel casting foundries, and one from an aluminum casting foundry. Hydraulic efficiencies of the foundry sands were assessed by measuring hydraulic conductivity with twice replicated falling-head permeability tests. Batch tests were employed to evaluate foundry sand potential to treat water containing nitrate and phosphate nutrients, along with the pesticide, atrazine. Five of the six foundry sand samples had measured hydraulic conductivity values from 7.6 x 10-3 cm/s to 3.8 x 10-2 cm/s, which is in the range of hydraulic conductivity values found for clean sand. The one foundry sand that was an exception had much lower measured hydraulic conductivity values of 2.75 x 10-5 cm/s and 5.76 x 10-5 cm/s. For the batch tests conducted, none of the nitrate was removed by any of the six foundry sands; however, conversely, almost all of the phosphate was removed by each foundry sand. Batch test atrazine removal results were much more varied. Compared with baseline batch tests, one foundry sand removed two thirds of the atrazine, one foundry sand removed about one half of the atrazine, three foundry sands removed about a third of the atrazine, and one

  20. Ontology Language to Support Description of Experiment Control System Semantics, Collaborative Knowledge-Base Design and Ontology Reuse

    SciTech Connect

    Vardan Gyurjyan, D Abbott, G Heyes, E Jastrzembski, B Moffit, C Timmer, E Wolin

    2009-10-01

    In this paper we discuss the control domain specific ontology that is built on top of the domain-neutral Resource Definition Framework (RDF). Specifically, we will discuss the relevant set of ontology concepts along with the relationships among them in order to describe experiment control components and generic event-based state machines. Control Oriented Ontology Language (COOL) is a meta-data modeling language that provides generic means for representation of physics experiment control processes and components, and their relationships, rules and axioms. It provides a semantic reference frame that is useful for automating the communication of information for configuration, deployment and operation. COOL has been successfully used to develop a complete and dynamic knowledge-base for experiment control systems, developed using the AFECS framework.

  1. GeoSciGraph: An Ontological Framework for EarthCube Semantic Infrastructure

    NASA Astrophysics Data System (ADS)

    Gupta, A.; Schachne, A.; Condit, C.; Valentine, D.; Richard, S.; Zaslavsky, I.

    2015-12-01

    The CINERGI (Community Inventory of EarthCube Resources for Geosciences Interoperability) project compiles an inventory of a wide variety of earth science resources including documents, catalogs, vocabularies, data models, data services, process models, information repositories, domain-specific ontologies etc. developed by research groups and data practitioners. We have developed a multidisciplinary semantic framework called GeoSciGraph semantic ingration of earth science resources. An integrated ontology is constructed with Basic Formal Ontology (BFO) as its upper ontology and currently ingests multiple component ontologies including the SWEET ontology, GeoSciML's lithology ontology, Tematres controlled vocabulary server, GeoNames, GCMD vocabularies on equipment, platforms and institutions, software ontology, CUAHSI hydrology vocabulary, the environmental ontology (ENVO) and several more. These ontologies are connected through bridging axioms; GeoSciGraph identifies lexically close terms and creates equivalence class or subclass relationships between them after human verification. GeoSciGraph allows a community to create community-specific customizations of the integrated ontology. GeoSciGraph uses the Neo4J,a graph database that can hold several billion concepts and relationships. GeoSciGraph provides a number of REST services that can be called by other software modules like the CINERGI information augmentation pipeline. 1) Vocabulary services are used to find exact and approximate terms, term categories (community-provided clusters of terms e.g., measurement-related terms or environmental material related terms), synonyms, term definitions and annotations. 2) Lexical services are used for text parsing to find entities, which can then be included into the ontology by a domain expert. 3) Graph services provide the ability to perform traversal centric operations e.g., finding paths and neighborhoods which can be used to perform ontological operations like

  2. The Synthetic Aperture Radar Science Data Processing Foundry Concept for Earth Science

    NASA Astrophysics Data System (ADS)

    Rosen, P. A.; Hua, H.; Norton, C. D.; Little, M. M.

    2015-12-01

    Since 2008, NASA's Earth Science Technology Office and the Advanced Information Systems Technology Program have invested in two technology evolutions to meet the needs of the community of scientists exploiting the rapidly growing database of international synthetic aperture radar (SAR) data. JPL, working with the science community, has developed the InSAR Scientific Computing Environment (ISCE), a next-generation interferometric SAR processing system that is designed to be flexible and extensible. ISCE currently supports many international space borne data sets but has been primarily focused on geodetic science and applications. A second evolutionary path, the Advanced Rapid Imaging and Analysis (ARIA) science data system, uses ISCE as its core science data processing engine and produces automated science and response products, quality assessments and metadata. The success of this two-front effort has been demonstrated in NASA's ability to respond to recent events with useful disaster support. JPL has enabled high-volume and low latency data production by the re-use of the hybrid cloud computing science data system (HySDS) that runs ARIA, leveraging on-premise cloud computing assets that are able to burst onto the Amazon Web Services (AWS) services as needed. Beyond geodetic applications, needs have emerged to process large volumes of time-series SAR data collected for estimation of biomass and its change, in such campaigns as the upcoming AfriSAR field campaign. ESTO is funding JPL to extend the ISCE-ARIA model to a "SAR Science Data Processing Foundry" to on-ramp new data sources and to produce new science data products to meet the needs of science teams and, in general, science community members. An extension of the ISCE-ARIA model to support on-demand processing will permit PIs to leverage this Foundry to produce data products from accepted data sources when they need them. This paper will describe each of the elements of the SAR SDP Foundry and describe their

  3. Building medical ontologies based on terminology extraction from texts: an experimentation in pneumology.

    PubMed

    Baneyx, Audrey; Charlet, Jean; Jaulent, Marie-Christine

    2005-01-01

    Pathologies and acts are classified in thesauri to help physicians to code their activity. In practice, the use of thesauri is not sufficient to reduce variability in coding and thesauri do not fit computer processing. We think the automation of the coding task requires a conceptual modelling of medical items: an ontology. Our objective is to help pneumologists code acts and diagnoses with a software that represents medical knowledge by an ontology of the concerned specialty. The main research hypothesis is to apply natural language processing tools to corpora to develop the resources needed to build the ontology. In this paper, our objective is twofold: we have to build the ontology of pneumology and we want to develop a methodology for the knowledge engineer to build various types of medical ontologies based on terminology extraction from texts.

  4. Ontology Re-engineering Use Case: Extending SWEET to map Climate and Forecasting Vocabulary Terms

    NASA Astrophysics Data System (ADS)

    Ramachandran, R.; Graves, S.; Raskin, R.

    2006-05-01

    A common problem faced while developing metadata for scientific data archives is that of keywords. Although keywords are an effective way for searching the resource catalogs, data archive designers may select from one of many different controlled vocabularies to describe their holdings. For example, in Earth Science, Climate and Forecasting (CF Convention) is a controlled vocabulary commonly used within the Modeling community. Similarly, the Global Change Master Directory (GCMD) keywords list is the convention used within the NASA Earth Science Program. The use of controlled vocabularies allows searches on the resource catalogs to be accurate and complete, but the burden of framing the precise query falls on the shoulders of the users. The user has to know the keyword before hand in order to perform a "free text" search. This might be perfectly acceptable in smaller projects where the users are specialized and have the required knowledge, but is impractical in larger projects where the users may have varied levels of domain knowledge. One solution to this problem is the use of an ontology, where the ontology contains higher level abstract concepts and the corresponding mapping to the different controlled vocabulary terms. This use of ontologies eliminates the barrier of entry based on domain knowledge and provides easy-to-use search capabilities to the users. In this presentation, we will describe an ontology designed and created to address this problem. However, this ontology required re-engineering of higher level ontologies, namely the Semantic Web for Earth and Environmental Terminology (SWEET) ontologies, instead of the initial creation of an ontology. Since the traditional methodologies for creating an ontology do not account for reengineering and reuse of higher level ontologies, we propose a new modified methodology. This presentation will describe this methodology and also explore some of the issues and challenges involved in the construction of an

  5. A Lexical-Ontological Resource for Consumer Heathcare

    NASA Astrophysics Data System (ADS)

    Cardillo, Elena

    In Consumer Healthcare Informatics it is still difficult for laypersons to understand and act on health information, due to the persistent communication gap between specialized medical terminology and that used by healthcare consumers. Furthermore, existing clinically-oriented terminologies cannot provide sufficient support when integrated into consumer-oriented applications, so there is a need to create consumer-friendly terminologies reflecting the different ways healthcare consumers express and think about health topics. Following this direction, this work suggests a way to support the design of an ontology-based system that mitigates this gap, using knowledge engineering and Semantic Web technologies. The system is based on the development of a consumer-oriented medical terminology which will be integrated with other existing domain ontologies/terminologies into a medical ontology repository. This will support consumer-oriented healthcare systems by providing many knowledge services to help users in accessing and managing their healthcare data.

  6. A Lexical-Ontological Resource for Consumer Healthcare

    NASA Astrophysics Data System (ADS)

    Cardillo, Elena; Serafini, Luciano; Tamilin, Andrei

    In Consumer Healthcare Informatics it is still difficult for laypeople to find, understand and act on health information, due to the persistent communication gap between specialized medical terminology and that used by healthcare consumers. Furthermore, existing clinically-oriented terminologies cannot provide sufficient support when integrated into consumer-oriented applications, so there is a need to create consumer-friendly terminologies reflecting the different ways healthcare consumers express and think about health topics. Following this direction, this work suggests a way to support the design of an ontology-based system that mitigates this gap, using knowledge engineering and semantic web technologies. The system is based on the development of a consumer-oriented medical terminology that will be integrated with other medical domain ontologies and terminologies into a medical ontology repository. This will support consumer-oriented healthcare systems, such as Personal Health Records, by providing many knowledge services to help users in accessing and managing their healthcare data.

  7. Ontology-based federated data access to human studies information.

    PubMed

    Sim, Ida; Carini, Simona; Tu, Samson W; Detwiler, Landon T; Brinkley, James; Mollah, Shamim A; Burke, Karl; Lehmann, Harold P; Chakraborty, Swati; Wittkowski, Knut M; Pollock, Brad H; Johnson, Thomas M; Huser, Vojtech

    2012-01-01

    Human studies are one of the most valuable sources of knowledge in biomedical research, but data about their design and results are currently widely dispersed in siloed systems. Federation of these data is needed to facilitate large-scale data analysis to realize the goals of evidence-based medicine. The Human Studies Database project has developed an informatics infrastructure for federated query of human studies databases, using a generalizable approach to ontology-based data access. Our approach has three main components. First, the Ontology of Clinical Research (OCRe) provides the reference semantics. Second, a data model, automatically derived from OCRe into XSD, maintains semantic synchrony of the underlying representations while facilitating data acquisition using common XML technologies. Finally, the Query Integrator issues queries distributed over the data, OCRe, and other ontologies such as SNOMED in BioPortal. We report on a demonstration of this infrastructure on data acquired from institutional systems and from ClinicalTrials.gov. PMID:23304360

  8. Combining ontologies and workflows to design formal protocols for biological laboratories

    PubMed Central

    2010-01-01

    Background Laboratory protocols in life sciences tend to be written in natural language, with negative consequences on repeatability, distribution and automation of scientific experiments. Formalization of knowledge is becoming popular in science. In the case of laboratory protocols two levels of formalization are needed: one for the entities and individuals operations involved in protocols and another one for the procedures, which can be manually or automatically executed. This study aims to combine ontologies and workflows for protocol formalization. Results A laboratory domain specific ontology and the COW (Combining Ontologies with Workflows) software tool were developed to formalize workflows built on ontologies. A method was specifically set up to support the design of structured protocols for biological laboratory experiments. The workflows were enhanced with ontological concepts taken from the developed domain specific ontology. The experimental protocols represented as workflows are saved in two linked files using two standard interchange languages (i.e. XPDL for workflows and OWL for ontologies). A distribution package of COW including installation procedure, ontology and workflow examples, is freely available from http://www.bmr-genomics.it/farm/cow. Conclusions Using COW, a laboratory protocol may be directly defined by wet-lab scientists without writing code, which will keep the resulting protocol's specifications clear and easy to read and maintain. PMID:20416048

  9. From classification to epilepsy ontology and informatics.

    PubMed

    Zhang, Guo-Qiang; Sahoo, Satya S; Lhatoo, Samden D

    2012-07-01

    The 2010 International League Against Epilepsy (ILAE) classification and terminology commission report proposed a much needed departure from previous classifications to incorporate advances in molecular biology, neuroimaging, and genetics. It proposed an interim classification and defined two key requirements that need to be satisfied. The first is the ability to classify epilepsy in dimensions according to a variety of purposes including clinical research, patient care, and drug discovery. The second is the ability of the classification system to evolve with new discoveries. Multidimensionality and flexibility are crucial to the success of any future classification. In addition, a successful classification system must play a central role in the rapidly growing field of epilepsy informatics. An epilepsy ontology, based on classification, will allow information systems to facilitate data-intensive studies and provide a proven route to meeting the two foregoing key requirements. Epilepsy ontology will be a structured terminology system that accommodates proposed and evolving ILAE classifications, the National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) Common Data Elements, the International Classification of Diseases (ICD) systems and explicitly specifies all known relationships between epilepsy concepts in a proper framework. This will aid evidence-based epilepsy diagnosis, investigation, treatment and research for a diverse community of clinicians and researchers. Benefits range from systematization of electronic patient records to multimodal data repositories for research and training manuals for those involved in epilepsy care. Given the complexity, heterogeneity, and pace of research advances in the epilepsy domain, such an ontology must be collaboratively developed by key stakeholders in the epilepsy community and experts in knowledge engineering and computer science. PMID:22765502

  10. ODISEES: Ontology-Driven Interactive Search Environment for Earth Sciences

    NASA Technical Reports Server (NTRS)

    Rutherford, Matthew T.; Huffer, Elisabeth B.; Kusterer, John M.; Quam, Brandi M.

    2015-01-01

    This paper discusses the Ontology-driven Interactive Search Environment for Earth Sciences (ODISEES) project currently being developed to aid researchers attempting to find usable data among an overabundance of closely related data. ODISEES' ontological structure relies on a modular, adaptable concept modeling approach, which allows the domain to be modeled more or less as it is without worrying about terminology or external requirements. In the model, variables are individually assigned semantic content based on the characteristics of the measurements they represent, allowing intuitive discovery and comparison of data without requiring the user to sift through large numbers of data sets and variables to find the desired information.

  11. DataFoundry: Warehousing techniques for dynamic environments

    SciTech Connect

    Critchlow, T.; Fidelis, K.; Ganesh, M.; Musick, R.; Slezak, T., LLNL

    1998-01-29

    Data warehouses and data marts have been successfully applied to a multitude of commercial business applications as tools for integrating and providing access to data located across an enterprise. Although the need for this capability is as vital in the scientific world as in the business domain, working warehouses in our community are scarce. A primary technical reason for this is that our understanding of the concepts being explored in an evolving scientific domain change constantly, leading to rapid changes in the data representation. When any database providing information to a warehouse changes its format, the warehouse must be updated to reflect these changes, or it will not function properly. The cost of maintaining a warehouse using traditional techniques in this environment is prohibitive. This paper describes ideas for dramatically reducing the amount of work that must be done to keep a warehouse up to date in a dynamic, scientific environment. The ideas are being applied in a prototype warehouse called DataFoundry. DataFoundry, currently in use by structural biologists at LLNL, will eventually support scientists at the Department of Energy`s Joint Genome Institute.

  12. Reducing exposures during the pouring operations of a brass foundry.

    PubMed

    Edmonds, M A; Gressel, M G; O'Brien, D M; Clark, N J

    1993-05-01

    The focus of this exposure assessment and control technology study was a brass foundry and the lead exposures of workers involved in the transportation and pouring of metal. Controls in place at the foundry included ventilation systems at the furnace and along the continuous and stationary pouring lines. Real-time measurements were made to determine which tasks were the primary exposure sources, and a hand-held aerosol monitor was used to measure real-time aerosol exposures (as a surrogate for lead) in the workers' breathing zones. Data were collected over two 30-min sampling periods while worker activities were monitored using a video camera. Analysis of the data showed that the greatest aerosol exposures occurred during the transportation of an unventilated, full ladle, resulting in an average concentration of at least twice that of the other tasks. The study concluded that the addition of exhaust ventilation such as a moveable hood and duct system during the ladle transport and pouring tasks, and the implementation of a side draft hood at the pigging area, could result in a reduction of worker exposure to aerosols during the continuous pouring operation by up to 40%. The controls and techniques suggested in this study could be applied to pouring operations throughout the industry to reduce worker exposure to metal fumes.

  13. Total dose hardness of three commercial CMOS microelectronics foundries

    SciTech Connect

    Osborn, J.V.; Lacoe, R.C.; Mayer, D.C.; Yabiku, G.

    1998-06-01

    The authors have measured the effects of total ionizing dose (TID) on CMOS FETs, ring oscillators and field-oxide transistor test structures fabricated at three different commercial foundries with four different processes. The foundries spanned a range of integration levels and included Hewlett-Packard (HP) 0.5 {micro}m and 0.8 {micro}m processes, an Orbit 1.2 {micro}m process, and an AMI 1.6 {micro}m process. They found that the highest tolerance to TID was for the HP 0.5 {micro}m process, where the shift in NMOS threshold voltage was less than 40 mV at 300 krad. An examination of the dependence of the threshold voltage shift on gate oxide thickness indicated that oxides of the different commercial processes were of similar quality, and that the improvement in the total dose tolerance of the HP 0.5 {micro}m technology is associated with the scaling of the gate oxide. Measurements on field-oxide transistors from the HP 0.5 {micro}m process were shown not to invert for signal voltages at 300 krad, maintaining the integrity of the LOCOS isolation.

  14. Ultrafine and respirable particles in an automotive grey iron foundry.

    PubMed

    Evans, Douglas E; Heitbrink, William A; Slavin, Thomas J; Peters, Thomas M

    2008-01-01

    Ultrafine particle number and respirable particle mass concentrations were measured throughout an automotive grey iron foundry during winter, spring and summer using a particle concentration mapping procedure. Substantial temporal and spatial variability was observed in all seasons and attributed, in part, to the batch nature of operations, process emission variability and frequent work interruptions. The need for fine mapping grids was demonstrated, where elevations in particle concentrations were highly localized. Ultrafine particle concentrations were generally greatest during winter when incoming make-up air was heated with direct fire, natural gas burners. Make-up air drawn from roof level had elevated respirable mass and ultrafine number concentrations above ambient outdoor levels, suggesting inadvertent recirculation of foundry process emissions. Elevated respirable mass concentrations were highly localized on occasions (e.g. abrasive blasting and grinding), depended on the area within the facility where measurements were obtained, but were largely unaffected by season. Particle sources were further characterized by measuring their respective number and mass concentrations by particle size. Sources that contributed to ultrafine particles included process-specific sources (e.g. melting and pouring operations), and non-process sources (e.g. direct fire natural gas heating units, a liquid propane-fuelled sweeper and cigarette smoking) were additionally identified. PMID:18056626

  15. An ontological model of the practice transformation process.

    PubMed

    Sen, Arun; Sinha, Atish P

    2016-06-01

    Patient-centered medical home is defined as an approach for providing comprehensive primary care that facilitates partnerships between individual patients and their personal providers. The current state of the practice transformation process is ad hoc and no methodological basis exists for transforming a practice into a patient-centered medical home. Practices and hospitals somehow accomplish the transformation and send the transformation information to a certification agency, such as the National Committee for Quality Assurance, completely ignoring the development and maintenance of the processes that keep the medical home concept alive. Many recent studies point out that such a transformation is hard as it requires an ambitious whole-practice reengineering and redesign. As a result, the practices suffer change fatigue in getting the transformation done. In this paper, we focus on the complexities of the practice transformation process and present a robust ontological model for practice transformation. The objective of the model is to create an understanding of the practice transformation process in terms of key process areas and their activities. We describe how our ontology captures the knowledge of the practice transformation process, elicited from domain experts, and also discuss how, in the future, that knowledge could be diffused across stakeholders in a healthcare organization. Our research is the first effort in practice transformation process modeling. To build an ontological model for practice transformation, we adopt the Methontology approach. Based on the literature, we first identify the key process areas essential for a practice transformation process to achieve certification status. Next, we develop the practice transformation ontology by creating key activities and precedence relationships among the key process areas using process maturity concepts. At each step, we employ a panel of domain experts to verify the intermediate representations of the

  16. An ontological model of the practice transformation process.

    PubMed

    Sen, Arun; Sinha, Atish P

    2016-06-01

    Patient-centered medical home is defined as an approach for providing comprehensive primary care that facilitates partnerships between individual patients and their personal providers. The current state of the practice transformation process is ad hoc and no methodological basis exists for transforming a practice into a patient-centered medical home. Practices and hospitals somehow accomplish the transformation and send the transformation information to a certification agency, such as the National Committee for Quality Assurance, completely ignoring the development and maintenance of the processes that keep the medical home concept alive. Many recent studies point out that such a transformation is hard as it requires an ambitious whole-practice reengineering and redesign. As a result, the practices suffer change fatigue in getting the transformation done. In this paper, we focus on the complexities of the practice transformation process and present a robust ontological model for practice transformation. The objective of the model is to create an understanding of the practice transformation process in terms of key process areas and their activities. We describe how our ontology captures the knowledge of the practice transformation process, elicited from domain experts, and also discuss how, in the future, that knowledge could be diffused across stakeholders in a healthcare organization. Our research is the first effort in practice transformation process modeling. To build an ontological model for practice transformation, we adopt the Methontology approach. Based on the literature, we first identify the key process areas essential for a practice transformation process to achieve certification status. Next, we develop the practice transformation ontology by creating key activities and precedence relationships among the key process areas using process maturity concepts. At each step, we employ a panel of domain experts to verify the intermediate representations of the

  17. Excess Foundry Sand Characterization and Experimental Investigation in Controlled Low-Strength Material and Hot-Mixing Asphalt

    SciTech Connect

    Pauul J. Tikalsky

    2004-10-31

    This report provides technical data regarding the reuse of excess foundry sand. The report addresses three topics: (1) a statistically sound evaluation of the characterization of foundry sand, (2) a laboratory investigation to qualify excess foundry sand as a major component in controlled low-strength material (CLSM), and (3) the identification of the best methods for using foundry sand as a replacement for natural aggregates for construction purposes, specifically in asphalt paving materials. The survival analysis statistical technique was used to characterize foundry sand over a full spectrum of general chemical parameters, metallic elements, and organic compounds regarding bulk analysis and leachate characterization. Not limited to characterization and environmental impact, foundry sand was evaluated by factor analyses, which contributes to proper selection of factor and maximization of the reuse marketplace for foundry sand. Regarding the integration of foundry sand into CLSM, excavatable CLSM and structural CLSM containing different types of excess foundry sands were investigated through laboratory experiments. Foundry sand was approved to constitute a major component in CLSM. Regarding the integration of foundry sand into asphalt paving materials, the optimum asphalt content was determined for each mixture, as well as the bulk density, maximum density, asphalt absorption, and air voids at N{sub ini}, N{sub des}, and N{sub max}. It was found that foundry sands can be used as an aggregate in hot-mix asphalt production, but each sand should be evaluated individually. Foundry sands tend to lower the strength of mixtures and also may make them more susceptible to moisture damage. Finally, traditional anti-stripping additives may decrease the moisture sensitivity of a mixture containing foundry sand, but not to the level allowed by most highway agencies.

  18. Excess Foundry Sand Characterization and Experimental Investigation in Controlled Low-Strength Material and Hot-Mixing Asphalt

    SciTech Connect

    Tikalsky, Paul J.; Bahia, Hussain U.; Deng, An; Snyder, Thomas

    2004-10-15

    This report provides technical data regarding the reuse of excess foundry sand. The report addresses three topics: a statistically sound evaluation of the characterization of foundry sand, a laboratory investigation to qualify excess foundry sand as a major component in controlled low-strength material (CLSM), and the identification of the best methods for using foundry sand as a replacement for natural aggregates for construction purposes, specifically in asphalt paving materials. The survival analysis statistical technique was used to characterize foundry sand over a full spectrum of general chemical parameters, metallic elements, and organic compounds regarding bulk analysis and leachate characterization. Not limited to characterization and environmental impact, foundry sand was evaluated by factor analyses, which contributes to proper selection of factor and maximization of the reuse marketplace for foundry sand. Regarding the integration of foundry sand into CLSM, excavatable CLSM and structural CLSM containing different types of excess foundry sands were investigated through laboratory experiments. Foundry sand was approved to constitute a major component in CLSM. Regarding the integration of foundry sand into asphalt paving materials, the optimum asphalt content was determined for each mixture, as well as the bulk density, maximum density, asphalt absorption, and air voids at Nini, Ndes, and Nmax. It was found that foundry sands can be used as an aggregate in hot-mix asphalt production, but each sand should be evaluated individually. Foundry sands tend to lower the strength of mixtures and also may make them more susceptible to moisture damage. Finally, traditional anti-stripping additives may decrease the moisture sensitivity of a mixture containing foundry sand, but not to the level allowed by most highway agencies.

  19. Cause-Specific Mortality Due to Malignant and Non-Malignant Disease in Korean Foundry Workers

    PubMed Central

    Yoon, Jin-Ha; Ahn, Yeon-Soon

    2014-01-01

    Background Foundry work is associated with serious occupational hazards. Although several studies have investigated the health risks associated with foundry work, the results of these studies have been inconsistent with the exception of an increased lung cancer risk. The current study evaluated the mortality of Korean foundry workers due to malignant and non-malignant diseases. Methods This study is part of an ongoing investigation of Korean foundry workers. To date, we have observed more than 150,000 person-years in male foundry production workers. In the current study, we stratified mortality ratios by the following job categories: melting-pouring, molding-coremaking, fettling, and uncategorized production work. We calculated standard mortality ratios (SMR) of foundry workers compare to general Korean men and relative risk (RR) of mortality of foundry production workers reference to non-production worker, respectively. Results Korean foundry production workers had a significantly higher risk of mortality due to malignant disease, including stomach (RR: 3.96; 95% CI: 1.41–11.06) and lung cancer (RR: 2.08; 95% CI: 1.01–4.30), compared with non-production workers. High mortality ratios were also observed for non-malignant diseases, including diseases of the circulatory (RR: 1.92; 95% CI: 1.18–3.14), respiratory (RR: 1.71; 95% CI: 1.52–21.42 for uncategorized production worker), and digestive (RR: 2.27; 95% CI: 1.22–4.24) systems, as well as for injuries (RR: 2.36; 95% CI: 1.52–3.66) including suicide (RR: 3.64; 95% CI: 1.32–10.01). Conclusion This study suggests that foundry production work significantly increases the risk of mortality due to some kinds of malignant and non-malignant diseases compared with non-production work. PMID:24505454

  20. Ontology-supported Research on Vaccine Efficacy, Safety, and Integrative Biological Networks

    PubMed Central

    He, Yongqun

    2016-01-01

    Summary While vaccine efficacy and safety research has dramatically progressed with the methods of in silico prediction and data mining, many challenges still exist. A formal ontology is a human- and computer-interpretable set of terms and relations that represent entities in a specific domain and how these terms relate to each other. Several community-based ontologies (including the Vaccine Ontology, Ontology of Adverse Events, and Ontology of Vaccine Adverse Events) have been developed to support vaccine and adverse event representation, classification, data integration, literature mining of host-vaccine interaction networks, and analysis of vaccine adverse events. The author further proposes minimal vaccine information standards and their ontology representations, ontology-based linked open vaccine data and meta-analysis, an integrative One Network (“OneNet”) Theory of Life, and ontology-based approaches to study and apply the OneNet theory. In the Big Data era, these proposed strategies provide a novel framework for advanced data integration and analysis of fundamental biological networks including vaccine immune mechanisms. PMID:24909153

  1. Assessing the threat of firearms: new threat formula, resources, and ontological linking algorithms

    NASA Astrophysics Data System (ADS)

    Hempelmann, Christian F.; Arslan, Abdullah N.; Attardo, Salvatore; Blount, Grady P.; Sirakov, Nikolay Metodiev

    2014-06-01

    The present work is part of an ongoing larger project.2, 3, 11, 12 The goal of this project is to develop a system capable of automatic threat assessment for instances of firearms use in public places. The main components of the system are: an ontology of firearms;1, 14 algorithms to create the visual footprint of the firearms,1, 14 to compare visual information,2, 3, 11, 12 to facilitate search in the ontology, and to generate the links between the conceptual and visual ontologies; as well as a formula to calculate the threat of individual firearms, firearms classes, and ammunition types in different environments. One part of the dual-level ontology for the properties of the firearms captures key visual features used to identify their type or class in images, while the other part captures their threat-relevant conceptual properties. The visual ontology is the result of image segmentation and matching methods, while the conceptual ontology is designed using knowledge-engineering principles and populated semi-automatically from Web resources. The focus of the present paper is two-fold. On the one hand, we will report on an update of the initial threat formula, based on the substantially increased population of the firearm ontology, including ammunition types and comparisons to actual incidents, and allowing for an overall more accurate assessment. On the other hand, the linking algorithms between the visual and conceptual ontologies are elaborated for faster transfer of information leading to an improvement in accuracy of the threat assessment.

  2. A unified software framework for deriving, visualizing, and exploring abstraction networks for ontologies.

    PubMed

    Ochs, Christopher; Geller, James; Perl, Yehoshua; Musen, Mark A

    2016-08-01

    Software tools play a critical role in the development and maintenance of biomedical ontologies. One important task that is difficult without software tools is ontology quality assurance. In previous work, we have introduced different kinds of abstraction networks to provide a theoretical foundation for ontology quality assurance tools. Abstraction networks summarize the structure and content of ontologies. One kind of abstraction network that we have used repeatedly to support ontology quality assurance is the partial-area taxonomy. It summarizes structurally and semantically similar concepts within an ontology. However, the use of partial-area taxonomies was ad hoc and not generalizable. In this paper, we describe the Ontology Abstraction Framework (OAF), a unified framework and software system for deriving, visualizing, and exploring partial-area taxonomy abstraction networks. The OAF includes support for various ontology representations (e.g., OWL and SNOMED CT's relational format). A Protégé plugin for deriving "live partial-area taxonomies" is demonstrated. PMID:27345947

  3. Generative Graph Grammar of Neo-Vaiśeṣika Formal Ontology (NVFO)

    NASA Astrophysics Data System (ADS)

    Tavva, Rajesh; Singh, Navjyoti

    NLP applications for Sanskrit so far work within computational paradigm of string grammars. However, to compute 'meanings', as in traditional śā bdabodha prakriyā-s, there is a need to develop suitable graph grammars. Ontological structures are fundamentally graphs. We work within the formal framework of Neo-Vaiśeṣika Formal Ontology (NVFO) to propose a generative graph grammar. The proposed formal grammar only produces well-formed graphs that can be readily interpreted in accordance with Vaiśeṣ ika Ontology. We show that graphs not permitted by Vaiśeṣ ika ontology are not generated by the proposed grammar. Further, we write Interpreter of these graphical structures. This creates computational environment which can be deployed for writing computational applications of Vaiśeṣ ika ontology. We illustrate how this environment can be used to create applications like computing śā bdabodha of sentences.

  4. NeXO Web: the NeXO ontology database and visualization platform

    PubMed Central

    Dutkowski, Janusz; Ono, Keiichiro; Kramer, Michael; Yu, Michael; Pratt, Dexter; Demchak, Barry; Ideker, Trey

    2014-01-01

    The Network-extracted Ontology (NeXO) is a gene ontology inferred directly from large-scale molecular networks. While most ontologies are constructed through manual expert curation, NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a global hierarchy of cellular components and processes. Here, we describe the development of the NeXO Web platform (http://www.nexontology.org)—an online database and graphical user interface for visualizing, browsing and performing term enrichment analysis using NeXO and the gene ontology. The platform applies state-of-the-art web technology and visualization techniques to provide an intuitive framework for investigating biological machinery captured by both data-driven and manually curated ontologies. PMID:24271398

  5. Visualization of Large Ontologies in University Education from a Tool Point of View.

    PubMed

    Schaaf, Michael; Jahn, Franziska; Tahar, Kais; Kücherer, Christian; Winter, Alfred; Paech, Barbara

    2016-01-01

    The realization of ontology visualization requirements in university education is a challenging task and should be supported by appropriate tools. This applies in particular, if the ontology to be visualized is based on a large text corpus that comprises a huge number of concepts, relations and annotations. In SNIK, we developed such an ontology of information management in hospitals in order to support the transfer of knowledge in the context of the university education. The challenge is to identify tools and methods, which are capable to support ontology visualization and usage as efficiently as possible. Related research fields (e.g. bioinformatics) are confronted with similar visualization problems. These tools and methods used could provide a suitable solution in our research field. In total, we assessed eight tools concerning the visualization of large ontologies to evaluate their suitability representing knowledge in the field of medical informatics.

  6. Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting

    PubMed Central

    2012-01-01

    Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data. PMID:22541591

  7. Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.

    PubMed

    Soldatova, Larisa N; Sansone, Susanna-Assunta; Dumontier, Michel; Shah, Nigam H

    2012-01-01

    Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data. PMID:22541591

  8. Visualization of Large Ontologies in University Education from a Tool Point of View.

    PubMed

    Schaaf, Michael; Jahn, Franziska; Tahar, Kais; Kücherer, Christian; Winter, Alfred; Paech, Barbara

    2016-01-01

    The realization of ontology visualization requirements in university education is a challenging task and should be supported by appropriate tools. This applies in particular, if the ontology to be visualized is based on a large text corpus that comprises a huge number of concepts, relations and annotations. In SNIK, we developed such an ontology of information management in hospitals in order to support the transfer of knowledge in the context of the university education. The challenge is to identify tools and methods, which are capable to support ontology visualization and usage as efficiently as possible. Related research fields (e.g. bioinformatics) are confronted with similar visualization problems. These tools and methods used could provide a suitable solution in our research field. In total, we assessed eight tools concerning the visualization of large ontologies to evaluate their suitability representing knowledge in the field of medical informatics. PMID:27577402

  9. Issues in the design of medical ontologies used for knowledge sharing.

    PubMed

    Burgun, A; Botti, G; Fieschi, M; Le Beux, P

    2001-04-01

    Recent work in Medical Informatics is exploring the development and the use of formal ontologies as a way of specifying content-specific agreements for the sharing and reuse of knowledge among several computer systems. We describe the role of ontologies in supporting knowledge sharing activities in medicine Principles for the design of ontologies have been proposed, mainly in other domains: these principles include parsimony, clarity, representation of categories versus terms, and coherence. We analyze how and why these principles can or cannot be applied from case studies from medical systems. Regarding the fact that most of medical concepts are empirical, selected design decisions are discussed. An alternative representation choice consists in mapping principled general core ontologies and domain ontologies.

  10. Selected papers from the 14th Annual Bio-Ontologies Special Interest Group Meeting.

    PubMed

    Soldatova, Larisa N; Sansone, Susanna-Assunta; Dumontier, Michel; Shah, Nigam H

    2012-01-01

    Over the 14 years, the Bio-Ontologies SIG at ISMB has provided a forum for discussion of the latest and most innovative research in the bio-ontologies development, its applications to biomedicine and more generally the organisation, presentation and dissemination of knowledge in biomedicine and the life sciences. The seven papers selected for this supplement span a wide range of topics including: web-based querying over multiple ontologies, integration of data from wikis, innovative methods of annotating and mining electronic health records, advances in annotating web documents and biomedical literature, quality control of ontology alignments, and the ontology support for predictive models about toxicity and open access to the toxicity data.

  11. Reduction in Energy Consumption & Variability in Steel Foundry Operations

    SciTech Connect

    Frank Peters

    2005-05-04

    This project worked to improve the efficiency of the steel casting industry by reducing the variability that occurs because of process and product variation. The project focused on the post shakeout operations since roughly half of the production costs are in this area. These improvements will reduce the amount of variability, making it easier to manage the operation and improve the competitiveness. The reduction in variability will also reduce the need for many rework operations, which will result in a direct reduction of energy usage, particularly by the reduction of repeated heat treatment operations. Further energy savings will be realized from the reduction of scrap and reduced handling. Field studies were conducted at ten steel foundries that represented the U.S. steel casting industry, for a total of over 100 weeks of production observation. These studies quantified the amount of variability, and looked toward determining the source. A focus of the data collected was the grinding operations since this is a major effort in the cleaning room, and it represents the overall casting quality. The grinding was divided into two categories, expected and unexpected. Expected grinding is that in which the location of the effort is known prior to making the casting, such as smoothing parting lines, gates, and riser contacts. Unexpected grinding, which was approximately 80% of the effort, was done to improve the surfaces at weld repair locations, to rectify burnt on sand, and other surface anomalies at random locations. Unexpected grinding represents about 80% of the grinding effort. By quantifying this effort, the project raised awareness within the industry and the industry is continuing to make improvements. The field studies showed that the amount of variation of grinding operations (normalized because of the diverse set of parts studied) was very consistent across the industry. The field studies identified several specific sources that individually contributed to

  12. Construction of a Clinical Decision Support System for Undergoing Surgery Based on Domain Ontology and Rules Reasoning

    PubMed Central

    Bau, Cho-Tsan; Huang, Chung-Yi

    2014-01-01

    Abstract Objective: To construct a clinical decision support system (CDSS) for undergoing surgery based on domain ontology and rules reasoning in the setting of hospitalized diabetic patients. Materials and Methods: The ontology was created with a modified ontology development method, including specification and conceptualization, formalization, implementation, and evaluation and maintenance. The Protégé–Web Ontology Language editor was used to implement the ontology. Embedded clinical knowledge was elicited to complement the domain ontology with formal concept analysis. The decision rules were translated into JENA format, which JENA can use to infer recommendations based on patient clinical situations. Results: The ontology includes 31 classes and 13 properties, plus 38 JENA rules that were built to generate recommendations. The evaluation studies confirmed the correctness of the ontology, acceptance of recommendations, satisfaction with the system, and usefulness of the ontology for glycemic management of diabetic patients undergoing surgery, especially for domain experts. Conclusions: The contribution of this research is to set up an evidence-based hybrid ontology and an evaluation method for CDSS. The system can help clinicians to achieve inpatient glycemic control in diabetic patients undergoing surgery while avoiding hypoglycemia. PMID:24730353

  13. Techni-Cast: Foundry Saves Energy with Compressed Air System Retrofit

    SciTech Connect

    none,

    2004-03-01

    In 2002, Techni-Cast improved its compressed air system at its foundry in Southgate, California. The project allowed the foundry to reduce its compressor capacity by 50%, which greatly reduced the foundry's energy and maintenance costs. The annual energy and maintenance savings from the project implementation are 242,000 kWh and $24,200, and the project's cost was $38,000. Because the plant received a $10,000 incentive payment from the California Public Utilities Commission, the total project cost was reduced to $28,000, yielding a 14-month simple payback.

  14. Revealing ontological commitments by magic.

    PubMed

    Griffiths, Thomas L

    2015-03-01

    Considering the appeal of different magical transformations exposes some systematic asymmetries. For example, it is more interesting to transform a vase into a rose than a rose into a vase. An experiment in which people judged how interesting they found different magic tricks showed that these asymmetries reflect the direction a transformation moves in an ontological hierarchy: transformations in the direction of animacy and intelligence are favored over the opposite. A second and third experiment demonstrated that judgments of the plausibility of machines that perform the same transformations do not show the same asymmetries, but judgments of the interestingness of such machines do. A formal argument relates this sense of interestingness to evidence for an alternative to our current physical theory, with magic tricks being a particularly pure source of such evidence. These results suggest that people's intuitions about magic tricks can reveal the ontological commitments that underlie human cognition.

  15. An Evolutionary Ontology Approach for Community-Based Competency Management

    NASA Astrophysics Data System (ADS)

    de Baer, Peter; Meersman, Robert; Zhao, Gang

    In this article we describe an evolutionary ontology approach that distinguishes between major ontology changes and minor ontology changes. We divide the community in three (possibly overlapping) groups, i.e. facilitators, contributors, and users. Facilitators are a selected group of domain experts who represent the intended community. These facilitators define the intended goals of the ontology and will be responsible for major ontology and ontology platform changes. A larger group of contributors consists of all participating domain experts. The contributors will carry out minor ontology changes, like instantiation of concepts and description of concept instances. Users of the ontology may explore the ontology content via the ontology platform and/or make use of the published ontology content in XML or HTML format. The approach makes use of goal and group specific user interfaces to guide the ontology evolution process. For the minor ontology changes, the approach relies on the wisdom of crowds.

  16. Ontology for E-Learning: A Case Study

    ERIC Educational Resources Information Center

    Colace, Francesco; De Santo, Massimo; Gaeta, Matteo

    2009-01-01

    Purpose: The development of adaptable and intelligent educational systems is widely considered one of the great challenges in scientific research. Among key elements for building advanced training systems, an important role is played by methodologies chosen for knowledge representation. In this scenario, the introduction of ontology formalism can…

  17. Foundries Footprint, October 2012 (MECS 2006)

    SciTech Connect

    2012-10-17

    Manufacturing energy and carbon footprints map energy consumption and losses, as well as greenhouse gas emissions from fuel consumption, for fifteen individual U.S. manufacturing sectors (representing 94% of all manufacturing energy use) and for the entire manufacturing sector. By providing energy consumption and emissions figures broken down by end use, the footprints allow for comparisons of energy use and emissions sources both within and across sectors. The footprints portray a large amount of information for each sector, including: * Comparison of the energy generated offsite and transferred to facilities versus that generated onsite * Nature and amount of energy consumed by end use within facilities * Magnitude of the energy lost both outside and inside facility boundaries * Magnitude of the greenhouse gas emissions released as a result of manufacturing energy use. Energy losses indicate opportunities to improve efficiency by implementing energy management best practices, upgrading energy systems, and developing new technologies. Footprints are available below for each sector. Data is presented in two levels of detail. The first page provides a high- level snapshot of the offsite and onsite energy flow, and the second page shows the detail for onsite generation and end use of energy. The principle energy use data source is the U.S. Department of Energy (DOE) Energy Information Administration's (EIA's) Manufacturing Energy Consumption Survey (MECS), for consumption in the year 2006, when the survey was last completed.

  18. Foundries Footprint, December 2010 (MECS 2006)

    SciTech Connect

    none,

    2010-06-01

    Manufacturing energy and carbon footprints map fuel energy consumption and losses, as well as greenhouse gas emissions from fuel consumption, for fifteen individual U.S. manufacturing sectors (representing 94% of all manufacturing energy use) and for the entire manufacturing industry sector. By providing energy consumption and emissions figures broken down by end use, the footprints allow for comparisons of energy use and emissions sources both within and across sectors. The footprints portray a large amount of information for each sector, including: * Comparison of the energy generated offsite and transferred to facilities versus that generated onsite * Nature and amount of energy consumed by end use within facilities * Magnitude of the energy lost both outside and inside facility boundaries * Magnitude of the greenhouse gas emissions released due to the combustion of fuel. Energy losses indicate opportunities to improve efficiency by implementing energy management best practices, upgrading energy systems, and developing new technologies. Footprints are available below for each sector. Data is presented in two levels of detail. The first page provides a high-level snapshot of the offsite and onsite energy flow, and the second page shows the detail for onsite generation and end use of energy. The energy data is primarily provided by the U.S. Department of Energy (DOE) Energy Information Administration's (EIA's) Manufacturing Energy Consumption Survey (MECS), and therefore reflects consumption in the year 2006, when the survey was last completed.

  19. Unification of multi-species vertebrate anatomy ontologies for comparative biology in Uberon

    PubMed Central

    2014-01-01

    Background Elucidating disease and developmental dysfunction requires understanding variation in phenotype. Single-species model organism anatomy ontologies (ssAOs) have been established to represent this variation. Multi-species anatomy ontologies (msAOs; vertebrate skeletal, vertebrate homologous, teleost, amphibian AOs) have been developed to represent ‘natural’ phenotypic variation across species. Our aim has been to integrate ssAOs and msAOs for various purposes, including establishing links between phenotypic variation and candidate genes. Results Previously, msAOs contained a mixture of unique and overlapping content. This hampered integration and coordination due to the need to maintain cross-references or inter-ontology equivalence axioms to the ssAOs, or to perform large-scale obsolescence and modular import. Here we present the unification of anatomy ontologies into Uberon, a single ontology resource that enables interoperability among disparate data and research groups. As a consequence, independent development of TAO, VSAO, AAO, and vHOG has been discontinued. Conclusions The newly broadened Uberon ontology is a unified cross-taxon resource for metazoans (animals) that has been substantially expanded to include a broad diversity of vertebrate anatomical structures, permitting reasoning across anatomical variation in extinct and extant taxa. Uberon is a core resource that supports single- and cross-species queries for candidate genes using annotations for phenotypes from the systematics, biodiversity, medical, and model organism communities, while also providing entities for logical definitions in the Cell and Gene Ontologies. The ontology release files associated with the ontology merge described in this manuscript are available at: http://purl.obolibrary.org/obo/uberon/releases/2013-02-21/ Current ontology release files are available always available at: http://purl.obolibrary.org/obo/uberon/releases/ PMID:25009735

  20. Ontology-Based Analysis of Microarray Data.

    PubMed

    Giuseppe, Agapito; Milano, Marianna

    2016-01-01

    The importance of semantic-based methods and algorithms for the analysis and management of biological data is growing for two main reasons. From a biological side, knowledge contained in ontologies is more and more accurate and complete, from a computational side, recent algorithms are using in a valuable way such knowledge. Here we focus on semantic-based management and analysis of protein interaction networks referring to all the approaches of analysis of protein-protein interaction data that uses knowledge encoded into biological ontologies. Semantic approaches for studying high-throughput data have been largely used in the past to mine genomic and expression data. Recently, the emergence of network approaches for investigating molecular machineries has stimulated in a parallel way the introduction of semantic-based techniques for analysis and management of network data. The application of these computational approaches to the study of microarray data can broad the application scenario of them and simultaneously can help the understanding of disease development and progress.

  1. Ontology patterns for complex topographic feature yypes

    USGS Publications Warehouse

    Varanka, Dalia E.

    2011-01-01

    Complex feature types are defined as integrated relations between basic features for a shared meaning or concept. The shared semantic concept is difficult to define in commonly used geographic information systems (GIS) and remote sensing technologies. The role of spatial relations between complex feature parts was recognized in early GIS literature, but had limited representation in the feature or coverage data models of GIS. Spatial relations are more explicitly specified in semantic technology. In this paper, semantics for topographic feature ontology design patterns (ODP) are developed as data models for the representation of complex features. In the context of topographic processes, component assemblages are supported by resource systems and are found on local landscapes. The topographic ontology is organized across six thematic modules that can account for basic feature types, resource systems, and landscape types. Types of complex feature attributes include location, generative processes and physical description. Node/edge networks model standard spatial relations and relations specific to topographic science to represent complex features. To demonstrate these concepts, data from The National Map of the U. S. Geological Survey was converted and assembled into ODP.

  2. Geographic spatial reasoning strategy based on ontology

    NASA Astrophysics Data System (ADS)

    Du, Xiaochu; Guo, Qingsheng; Wang, Quanfang

    2009-10-01

    Research on geographical spatial reasoning aims at expression of spatial relationships, geo-spatial reasoning rules and reasoning mechanism that could be used for geo-spatial knowledge discovery and spatial analysis. Spatial reasoning is intelligent spatial data processing technology in support of geo-spatial decision-making. Geographic ontology is clear formal definition of geographical concepts, which defines the basic terms and relations of these concepts, and the rules combining these terms and relationship. Therefore, it can well meet the formal knowledge representation requirement for geo-spatial reasoning that carry out reasoning by using geographic ontology. In this paper, methods of creating geographic ontology are discussed, and the rules based on spatial reasoning are summarized. Furthermore, a path query method based on geographic ontology is proposed, by creating a road ontology system and the corresponding administrative region ontology system, it can be used to solve large-scale spatial path query problem.

  3. Anatomy Ontology Matching Using Markov Logic Networks

    PubMed Central

    Li, Chunhua; Zhao, Pengpeng; Wu, Jian; Cui, Zhiming

    2016-01-01

    The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relationships between ontologies describing different species. Ontology matching is a kind of solutions to find semantic correspondences between entities of different ontologies. Markov logic networks which unify probabilistic graphical model and first-order logic provide an excellent framework for ontology matching. We combine several different matching strategies through first-order logic formulas according to the structure of anatomy ontologies. Experiments on the adult mouse anatomy and the human anatomy have demonstrated the effectiveness of proposed approach in terms of the quality of result alignment. PMID:27382498

  4. Incorporating Community Input into the SWEET Ontologies

    NASA Astrophysics Data System (ADS)

    Raskin, R. G.

    2006-05-01

    The Semantic Web for Earth and Environmental Terminology (SWEET) includes a comprehensive set of ontologies that are expandable by specialized user communities. SWEET provides shared understanding of concepts and relations that cross multiple Earth system science disciplines (such as nitrogen, conduction, pressure). A procedure has been established to elicit community input, to expand or edit the ontologies, and to align and map SWEET elements to concepts in other ontologies. The process includes a discussion wiki, ontology alignment tools, and community workshops and oversight committees. SWEET is being expanded to the entire planetary system (including solid Earth and heliosphere) based on a NASA ROSE/ACCESS grant.

  5. Temperature influence on structural changes of foundry bentonites

    NASA Astrophysics Data System (ADS)

    Holtzer, Mariusz; Bobrowski, Artur; Żymankowska-Kumon, Sylwia

    2011-10-01

    The results of investigations of three calcium bentonites, activated by sodium carbonate, applied in the foundry industry as binding material for moulding sands, subjected to the influence of high temperatures - are presented in the paper. Investigations were performed by the thermal analysis (TG) method, the infrared spectroscopy (FTIR) method and the modern Cu(II)-TET complex method (used for the determination of the montmorillonite content in bentonite samples). The occurrence of the dehydration process and two-stage dehydroxylation process was confirmed only for bentonite no. 2. This probably indicates that cis- and trans-isomers are present in the octahedric bentonite structure. Tests were performed at temperatures: 500, 550, 700, 900, 1000, 1100, 1200 °C.

  6. Laboratories for the 21st Century: Case Studies, Molecular Foundry, Berkeley, California

    SciTech Connect

    Not Available

    2010-11-01

    This case study provides information on the Molecular Foundry, which incorporates Labs21 principles in its design and construction. The design includes many of the strategies researched at Lawrence Berkeley Laboratory for energy efficient cleanroom and data centers.

  7. View northwest from floor of drydock no. 2; foundry/propeller shop ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    View northwest from floor of drydock no. 2; foundry/propeller shop in background. - Naval Base Philadelphia-Philadelphia Naval Shipyard, Drydock No. 2, League Island, Philadelphia, Philadelphia County, PA

  8. Drydock no. 2, view north from caisson; foundry/propeller shop (Haer ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    Drydock no. 2, view north from caisson; foundry/propeller shop (Haer no. Pa-387-O) in backgound and crane AL138 at left. - Naval Base Philadelphia-Philadelphia Naval Shipyard, Drydock No. 2, League Island, Philadelphia, Philadelphia County, PA

  9. 3. ANACONDA FOUNDRY DEPARTMENT LOOKING WEST. THE STEAM/BOILER HOUSE IS ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    3. ANACONDA FOUNDRY DEPARTMENT LOOKING WEST. THE STEAM/BOILER HOUSE IS IN THE FOREGROUND, WITH THE COMPRESSOR HOUSE AND MACHINE SHOP BEYOND - Anaconda Reduction Department, Southeast side of Warm Springs Valley, Anaconda, Deer Lodge County, MT

  10. The National Center for Biomedical Ontology: Advancing Biomedicinethrough Structured Organization of Scientific Knowledge

    SciTech Connect

    Rubin, Daniel L.; Lewis, Suzanna E.; Mungall, Chris J.; Misra,Sima; Westerfield, Monte; Ashburner, Michael; Sim, Ida; Chute,Christopher G.; Solbrig, Harold; Storey, Margaret-Anne; Smith, Barry; Day-Richter, John; Noy, Natalya F.; Musen, Mark A.

    2006-01-23

    The National Center for Biomedical Ontology(http://bioontology.org) is a consortium that comprises leadinginformaticians, biologists, clinicians, and ontologists funded by the NIHRoadmap to develop innovative technology and methods that allowscientists to record, manage, and disseminate biomedical information andknowledge in machine-processable form. The goals of the Center are: (1)to help unify the divergent and isolated efforts in ontology developmentby promoting high quality open-source, standards-based tools to create,manage, and use ontologies, (2) to create new software tools so thatscientists can use ontologies to annotate and analyze biomedical data,(3) to provide a national resource for the ongoing evaluation,integration, and evolution of biomedical ontologies and associated toolsand theories in the context of driving biomedical projects (DBPs), and(4) to disseminate the tools and resources of the Center and to identify,evaluate, and communicate best practices of ontology development to thebiomedical community. The Center is working toward these objectives byproviding tools to develop ontologies and to annotate experimental data,and by developing resources to integrate and relate existing ontologiesas well as by creating repositories of biomedical data that are annotatedusing those ontologies. The Center is providing training workshops inontology design, development, and usage, and is also pursuing research inontology evaluation, quality, and use of ontologies to promote scientificdiscovery. Through the research activities within the Center,collaborations with the DBPs, and interactions with the biomedicalcommunity, our goal is to help scientists to work more effectively in thee-science paradigm, enhancing experiment design, experiment execution,data analysis, information synthesis, hypothesis generation and testing,and understand human disease.

  11. Ontology of Serious Games

    ERIC Educational Resources Information Center

    Prayaga, Lakshmi; Rasmussen, Karen L.

    2008-01-01

    Computer games are no longer just for entertainment; they have also become a useful instructional strategy for acquiring knowledge. When games are used for purposes other than strict entertainment they become serious games. The goal of serious games is to enable the player to learn a task, master a strategy or develop a skill. Serious games can be…

  12. Variation Ontology for annotation of variation effects and mechanisms

    PubMed Central

    Vihinen, Mauno

    2014-01-01

    Ontology organizes and formally conceptualizes information in a knowledge domain with a controlled vocabulary having defined terms and relationships between them. Several ontologies have been used to annotate numerous databases in biology and medicine. Due to their unambiguous nature, ontological annotations facilitate systematic description and data organization, data integration and mining, and pattern recognition and statistics, as well as development of analysis and prediction tools. The Variation Ontology (VariO) was developed to allow the annotation of effects, consequences, and mechanisms of DNA, RNA, and protein variations. Variation types are systematically organized, and a detailed description of effects and mechanisms is possible. VariO is for annotating the variant, not the normal-state features or properties, and requires a reference (e.g., reference sequence, reference-state property, activity, etc.) compared to which the changes are indicated. VariO is versatile and can be used for variations ranging from genomic multiplications to single nucleotide or amino acid changes, whether of genetic or nongenetic origin. VariO annotations are position-specific and can be used for variations in any organism. PMID:24162187

  13. OGO: an ontological approach for integrating knowledge about orthology

    PubMed Central

    Miñarro-Gimenez, Jose Antonio; Madrid, Marisa; Fernandez-Breis, Jesualdo Tomas

    2009-01-01

    Background There exist several information resources about orthology of genes and proteins, and there are also systems for querying those resources in an integrated way. However, caveats with current approaches include lack of integration, since results are shown sequentially by resource, meaning that there is redundant information and the users are required to combine the results obtained manually. Results In this paper we have applied the Ontological Gene Orthology approach, which makes use of a domain ontology to integrate the information output from selected orthology resources. The integrated information is stored in a knowledge base, which can be queried through semantic languages. A friendly user interface has been developed to facilitate the search; consequently, users do not need to have knowledge on ontologies or ontological languages to obtain the relevant information. Conclusion The development and application of our approach allows users to retrieve integrated results when querying orthology information, providing a gene product-oriented output instead of a traditional information resource-oriented one. Besides this benefit for users, it also allows a better exploitation and management of orthology information and knowledge. PMID:19796397

  14. Ontology Driven Analysis of Spatio-temporal Phenomena, Aimed At Spatial Planning And Environmental Forecasting

    NASA Astrophysics Data System (ADS)

    Iwaniak, A.; Łukowicz, J.; Strzelecki, M.; Kaczmarek, I.

    2013-10-01

    Spatial planning is a crucial area for balancing civilization development with environmental protection. Spatial planning has a multidisciplinary nature. It must take into account the dynamics of the processes, which could affect the integrity of the environmental system. That is why we need a new approach to modelling phenomena occurring in space. Such approach is offered by ontologies, based on Description Logic (DL) and related to inference systems. Ontology is a system for the knowledge representation, including conceptual scheme and based on this scheme representation of reality. Ontologies can be enriched with additional logical systems. The authors present a way of building domain ontologies for spatial planning, including the representation of spatio-temporal phenomena. Description Logic is supplemented by structures of temporal logic. As a result, the analysis for exploring the topological relations between spatial objects will be extended to include temporal relationships: coincidence, precedence and succession, cause and effect relationship. Spatio-temporal models with temporal logic structures, encoded in ontologies, could be a subject of inference process, performed by semantic reasoners (reasoner engines). Spatio-temporal representations are offered, by so-called upper ontologies, such as GFO, BFO, OCHRE and others. Temporal structures provided in such ontologies, are useful for the analysis of data obtained from environmental and development monitoring systems and for description and representation of historical phenomena. They allow creating the models and scenarios of expected spatial transformation. They will support analysis for spatial development design, decision-making in spatial planning and forecasting of environmental impact.

  15. Arthrogryposis as a Syndrome: Gene Ontology Analysis.

    PubMed

    Hall, Judith G; Kiefer, Jeff

    2016-07-01

    Arthrogryposis by definition has multiple congenital contractures. All types of arthrogryposis have decreased in utero fetal movement. Because so many things are involved in normal fetal movement, there are many causes and processes that can go awry. In this era of molecular genetics, we have tried to place the known mutated genes seen in genetic forms of arthrogryposis into biological processes or cellular functions as defined by gene ontology. We hope this leads to better identification of all interacting pathways and processes involved in the development of fetal movement in order to improve diagnosis of the genetic forms of arthrogryposis, to lead to the development of molecular therapies, and to help better define the natural history of various types of arthrogryposis. PMID:27587986

  16. Cancer mortality in a cohort of United Kingdom steel foundry workers: 1946-85.

    PubMed Central

    Sorahan, T; Cooke, M A

    1989-01-01

    The mortality experienced by a cohort of 10,491 United Kingdom steel foundry workers during the period 1946-85 has been investigated. These workers were all male operatives first employed in any one of the 10 participating foundries in 1946-65; all had worked in the industry for a minimum period of one year. Compared with the general population of England and Wales, statistically significant excesses relating to cancer mortality were found for cancer of the stomach (E = 77.4, O = 106, SMR = 137) and cancer of the lung (E = 229.2, O = 441, SMR = 147). A statistically significant deficit was found for cancer of the brain (E = 19.4, O = 10, SMR = 51). Involvement of occupational exposures was assessed by the method of regression models and life tables (RMLT). This method was used to compare the duration of employment in the industry, in "dust exposed" jobs, in "fume exposed" jobs, in foundry area jobs, in fettling shop jobs, and in foundry area or fettling shop jobs, of those dying from cancers of the stomach and lung with those of all matching survivors. The RMLT analyses provided evidence of an occupational involvement in the risk of death from lung cancer from work in the foundry area or fettling shop, and weaker evidence of an occupational involvement in the risk of death from stomach cancer from work in the foundry area. PMID:2923828

  17. The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia

    PubMed Central

    Mizuno, Satoshi; Ogishima, Soichi; Nishigori, Hidekazu; Jamieson, Daniel G.; Verspoor, Karin; Tanaka, Hiroshi; Yaegashi, Nobuo; Nakaya, Jun

    2016-01-01

    Pre-eclampsia (PE) is a clinical syndrome characterized by new-onset hypertension and proteinuria at ≥20 weeks of gestation, and is a leading cause of maternal and perinatal morbidity and mortality. Previous studies have gathered abundant data about PE such as risk factors and pathological findings. However, most of these data are not semantically structured. Clinical data on PE patients are often generated with semantic heterogeneity such as using disparate terminology to describe the same phenomena. In clinical studies, interoperability of heterogenic clinical data is required in various situations. In such a situation, it is necessary to develop an interoperable and standardized semantic framework to research the pathology of PE more comprehensively and to achieve interoperability of heterogenic clinical data of PE patients. In this study, we developed an ontology representing clinical features, treatments, genetic factors, environmental factors, and other aspects of the current knowledge in the domain of PE. We call this pre-eclampsia ontology “PEO”. To achieve interoperability with other ontologies, the core structure of PEO was compliant with the hierarchy of the Basic Formal Ontology (BFO). The PEO incorporates a wide range of key concepts and terms of PE from clinical and biomedical research in structuring the knowledge base that is specific to PE; therefore, PEO is expected to enhance PE-specific information retrieval and knowledge discovery in both clinical and biomedical research fields. PMID:27788142

  18. Issues in learning an ontology from text

    PubMed Central

    Brewster, Christopher; Jupp, Simon; Luciano, Joanne; Shotton, David; Stevens, Robert D; Zhang, Ziqi

    2009-01-01

    Ontology construction for any domain is a labour intensive and complex process. Any methodology that can reduce the cost and increase efficiency has the potential to make a major impact in the life sciences. This paper describes an experiment in ontology construction from text for the animal behaviour domain. Our objective was to see how much could be done in a simple and relatively rapid manner using a corpus of journal papers. We used a sequence of pre-existing text processing steps, and here describe the different choices made to clean the input, to derive a set of terms and to structure those terms in a number of hierarchies. We describe some of the challenges, especially that of focusing the ontology appropriately given a starting point of a heterogeneous corpus. Using mainly automated techniques, we were able to construct an 18055 term ontology-like structure with 73% recall of animal behaviour terms, but a precision of only 26%. We were able to clean unwanted terms from the nascent ontology using lexico-syntactic patterns that tested the validity of term inclusion within the ontology. We used the same technique to test for subsumption relationships between the remaining terms to add structure to the initially broad and shallow structure we generated. All outputs are available at . We present a systematic method for the initial steps of ontology or structured vocabulary construction for scientific domains that requires limited human effort and can make a contribution both to ontology learning and maintenance. The method is useful both for the exploration of a scientific domain and as a stepping stone towards formally rigourous ontologies. The filtering of recognised terms from a heterogeneous corpus to focus upon those that are the topic of the ontology is identified to be one of the main challenges for research in ontology learning. PMID:19426458

  19. Hybrid Ontology for Semantic Information Retrieval Model Using Keyword Matching Indexing System

    PubMed Central

    Uthayan, K. R.; Anandha Mala, G. S.

    2015-01-01

    Ontology is the process of growth and elucidation of concepts of an information domain being common for a group of users. Establishing ontology into information retrieval is a normal method to develop searching effects of relevant information users require. Keywords matching process with historical or information domain is significant in recent calculations for assisting the best match for specific input queries. This research presents a better querying mechanism for information retrieval which integrates the ontology queries with keyword search. The ontology-based query is changed into a primary order to predicate logic uncertainty which is used for routing the query to the appropriate servers. Matching algorithms characterize warm area of researches in computer science and artificial intelligence. In text matching, it is more dependable to study semantics model and query for conditions of semantic matching. This research develops the semantic matching results between input queries and information in ontology field. The contributed algorithm is a hybrid method that is based on matching extracted instances from the queries and information field. The queries and information domain is focused on semantic matching, to discover the best match and to progress the executive process. In conclusion, the hybrid ontology in semantic web is sufficient to retrieve the documents when compared to standard ontology. PMID:25922851

  20. Research and application of role theory in ocean carbon cycle ontology construction

    NASA Astrophysics Data System (ADS)

    Jia, Haipeng; Xiong, Jing; Xu, Jianliang; Wang, Jipeng

    2014-12-01

    Many researchers have studied the ocean carbon cycle model trying to regulate the level of CO2 in atmosphere from viewpoint of quantification. Unlike other researches, this paper analyzes the conversion process of carbon element in the ocean from the qualitative viewpoint. There are many complex roles in the ocean carbon cycle, and it is hard to represent the case that an entity plays different role in different environment. An ontology technology Hozo role theory developed by Osaka University Mizoguchi Laboratory is proposed as a solution. The basic concepts and representation mode of Hozo role theory is introduced. The conversion process of ocean carbon cycle is abstracted and an ontology model using Hozo role theory is proposed. Instead of comprehensive common ontology construction method, we propose our own ontology development steps. Then an ontology about ocean carbon cycle is built in order to describe and share the basic knowledge of ocean carbon cycle. A knowledge base of material circulation is proposed based on the ontology. Its construction framework is described and some knowledge base query examples are also illustrated. Conclusions show that the role theory can effectively solve the problem of multirole description in ocean carbon cycle, and knowledge reasoning based on ontology is also effective.