Molecular Foundry

Science.gov Websites

Molecular Foundry? Research Themes Strategic Plan (PDF) Foundry Careers Foundry Facts Bay Cam Other User -art instrumentation and expertise. Having merged with the Molecular Foundry in 2014, the facility

IDOMAL: an ontology for malaria.

PubMed

Topalis, Pantelis; Mitraka, Elvira; Bujila, Ioana; Deligianni, Elena; Dialynas, Emmanuel; Siden-Kiamos, Inga; Troye-Blomberg, Marita; Louis, Christos

2010-08-10

Ontologies are rapidly becoming a necessity for the design of efficient information technology tools, especially databases, because they permit the organization of stored data using logical rules and defined terms that are understood by both humans and machines. This has as consequence both an enhanced usage and interoperability of databases and related resources. It is hoped that IDOMAL, the ontology of malaria will prove a valuable instrument when implemented in both malaria research and control measures. The OBOEdit2 software was used for the construction of the ontology. IDOMAL is based on the Basic Formal Ontology (BFO) and follows the rules set by the OBO Foundry consortium. The first version of the malaria ontology covers both clinical and epidemiological aspects of the disease, as well as disease and vector biology. IDOMAL is meant to later become the nucleation site for a much larger ontology of vector borne diseases, which will itself be an extension of a large ontology of infectious diseases (IDO). The latter is currently being developed in the frame of a large international collaborative effort. IDOMAL, already freely available in its first version, will form part of a suite of ontologies that will be used to drive IT tools and databases specifically constructed to help control malaria and, later, other vector-borne diseases. This suite already consists of the ontology described here as well as the one on insecticide resistance that has been available for some time. Additional components are being developed and introduced into IDOMAL.

Semi-automated ontology generation within OBO-Edit.

PubMed

Wächter, Thomas; Schroeder, Michael

2010-06-15

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. 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. DOG4DAG is available within OBO-Edit 2.1 at http://www.oboedit.org. Supplementary data are available at Bioinformatics online.

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

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.

Tutorial on Protein Ontology Resources

PubMed Central

Arighi, Cecilia; Drabkin, Harold; Christie, Karen R.; Ross, Karen; Natale, Darren

2017-01-01

The Protein Ontology (PRO) is the reference ontology for proteins in the Open Biomedical Ontologies (OBO) foundry and consists of three sub-ontologies representing protein classes of homologous genes, proteoforms (e.g., splice isoforms, sequence variants, and post-translationally modified forms), and protein complexes. PRO defines classes of proteins and protein complexes, both species-specific and species non-specific, and indicates their relationships in a hierarchical framework, supporting accurate protein annotation at the appropriate level of granularity, analyses of protein conservation across species, and semantic reasoning. In this first section of this chapter, we describe the PRO framework including categories of PRO terms and the relationship of PRO to other ontologies and protein resources. Next, we provide a tutorial about the PRO website (proconsortium.org) where users can browse and search the PRO hierarchy, view reports on individual PRO terms, and visualize relationships among PRO terms in a hierarchical table view, a multiple sequence alignment view, and a Cytoscape network view. Finally, we describe several examples illustrating the unique and rich information available in PRO. PMID:28150233

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.

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

Solar-Terrestrial Ontology Development

NASA Astrophysics Data System (ADS)

McGuinness, D.; Fox, P.; Middleton, D.; Garcia, J.; Cinquni, L.; West, P.; Darnell, J. A.; Benedict, J.

2005-12-01

The development of an interdisciplinary virtual observatory (the Virtual Solar-Terrestrial Observatory; VSTO) as a scalable environment for searching, integrating, and analyzing databases distributed over the Internet requires a higher level of semantic interoperability than here-to-fore required by most (if not all) distributed data systems or discipline specific virtual observatories. The formalization of semantics using ontologies and their encodings for the internet (e.g. OWL - the Web Ontology Language), as well as the use of accompanying tools, such as reasoning, inference and explanation, open up both a substantial leap in options for interoperability and in the need for formal development principles to guide ontology development and use within modern, multi-tiered network data environments. In this presentation, we outline the formal methodologies we utilize in the VSTO project, the currently developed use-cases, ontologies and their relation to existing ontologies (such as SWEET).

The eXtensible ontology development (XOD) principles and tool implementation to support ontology interoperability.

PubMed

He, Yongqun; Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; Overton, James A; Ong, Edison

2018-01-12

Ontologies are critical to data/metadata and knowledge standardization, sharing, and analysis. With hundreds of biological and biomedical ontologies developed, it has become critical to ensure ontology interoperability and the usage of interoperable ontologies for standardized data representation and integration. The suite of web-based Ontoanimal tools (e.g., Ontofox, Ontorat, and Ontobee) support different aspects of extensible ontology development. By summarizing the common features of Ontoanimal and other similar tools, we identified and proposed an "eXtensible Ontology Development" (XOD) strategy and its associated four principles. These XOD principles reuse existing terms and semantic relations from reliable ontologies, develop and apply well-established ontology design patterns (ODPs), and involve community efforts to support new ontology development, promoting standardized and interoperable data and knowledge representation and integration. The adoption of the XOD strategy, together with robust XOD tool development, will greatly support ontology interoperability and robust ontology applications to support data to be Findable, Accessible, Interoperable and Reusable (i.e., FAIR).

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

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

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

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…

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

Development and Packaging of Microsystems Using Foundry Services

DTIC Science & Technology

1998-06-01

DEVELOPMENT AND PACKAGING OF MICROSYSTEMS USING FOUNDRY SERVICES Jeffrey T. Butler, BSEE, MSEE Captain, USAF Approved: Paul H . Ostdiek, PhD, Lt...structural polysilicon layers. CMOS Device Area Micromechanical Device Area arsenic-daped epitaxial layer >J1M* ’ MM t° H 0J n-type ailioon...Ö ♦ * ♦ m B 1 —i ft H 035 0.045 0.055 0.065 0.075 Power Applied to Driver (W) (b) Figure 4-4. (a) Driver output loading

Molecular Foundry

Science.gov Websites

Artificial Photosynthesis Foundry users, along with staff, have developed a fabrication method to make a square-inch sized artificial photosystem, in the form of an inorganic core-shell nanotube array, that awarded for his pioneering work in the area of advanced x-ray gratings New Catalyst Gives Artificial

TGF-beta signaling proteins and the Protein Ontology.

PubMed

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

2009-05-06

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. 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 modifications. PRO provides

The Orthology Ontology: development and applications.

PubMed

Fernández-Breis, Jesualdo Tomás; Chiba, Hirokazu; Legaz-García, María Del Carmen; Uchiyama, Ikuo

2016-06-04

Computational comparative analysis of multiple genomes provides valuable opportunities to biomedical research. In particular, orthology analysis can play a central role in comparative genomics; it guides establishing evolutionary relations among genes of organisms and allows functional inference of gene products. However, the wide variations in current orthology databases necessitate the research toward the shareability of the content that is generated by different tools and stored in different structures. Exchanging the content with other research communities requires making the meaning of the content explicit. The need for a common ontology has led to the creation of the Orthology Ontology (ORTH) following the best practices in ontology construction. Here, we describe our model and major entities of the ontology that is implemented in the Web Ontology Language (OWL), followed by the assessment of the quality of the ontology and the application of the ORTH to existing orthology datasets. This shareable ontology enables the possibility to develop Linked Orthology Datasets and a meta-predictor of orthology through standardization for the representation of orthology databases. The ORTH is freely available in OWL format to all users at http://purl.org/net/orth . The Orthology Ontology can serve as a framework for the semantic standardization of orthology content and it will contribute to a better exploitation of orthology resources in biomedical research. The results demonstrate the feasibility of developing shareable datasets using this ontology. Further applications will maximize the usefulness of this ontology.

[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.

Web-based expert system for foundry pollution prevention

NASA Astrophysics Data System (ADS)

Moynihan, Gary P.

2004-02-01

Pollution prevention is a complex task. Many small foundries lack the in-house expertise to perform these tasks. Expert systems are a type of computer information system that incorporates artificial intelligence. As noted in the literature, they provide a means of automating specialized expertise. This approach may be further leveraged by implementing the expert system on the internet (or world-wide web). This will allow distribution of the expertise to a variety of geographically-dispersed foundries. The purpose of this research is to develop a prototype web-based expert system to support pollution prevention for the foundry industry. The prototype system identifies potential emissions for a specified process, and also provides recommendations for the prevention of these contaminants. The system is viewed as an initial step toward assisting the foundry industry in better meeting government pollution regulations, as well as improving operating efficiencies within these companies.

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.

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

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,…

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

DOE PAGES

Buttigieg, Pier Luigi; Pafilis, Evangelos; Lewis, Suzanna E.; ...

2016-09-23

Background: The Environment Ontology (ENVO; http://www.environmentontology.org/), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications. Methods: We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVOmore » in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO. Results: Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl. Conclusions: ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation

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

Buttigieg, Pier Luigi; Pafilis, Evangelos; Lewis, Suzanna E.

Background: The Environment Ontology (ENVO; http://www.environmentontology.org/), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications. Methods: We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVOmore » in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO. Results: Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl. Conclusions: ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology

The environment ontology in 2016: bridging domains with increased scope, semantic density, and interoperation.

PubMed

Buttigieg, Pier Luigi; Pafilis, Evangelos; Lewis, Suzanna E; Schildhauer, Mark P; Walls, Ramona L; Mungall, Christopher J

2016-09-23

The Environment Ontology (ENVO; http://www.environmentontology.org/ ), first described in 2013, is a resource and research target for the semantically controlled description of environmental entities. The ontology's initial aim was the representation of the biomes, environmental features, and environmental materials pertinent to genomic and microbiome-related investigations. However, the need for environmental semantics is common to a multitude of fields, and ENVO's use has steadily grown since its initial description. We have thus expanded, enhanced, and generalised the ontology to support its increasingly diverse applications. We have updated our development suite to promote expressivity, consistency, and speed: we now develop ENVO in the Web Ontology Language (OWL) and employ templating methods to accelerate class creation. We have also taken steps to better align ENVO with the Open Biological and Biomedical Ontologies (OBO) Foundry principles and interoperate with existing OBO ontologies. Further, we applied text-mining approaches to extract habitat information from the Encyclopedia of Life and automatically create experimental habitat classes within ENVO. Relative to its state in 2013, ENVO's content, scope, and implementation have been enhanced and much of its existing content revised for improved semantic representation. ENVO now offers representations of habitats, environmental processes, anthropogenic environments, and entities relevant to environmental health initiatives and the global Sustainable Development Agenda for 2030. Several branches of ENVO have been used to incubate and seed new ontologies in previously unrepresented domains such as food and agronomy. The current release version of the ontology, in OWL format, is available at http://purl.obolibrary.org/obo/envo.owl . ENVO has been shaped into an ontology which bridges multiple domains including biomedicine, natural and anthropogenic ecology, 'omics, and socioeconomic development. Through

Versioning System for Distributed Ontology Development

DTIC Science & Technology

2016-03-15

provides guidelines for evaluating the impact of the version changes. This page intentionally left blank. v...conformance to a clear set of development and versioning guidelines to assure that changes and extensions can be integrated back into the “main development... guidelines for evolution of an ontology would have considerably helped the users of the ontology in these situations. The currently accessible

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

PubMed

Waldemarin, Ricardo C; de Farias, Cléver R G

2018-04-01

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

[Cohort study of ischemic heart disease among 1817 workers in a foundry].

PubMed

Lu, Yang; Zhang, Min

2012-09-01

To determine the risk of ischemic heart disease among foundry workers and the exposure-response relationship between the risk and foundry work and cumulative exposure to silica dust, and to establish a regression model to predict the risk for developing ischemic heart disease by a given length of employment and exposure to silica dust in foundry workers. Cohort study was conducted, following-up workers in an automobile foundry employed for more than one year during January 1, 1980 to December 31, 1996 as cohort members. In total, 30 years were followed to December 31, 2009. In cohort, workers exposed to pouring, sand preparation, cast shakeout and finishing, melting, overhead crane operation, moulding and core-making were in foundry group, and auxiliary workers at the same factory, such as electricians, fitters, and inspectors were in control group. The risk of ischemic heart disease among foundry workers and the exposure-response relationship between the risk and foundry work and cumulative exposure to silica dust were analyzed with cox regression model using SPSS software, and a logistic regression model was established for prediction of risk for developing ischemic heart disease at a given length of employment and exposure to silica dust in foundry workers. Totally, 1817 workers were followed-up for 45 553.05 person-years during 30 years, with 156 cases of ischemic heart disease and incidence of 342.46 per 100 000 person-years. And the average age at onset was 51.46 years and duration of employment at onset was 21.61 years. Results showed that male, smoking, alcohol drinking, age and duration of employment were risk factors for ischemic heart disease. Risk of ischemic heart disease in foundry workers positively correlated with cumulative silica exposure, and the risk of ischemic heart disease increased by 75.8 percent (RR = 1.758, 95% CI 1.221-2.532) with cumulative silica exposure of 1 mg/m3 x year, adjusted for smoking. And risk of ischemic heart disease was

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…

Development of an Ontology for Periodontitis.

PubMed

Suzuki, Asami; Takai-Igarashi, Takako; Nakaya, Jun; Tanaka, Hiroshi

2015-01-01

In the clinical dentists and periodontal researchers' community, there is an obvious demand for a systems model capable of linking the clinical presentation of periodontitis to underlying molecular knowledge. A computer-readable representation of processes on disease development will give periodontal researchers opportunities to elucidate pathways and mechanisms of periodontitis. An ontology for periodontitis can be a model for integration of large variety of factors relating to a complex disease such as chronic inflammation in different organs accompanied by bone remodeling and immune system disorders, which has recently been referred to as osteoimmunology. Terms characteristic of descriptions related to the onset and progression of periodontitis were manually extracted from 194 review articles and PubMed abstracts by experts in periodontology. We specified all the relations between the extracted terms and constructed them into an ontology for periodontitis. We also investigated matching between classes of our ontology and that of Gene Ontology Biological Process. We developed an ontology for periodontitis called Periodontitis-Ontology (PeriO). The pathological progression of periodontitis is caused by complex, multi-factor interrelationships. PeriO consists of all the required concepts to represent the pathological progression and clinical treatment of periodontitis. The pathological processes were formalized with reference to Basic Formal Ontology and Relation Ontology, which accounts for participants in the processes realized by biological objects such as molecules and cells. We investigated the peculiarity of biological processes observed in pathological progression and medical treatments for the disease in comparison with Gene Ontology Biological Process (GO-BP) annotations. The results indicated that peculiarities of Perio existed in 1) granularity and context dependency of both the conceptualizations, and 2) causality intrinsic to the pathological processes

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.

Expert2OWL: A Methodology for Pattern-Based Ontology Development.

PubMed

Tahar, Kais; Xu, Jie; Herre, Heinrich

2017-01-01

The formalization of expert knowledge enables a broad spectrum of applications employing ontologies as underlying technology. These include eLearning, Semantic Web and expert systems. However, the manual construction of such ontologies is time-consuming and thus expensive. Moreover, experts are often unfamiliar with the syntax and semantics of formal ontology languages such as OWL and usually have no experience in developing formal ontologies. To overcome these barriers, we developed a new method and tool, called Expert2OWL that provides efficient features to support the construction of OWL ontologies using GFO (General Formal Ontology) as a top-level ontology. This method allows a close and effective collaboration between ontologists and domain experts. Essentially, this tool integrates Excel spreadsheets as part of a pattern-based ontology development and refinement process. Expert2OWL enables us to expedite the development process and modularize the resulting ontologies. We applied this method in the field of Chinese Herbal Medicine (CHM) and used Expert2OWL to automatically generate an accurate Chinese Herbology ontology (CHO). The expressivity of CHO was tested and evaluated using ontology query languages SPARQL and DL. CHO shows promising results and can generate answers to important scientific questions such as which Chinese herbal formulas contain which substances, which substances treat which diseases, and which ones are the most frequently used in CHM.

DMTO: a realistic ontology for standard diabetes mellitus treatment.

PubMed

El-Sappagh, Shaker; Kwak, Daehan; Ali, Farman; Kwak, Kyung-Sup

2018-02-06

Treatment of type 2 diabetes mellitus (T2DM) is a complex problem. A clinical decision support system (CDSS) based on massive and distributed electronic health record data can facilitate the automation of this process and enhance its accuracy. The most important component of any CDSS is its knowledge base. This knowledge base can be formulated using ontologies. The formal description logic of ontology supports the inference of hidden knowledge. Building a complete, coherent, consistent, interoperable, and sharable ontology is a challenge. This paper introduces the first version of the newly constructed Diabetes Mellitus Treatment Ontology (DMTO) as a basis for shared-semantics, domain-specific, standard, machine-readable, and interoperable knowledge relevant to T2DM treatment. It is a comprehensive ontology and provides the highest coverage and the most complete picture of coded knowledge about T2DM patients' current conditions, previous profiles, and T2DM-related aspects, including complications, symptoms, lab tests, interactions, treatment plan (TP) frameworks, and glucose-related diseases and medications. It adheres to the design principles recommended by the Open Biomedical Ontologies Foundry and is based on ontological realism that follows the principles of the Basic Formal Ontology and the Ontology for General Medical Science. DMTO is implemented under Protégé 5.0 in Web Ontology Language (OWL) 2 format and is publicly available through the National Center for Biomedical Ontology's BioPortal at http://bioportal.bioontology.org/ontologies/DMTO . The current version of DMTO includes more than 10,700 classes, 277 relations, 39,425 annotations, 214 semantic rules, and 62,974 axioms. We provide proof of concept for this approach to modeling TPs. The ontology is able to collect and analyze most features of T2DM as well as customize chronic TPs with the most appropriate drugs, foods, and physical exercises. DMTO is ready to be used as a knowledge base for

The Development of Ontology from Multiple Databases

NASA Astrophysics Data System (ADS)

Kasim, Shahreen; Aswa Omar, Nurul; Fudzee, Mohd Farhan Md; Azhar Ramli, Azizul; Aizi Salamat, Mohamad; Mahdin, Hairulnizam

2017-08-01

The area of halal industry is the fastest growing global business across the world. The halal food industry is thus crucial for Muslims all over the world as it serves to ensure them that the food items they consume daily are syariah compliant. Currently, ontology has been widely used in computer sciences area such as web on the heterogeneous information processing, semantic web, and information retrieval. However, ontology has still not been used widely in the halal industry. Today, Muslim community still have problem to verify halal status for products in the market especially foods consisting of E number. This research tried to solve problem in validating the halal status from various halal sources. There are various chemical ontology from multilple databases found to help this ontology development. The E numbers in this chemical ontology are codes for chemicals that can be used as food additives. With this E numbers ontology, Muslim community could identify and verify the halal status effectively for halal products in the market.

A document-centric approach for developing the tolAPC ontology.

PubMed

Blfgeh, Aisha; Warrender, Jennifer; Hilkens, Catharien M U; Lord, Phillip

2017-11-28

There are many challenges associated with ontology building, as the process often touches on many different subject areas; it needs knowledge of the problem domain, an understanding of the ontology formalism, software in use and, sometimes, an understanding of the philosophical background. In practice, it is very rare that an ontology can be completed by a single person, as they are unlikely to combine all of these skills. So people with these skills must collaborate. One solution to this is to use face-to-face meetings, but these can be expensive and time-consuming for teams that are not co-located. Remote collaboration is possible, of course, but one difficulty here is that domain specialists use a wide-variety of different "formalisms" to represent and share their data - by the far most common, however, is the "office file" either in the form of a word-processor document or a spreadsheet. Here we describe the development of an ontology of immunological cell types; this was initially developed by domain specialists using an Excel spreadsheet for collaboration. We have transformed this spreadsheet into an ontology using highly-programmatic and pattern-driven ontology development. Critically, the spreadsheet remains part of the source for the ontology; the domain specialists are free to update it, and changes will percolate to the end ontology. We have developed a new ontology describing immunological cell lines built by instantiating ontology design patterns written programmatically, using values from a spreadsheet catalogue. This method employs a spreadsheet that was developed by domain experts. The spreadsheet is unconstrained in its usage and can be freely updated resulting in a new ontology. This provides a general methodology for ontology development using data generated by domain specialists.

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

PubMed

Elayavilli, Ravikumar Komandur; Liu, Hongfang

2016-01-01

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. 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. 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. 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 and formalizing them in ontological

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…

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.

Development and Evaluation of an Adolescents' Depression Ontology for Analyzing Social Data.

PubMed

Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min

2016-01-01

This study aims to develop and evaluate an ontology for adolescents' depression to be used for collecting and analyzing social data. The ontology was developed according to the 'ontology development 101' methodology. Concepts were extracted from clinical practice guidelines and related literatures. The ontology is composed of five sub-ontologies which represent risk factors, sign and symptoms, measurement, diagnostic result and management care. The ontology was evaluated in four different ways: First, we examined the frequency of ontology concept appeared in social data; Second, the content coverage of ontology was evaluated by comparing ontology concepts with concepts extracted from the youth depression counseling records; Third, the structural and representational layer of the ontology were evaluated by 5 ontology and psychiatric nursing experts; Fourth, the scope of the ontology was examined by answering 59 competency questions. The ontology was improved by adding new concepts and synonyms and revising the level of structure.

[Occupational risk for development of respiratory diseases in foundry shop workers at machinery industries].

PubMed

Khamitova, R Ia; Loskutov, D V

2012-01-01

The paper provides the results of assessment of prior and posterior occupational risks and those of questionnaire analysis in foundry shop workers from machinery enterprises. According to the data of attestation of job places, the working conditions of major foundry occupations were ascertained to correspond to class 3, grades 1 to 3. The prior risk for occupational respiratory diseases (RD) was defined as moderate whereas the posterior risk was high. According to the results of a questionnaire survey, more than half of the workers sought medical advice for bronchopulmonary pathology. Determination of whether there is, in terms of the etiological share, a cause-and-effect relationship between RDs and working conditions has shown that the occupation was highly responsible, which suggests that harmful industrial factors make a considerable contribution to the development of RDs in the workers of the enterprises under study.

Development and Evaluation of an Ontology for Guiding Appropriate Antibiotic Prescribing

PubMed Central

Furuya, E. Yoko; Kuperman, Gilad J.; Cimino, James J.; Bakken, Suzanne

2011-01-01

Objectives To develop and apply formal ontology creation methods to the domain of antimicrobial prescribing and to formally evaluate the resulting ontology through intrinsic and extrinsic evaluation studies. Methods We extended existing ontology development methods to create the ontology and implemented the ontology using Protégé-OWL. Correctness of the ontology was assessed using a set of ontology design principles and domain expert review via the laddering technique. We created three artifacts to support the extrinsic evaluation (set of prescribing rules, alerts and an ontology-driven alert module, and a patient database) and evaluated the usefulness of the ontology for performing knowledge management tasks to maintain the ontology and for generating alerts to guide antibiotic prescribing. Results The ontology includes 199 classes, 10 properties, and 1,636 description logic restrictions. Twenty-three Semantic Web Rule Language rules were written to generate three prescribing alerts: 1) antibiotic-microorganism mismatch alert; 2) medication-allergy alert; and 3) non-recommended empiric antibiotic therapy alert. The evaluation studies confirmed the correctness of the ontology, usefulness of the ontology for representing and maintaining antimicrobial treatment knowledge rules, and usefulness of the ontology for generating alerts to provide feedback to clinicians during antibiotic prescribing. Conclusions This study contributes to the understanding of ontology development and evaluation methods and addresses one knowledge gap related to using ontologies as a clinical decision support system component—a need for formal ontology evaluation methods to measure their quality from the perspective of their intrinsic characteristics and their usefulness for specific tasks. PMID:22019377

Development and evaluation of an ontology for guiding appropriate antibiotic prescribing.

PubMed

Bright, Tiffani J; Yoko Furuya, E; Kuperman, Gilad J; Cimino, James J; Bakken, Suzanne

2012-02-01

To develop and apply formal ontology creation methods to the domain of antimicrobial prescribing and to formally evaluate the resulting ontology through intrinsic and extrinsic evaluation studies. We extended existing ontology development methods to create the ontology and implemented the ontology using Protégé-OWL. Correctness of the ontology was assessed using a set of ontology design principles and domain expert review via the laddering technique. We created three artifacts to support the extrinsic evaluation (set of prescribing rules, alerts and an ontology-driven alert module, and a patient database) and evaluated the usefulness of the ontology for performing knowledge management tasks to maintain the ontology and for generating alerts to guide antibiotic prescribing. The ontology includes 199 classes, 10 properties, and 1636 description logic restrictions. Twenty-three Semantic Web Rule Language rules were written to generate three prescribing alerts: (1) antibiotic-microorganism mismatch alert; (2) medication-allergy alert; and (3) non-recommended empiric antibiotic therapy alert. The evaluation studies confirmed the correctness of the ontology, usefulness of the ontology for representing and maintaining antimicrobial treatment knowledge rules, and usefulness of the ontology for generating alerts to provide feedback to clinicians during antibiotic prescribing. This study contributes to the understanding of ontology development and evaluation methods and addresses one knowledge gap related to using ontologies as a clinical decision support system component-a need for formal ontology evaluation methods to measure their quality from the perspective of their intrinsic characteristics and their usefulness for specific tasks. Copyright © 2011 Elsevier Inc. All rights reserved.

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...

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

Development of an Adolescent Depression Ontology for Analyzing Social Data.

PubMed

Jung, Hyesil; Park, Hyeoun-Ae; Song, Tae-Min; Jeon, Eunjoo; Kim, Ae Ran; Lee, Joo Yun

2015-01-01

Depression in adolescence is associated with significant suicidality. Therefore, it is important to detect the risk for depression and provide timely care to adolescents. This study aims to develop an ontology for collecting and analyzing social media data about adolescent depression. This ontology was developed using the 'ontology development 101'. The important terms were extracted from several clinical practice guidelines and postings on Social Network Service. We extracted 777 terms, which were categorized into 'risk factors', 'sign and symptoms', 'screening', 'diagnosis', 'treatment', and 'prevention'. An ontology developed in this study can be used as a framework to understand adolescent depression using unstructured data from social media.

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…

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.

Extending the DIDEO ontology to include entities from the natural product drug interaction domain of discourse.

PubMed

Judkins, John; Tay-Sontheimer, Jessica; Boyce, Richard D; Brochhausen, Mathias

2018-05-09

Prompted by the frequency of concomitant use of prescription drugs with natural products, and the lack of knowledge regarding the impact of pharmacokinetic-based natural product-drug interactions (PK-NPDIs), the United States National Center for Complementary and Integrative Health has established a center of excellence for PK-NPDI. The Center is creating a public database to help researchers (primarly pharmacologists and medicinal chemists) to share and access data, results, and methods from PK-NPDI studies. In order to represent the semantics of the data and foster interoperability, we are extending the Drug-Drug Interaction and Evidence Ontology (DIDEO) to include definitions for terms used by the data repository. This is feasible due to a number of similarities between pharmacokinetic drug-drug interactions and PK-NPDIs. To achieve this, we set up an iterative domain analysis in the following steps. In Step 1 PK-NPDI domain experts produce a list of terms and definitions based on data from PK-NPDI studies, in Step 2 an ontology expert creates ontologically appropriate classes and definitions from the list along with class axioms, in Step 3 there is an iterative editing process during which the domain experts and the ontology experts review, assess, and amend class labels and definitions and in Step 4 the ontology expert implements the new classes in the DIDEO development branch. This workflow often results in different labels and definitions for the new classes in DIDEO than the domain experts initially provided; the latter are preserved in DIDEO as separate annotations. Step 1 resulted in a list of 344 terms. During Step 2 we found that 9 of these terms already existed in DIDEO, and 6 existed in other OBO Foundry ontologies. These 6 were imported into DIDEO; additional terms from multiple OBO Foundry ontologies were also imported, either to serve as superclasses for new terms in the initial list or to build axioms for these terms. At the time of writing, 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…

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

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

Applications of Ontology Design Patterns in Biomedical Ontologies

PubMed Central

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

2012-01-01

Ontology design patterns (ODPs) are a proposed solution to facilitate ontology development, and to help users avoid some of the most frequent modeling mistakes. ODPs originate from similar approaches in software engineering, where software design patterns have become a critical aspect of software development. There is little empirical evidence for ODP prevalence or effectiveness thus far. In this work, we determine the use and applicability of ODPs in a case study of biomedical ontologies. We encoded ontology design patterns from two ODP catalogs. We then searched for these patterns in a set of eight ontologies. We found five patterns of the 69 patterns. Two of the eight ontologies contained these patterns. While ontology design patterns provide a vehicle for capturing formally reoccurring models and best practices in ontology design, we show that today their use in a case study of widely used biomedical ontologies is limited. PMID:23304337

Development of health information search engine based on metadata and ontology.

PubMed

Song, Tae-Min; Park, Hyeoun-Ae; Jin, Dal-Lae

2014-04-01

The aim of the study was to develop a metadata and ontology-based health information search engine ensuring semantic interoperability to collect and provide health information using different application programs. Health information metadata ontology was developed using a distributed semantic Web content publishing model based on vocabularies used to index the contents generated by the information producers as well as those used to search the contents by the users. Vocabulary for health information ontology was mapped to the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), and a list of about 1,500 terms was proposed. The metadata schema used in this study was developed by adding an element describing the target audience to the Dublin Core Metadata Element Set. A metadata schema and an ontology ensuring interoperability of health information available on the internet were developed. The metadata and ontology-based health information search engine developed in this study produced a better search result compared to existing search engines. Health information search engine based on metadata and ontology will provide reliable health information to both information producer and information consumers.

A high-resolution anatomical ontology of the developing murine genitourinary tract

PubMed Central

Little, Melissa H.; Brennan, Jane; Georgas, Kylie; Davies, Jamie A.; Davidson, Duncan R.; Baldock, Richard A.; Beverdam, Annemiek; Bertram, John F.; Capel, Blanche; Chiu, Han Sheng; Clements, Dave; Cullen-McEwen, Luise; Fleming, Jean; Gilbert, Thierry; Houghton, Derek; Kaufman, Matt H.; Kleymenova, Elena; Koopman, Peter A.; Lewis, Alfor G.; McMahon, Andrew P.; Mendelsohn, Cathy L.; Mitchell, Eleanor K.; Rumballe, Bree A.; Sweeney, Derina E.; Valerius, M. Todd; Yamada, Gen; Yang, Yiya; Yu., Jing

2007-01-01

Cataloguing gene expression during development of the genitourinary tract will increase our understanding not only of this process but also of congenital defects and disease affecting this organ system. We have developed a high-resolution ontology with which to describe the subcompartments of the developing murine genitourinary tract. This ontology incorporates what can be defined histologically and begins to encompass other structures and cell types already identified at the molecular level. The ontology is being used to annotate in situ hybridisation data generated as part of the Genitourinary Development Molecular Anatomy Project (GUDMAP), a publicly available data resource on gene and protein expression during genitourinary development. The GUDMAP ontology encompasses Theiler stage (TS) 17 to 27 of development as well as the sexually mature adult. It has been written as a partonomic, text-based, hierarchical ontology that, for the embryological stages, has been developed as a high-resolution expansion of the existing Edinburgh Mouse Atlas Project (EMAP) ontology. It also includes group terms for well-characterised structural and/or functional units comprising several sub-structures, such as the nephron and juxtaglomerular complex. Each term has been assigned a unique identification number. Synonyms have been used to improve the success of query searching and maintain wherever possible existing EMAP terms relating to this organ system. We describe here the principles and structure of the ontology and provide representative diagrammatic, histological, and whole mount and section RNA in situ hybridisation images to clarify the terms used within the ontology. Visual examples of how terms appear in different specimen types are also provided. PMID:17452023

Development and Evaluation of an Obesity Ontology for Social Big Data Analysis.

PubMed

Kim, Ae Ran; Park, Hyeoun-Ae; Song, Tae-Min

2017-07-01

The aim of this study was to develop and evaluate an obesity ontology as a framework for collecting and analyzing unstructured obesity-related social media posts. The obesity ontology was developed according to the 'Ontology Development 101'. The coverage rate of the developed ontology was examined by mapping concepts and terms of the ontology with concepts and terms extracted from obesity-related Twitter postings. The structure and representative ability of the ontology was evaluated by nurse experts. We applied the ontology to the density analysis of keywords related to obesity types and management strategies and to the sentiment analysis of obesity and diet using social big data. The developed obesity ontology was represented by 8 superclasses and 124 subordinate classes. The superclasses comprised 'risk factors,' 'types,' 'symptoms,' 'complications,' 'assessment,' 'diagnosis,' 'management strategies,' and 'settings.' The coverage rate of the ontology was 100% for the concepts and 87.8% for the terms. The evaluation scores for representative ability were higher than 4.0 out of 5.0 for all of the evaluation items. The density analysis of keywords revealed that the top-two posted types of obesity were abdomen and thigh, and the top-three posted management strategies were diet, exercise, and dietary supplements or drug therapy. Positive expressions of obesity-related postings has increased annually in the sentiment analysis. It was found that the developed obesity ontology was useful to identify the most frequently used terms on obesity and opinions and emotions toward obesity posted by the geneal population on social media.

MicrO: an ontology of phenotypic and metabolic characters, assays, and culture media found in prokaryotic taxonomic descriptions.

PubMed

Blank, Carrine E; Cui, Hong; Moore, Lisa R; Walls, Ramona L

2016-01-01

MicrO is an ontology of microbiological terms, including prokaryotic qualities and processes, material entities (such as cell components), chemical entities (such as microbiological culture media and medium ingredients), and assays. The ontology was built to support the ongoing development of a natural language processing algorithm, MicroPIE (or, Microbial Phenomics Information Extractor). During the MicroPIE design process, we realized there was a need for a prokaryotic ontology which would capture the evolutionary diversity of phenotypes and metabolic processes across the tree of life, capture the diversity of synonyms and information contained in the taxonomic literature, and relate microbiological entities and processes to terms in a large number of other ontologies, most particularly the Gene Ontology (GO), the Phenotypic Quality Ontology (PATO), and the Chemical Entities of Biological Interest (ChEBI). We thus constructed MicrO to be rich in logical axioms and synonyms gathered from the taxonomic literature. MicrO currently has ~14550 classes (~2550 of which are new, the remainder being microbiologically-relevant classes imported from other ontologies), connected by ~24,130 logical axioms (5,446 of which are new), and is available at (http://purl.obolibrary.org/obo/MicrO.owl) and on the project website at https://github.com/carrineblank/MicrO. MicrO has been integrated into the OBO Foundry Library (http://www.obofoundry.org/ontology/micro.html), so that other ontologies can borrow and re-use classes. Term requests and user feedback can be made using MicrO's Issue Tracker in GitHub. We designed MicrO such that it can support the ongoing and future development of algorithms that can leverage the controlled vocabulary and logical inference power provided by the ontology. By connecting microbial classes with large numbers of chemical entities, material entities, biological processes, molecular functions, and qualities using a dense array of logical axioms, we

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

Top-Level Categories of Constitutively Organized Material Entities - Suggestions for a Formal Top-Level Ontology

PubMed Central

Vogt, Lars; Grobe, Peter; Quast, Björn; Bartolomaeus, Thomas

2011-01-01

Background Application oriented ontologies are important for reliably communicating and managing data in databases. Unfortunately, they often differ in the definitions they use and thus do not live up to their potential. This problem can be reduced when using a standardized and ontologically consistent template for the top-level categories from a top-level formal foundational ontology. This would support ontological consistency within application oriented ontologies and compatibility between them. The Basic Formal Ontology (BFO) is such a foundational ontology for the biomedical domain that has been developed following the single inheritance policy. It provides the top-level template within the Open Biological and Biomedical Ontologies Foundry. If it wants to live up to its expected role, its three top-level categories of material entity (i.e., ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive, i.e. every concrete material entity must instantiate exactly one of them. Methodology/Principal Findings By systematically evaluating all possible basic configurations of material building blocks we show that BFO's top-level categories of material entity are not exhaustive. We provide examples from biology and everyday life that demonstrate the necessity for two additional categories: ‘fiat object part aggregate’ and ‘object with fiat object part aggregate’. By distinguishing topological coherence, topological adherence, and metric proximity we furthermore provide a differentiation of clusters and groups as two distinct subcategories for each of the three categories of material entity aggregates, resulting in six additional subcategories of material entity. Conclusions/Significance We suggest extending BFO to incorporate two additional categories of material entity as well as two subcategories for each of the three categories of material entity aggregates. With these additions, BFO would exhaustively cover all top-level types of

Development of Health Information Search Engine Based on Metadata and Ontology

PubMed Central

Song, Tae-Min; Jin, Dal-Lae

2014-01-01

Objectives The aim of the study was to develop a metadata and ontology-based health information search engine ensuring semantic interoperability to collect and provide health information using different application programs. Methods Health information metadata ontology was developed using a distributed semantic Web content publishing model based on vocabularies used to index the contents generated by the information producers as well as those used to search the contents by the users. Vocabulary for health information ontology was mapped to the Systematized Nomenclature of Medicine Clinical Terms (SNOMED CT), and a list of about 1,500 terms was proposed. The metadata schema used in this study was developed by adding an element describing the target audience to the Dublin Core Metadata Element Set. Results A metadata schema and an ontology ensuring interoperability of health information available on the internet were developed. The metadata and ontology-based health information search engine developed in this study produced a better search result compared to existing search engines. Conclusions Health information search engine based on metadata and ontology will provide reliable health information to both information producer and information consumers. PMID:24872907

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

OntoCheck: verifying ontology naming conventions and metadata completeness in Protégé 4

PubMed Central

2012-01-01

Background Although policy providers have outlined minimal metadata guidelines and naming conventions, ontologies of today still display inter- and intra-ontology heterogeneities in class labelling schemes and metadata completeness. This fact is at least partially due to missing or inappropriate tools. Software support can ease this situation and contribute to overall ontology consistency and quality by helping to enforce such conventions. Objective We provide a plugin for the Protégé Ontology editor to allow for easy checks on compliance towards ontology naming conventions and metadata completeness, as well as curation in case of found violations. Implementation In a requirement analysis, derived from a prior standardization approach carried out within the OBO Foundry, we investigate the needed capabilities for software tools to check, curate and maintain class naming conventions. A Protégé tab plugin was implemented accordingly using the Protégé 4.1 libraries. The plugin was tested on six different ontologies. Based on these test results, the plugin could be refined, also by the integration of new functionalities. Results The new Protégé plugin, OntoCheck, allows for ontology tests to be carried out on OWL ontologies. In particular the OntoCheck plugin helps to clean up an ontology with regard to lexical heterogeneity, i.e. enforcing naming conventions and metadata completeness, meeting most of the requirements outlined for such a tool. Found test violations can be corrected to foster consistency in entity naming and meta-annotation within an artefact. Once specified, check constraints like name patterns can be stored and exchanged for later re-use. Here we describe a first version of the software, illustrate its capabilities and use within running ontology development efforts and briefly outline improvements resulting from its application. Further, we discuss OntoChecks capabilities in the context of related tools and highlight potential future

OntoCheck: verifying ontology naming conventions and metadata completeness in Protégé 4.

PubMed

Schober, Daniel; Tudose, Ilinca; Svatek, Vojtech; Boeker, Martin

2012-09-21

Although policy providers have outlined minimal metadata guidelines and naming conventions, ontologies of today still display inter- and intra-ontology heterogeneities in class labelling schemes and metadata completeness. This fact is at least partially due to missing or inappropriate tools. Software support can ease this situation and contribute to overall ontology consistency and quality by helping to enforce such conventions. We provide a plugin for the Protégé Ontology editor to allow for easy checks on compliance towards ontology naming conventions and metadata completeness, as well as curation in case of found violations. In a requirement analysis, derived from a prior standardization approach carried out within the OBO Foundry, we investigate the needed capabilities for software tools to check, curate and maintain class naming conventions. A Protégé tab plugin was implemented accordingly using the Protégé 4.1 libraries. The plugin was tested on six different ontologies. Based on these test results, the plugin could be refined, also by the integration of new functionalities. The new Protégé plugin, OntoCheck, allows for ontology tests to be carried out on OWL ontologies. In particular the OntoCheck plugin helps to clean up an ontology with regard to lexical heterogeneity, i.e. enforcing naming conventions and metadata completeness, meeting most of the requirements outlined for such a tool. Found test violations can be corrected to foster consistency in entity naming and meta-annotation within an artefact. Once specified, check constraints like name patterns can be stored and exchanged for later re-use. Here we describe a first version of the software, illustrate its capabilities and use within running ontology development efforts and briefly outline improvements resulting from its application. Further, we discuss OntoChecks capabilities in the context of related tools and highlight potential future expansions. The OntoCheck plugin facilitates

Development and Evaluation of an Obesity Ontology for Social Big Data Analysis

PubMed Central

Kim, Ae Ran; Song, Tae-Min

2017-01-01

Objectives The aim of this study was to develop and evaluate an obesity ontology as a framework for collecting and analyzing unstructured obesity-related social media posts. Methods The obesity ontology was developed according to the ‘Ontology Development 101’. The coverage rate of the developed ontology was examined by mapping concepts and terms of the ontology with concepts and terms extracted from obesity-related Twitter postings. The structure and representative ability of the ontology was evaluated by nurse experts. We applied the ontology to the density analysis of keywords related to obesity types and management strategies and to the sentiment analysis of obesity and diet using social big data. Results The developed obesity ontology was represented by 8 superclasses and 124 subordinate classes. The superclasses comprised ‘risk factors,’ ‘types,’ ‘symptoms,’ ‘complications,’ ‘assessment,’ ‘diagnosis,’ ‘management strategies,’ and ‘settings.’ The coverage rate of the ontology was 100% for the concepts and 87.8% for the terms. The evaluation scores for representative ability were higher than 4.0 out of 5.0 for all of the evaluation items. The density analysis of keywords revealed that the top-two posted types of obesity were abdomen and thigh, and the top-three posted management strategies were diet, exercise, and dietary supplements or drug therapy. Positive expressions of obesity-related postings has increased annually in the sentiment analysis. Conclusions It was found that the developed obesity ontology was useful to identify the most frequently used terms on obesity and opinions and emotions toward obesity posted by the geneal population on social media. PMID:28875050

Environmental analysis of waste foundry sand via life cycle assessment.

PubMed

Mitterpach, Jozef; Hroncová, Emília; Ladomerský, Juraj; Balco, Karol

2017-01-01

The aim of this manuscript is to provide an environmental assessment of the creation and use of waste foundry sand (WFS) via an LCA in a foundry for grey cast iron. A life cycle impact assessment was carried out using SimaPro 8. This environmental analysis assessed the impact of creating waste foundry sand (WFS) in a foundry, Hronec (Slovakia, Central Europe). According to BREF, this foundry is classified as an iron foundry with a production capacity greater than 20 t/day with processes typical for grey cast iron foundries. Molten metal is poured into single-use sand moulds. We identified those factors influencing the creation and use of WFS which significantly affect the quality of the environment. The use of WFS from the production of cores in regenerated moulding mixtures with installed circuits brings marked minimisation of material and energy inputs in the processes of creating WFS and it positively influences the consumption of resources and the quality of the ecosystem. Space for lessening the impact of WFS processes upon the consumption of resources and ecosystem quality is mainly found in recycling WFS in the building sector. In the next step, it is necessary to thoroughly verify the eco-toxicological properties of not only the created WFS and other foundry waste, but mainly the building products for which this waste is used. In terms of transportation, it is important that waste is recycled at local level. The processes of creating WFS have a marked influence upon all the selected waste categories (consumption of resources, ecosystem quality, human health). By minimising material inputs into processes and the effective adjustment of production technology, a foundry can significantly lessen the impacts of processes for creating WFS upon the environment.

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.

Prevention of occupational injuries: Evidence for effective good practices in foundries.

PubMed

Porru, Stefano; Calza, Stefano; Arici, Cecilia

2017-02-01

Occupational injuries are a relevant research and practical issue. However, intervention studies evaluating the effectiveness of workplace injury prevention programs are seldom performed. The effectiveness of a multifaceted intervention aimed at reducing occupational injury rates (incidence/employment-based=IR, frequency/hours-based=FR, severity=SR) was evaluated between 2008 and 2013 in 29 Italian foundries (22 ferrous; 7 non-ferrous; 3,460 male blue collar workers/year) of varying sizes. Each foundry established an internal multidisciplinary prevention team for risk assessment, monitoring and prevention of occupational injuries, involving employers, occupational physicians, safety personnel, workers' representatives, supervisors. Targets of intervention were workers, equipment, organization, workplace, job tasks. An interrupted time series (ITS) design was applied. 4,604 occupational injuries and 83,156 lost workdays were registered between 2003 and 2013. Statistical analysis showed, after intervention, a reduction of all injury rates (-26% IR, -15% FR, -18% SR) in ferrous foundries and of SR (-4%) in non-ferrous foundries. A significant (p=0.021) 'step-effect' was shown for IR in ferrous foundries, independent of secular trends (p<0.001). Sector-specific benchmarks for all injury rates were developed separately for ferrous and non-ferrous foundries. Strengths of the study were: ITS design, according to standardized quality criteria (i.e., at least three data points before and three data points after intervention; clearly defined intervention point); pragmatic approach, with good external validity; promotion of effective good practices. Main limitations were the non-randomized nature and a medium length post-intervention period. In conclusion, a multifaceted, pragmatic and accountable intervention is effective in reducing the burden of occupational injuries in small-, medium- and large-sized foundries. Practical Applications: The study poses the basis for

Ontological Issues and the Possible Development of Cultural Psychology.

PubMed

Pérez-Campos, Gilberto

2017-12-01

Ontological issues have a bad reputation within mainstream psychology. This paper, however, is an attempt to argue that ontological reflection may play an important role in the development of cultural psychology. A cross-reading of two recent papers on the subject (Mammen & Mironenko, Integrative Psychological and Behavioral Science, 49(4), 681-713, 2015; Simão Integrative Psychological and Behavioral Science, 50, 568-585, 2016), aimed at characterizing their respective approaches to ontological issues, sets the stage for a presentation of Cornelius Castoriadis' ontological reflections. On this basis, a dialogue is initiated with E.E. Boesch's Symbolic Activity Theory that could contribute to a more refined understanding of human psychological functioning in its full complexity.

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.

Accommodating Ontologies to Biological Reality—Top-Level Categories of Cumulative-Constitutively Organized Material Entities

PubMed Central

Vogt, Lars; Grobe, Peter; Quast, Björn; Bartolomaeus, Thomas

2012-01-01

Background The Basic Formal Ontology (BFO) is a top-level formal foundational ontology for the biomedical domain. It has been developed with the purpose to serve as an ontologically consistent template for top-level categories of application oriented and domain reference ontologies within the Open Biological and Biomedical Ontologies Foundry (OBO). BFO is important for enabling OBO ontologies to facilitate in reliably communicating and managing data and metadata within and across biomedical databases. Following its intended single inheritance policy, BFO's three top-level categories of material entity (i.e. ‘object’, ‘fiat object part’, ‘object aggregate’) must be exhaustive and mutually disjoint. We have shown elsewhere that for accommodating all types of constitutively organized material entities, BFO must be extended by additional categories of material entity. Methodology/Principal Findings Unfortunately, most biomedical material entities are cumulative-constitutively organized. We show that even the extended BFO does not exhaustively cover cumulative-constitutively organized material entities. We provide examples from biology and everyday life that demonstrate the necessity for ‘portion of matter’ as another material building block. This implies the necessity for further extending BFO by ‘portion of matter’ as well as three additional categories that possess portions of matter as aggregate components. These extensions are necessary if the basic assumption that all parts that share the same granularity level exhaustively sum to the whole should also apply to cumulative-constitutively organized material entities. By suggesting a notion of granular representation we provide a way to maintain the single inheritance principle when dealing with cumulative-constitutively organized material entities. Conclusions/Significance We suggest to extend BFO to incorporate additional categories of material entity and to rearrange its top-level material

OMIT: dynamic, semi-automated ontology development for the microRNA domain.

PubMed

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.

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

77 FR 32998 - Foundry Coke From China

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-04

... China Determination On the basis of the record \\1\\ developed in the subject five-year review, the United... China would be likely to lead to continuation or recurrence of material injury to an industry in the... Publication 4326 (May 2012), entitled Foundry Coke from China: Investigation No. 731-TA-891 (Second Review...

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

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.

Development and Evaluation of a Low Fertility Ontology for Analyzing Social Data in Korea.

PubMed

Lee, Ji-Hyun; Park, Hyeoun-Ae; Song, Tae-Min

2016-01-01

The purpose of this study is to develop a low fertility ontology for collecting and analyzing social data. A low fertility ontology was developed according to Ontology Development 101 and formally represented using Protégé. The content coverage of the ontology was evaluated using 1,387 narratives posted by the public and 63 narratives posted by public servants. Six super-classes of the ontology were developed based on Bronfenbrenner's ecological system theory with an individual in the center and environmental systems impacting their as surroundings. In total, 568 unique concepts were extracted from the narratives. Out of these concepts, 424(74.6%) concepts were lexically or semantically mapped, 67(11.8%) were either broadly or narrowly mapped to the ontology concepts. Remaining 77(13.6%) concepts were not mapped to any of the ontology concepts. This ontology can be used as a framework to understand low fertility problems using social data in Korea.

The development of non-coding RNA ontology.

PubMed

Huang, Jingshan; Eilbeck, Karen; Smith, Barry; Blake, Judith A; Dou, Dejing; Huang, Weili; Natale, Darren A; Ruttenberg, Alan; Huan, Jun; Zimmermann, Michael T; Jiang, Guoqian; Lin, Yu; Wu, Bin; Strachan, Harrison J; de Silva, Nisansa; Kasukurthi, Mohan Vamsi; Jha, Vikash Kumar; He, Yongqun; Zhang, Shaojie; Wang, Xiaowei; Liu, Zixing; Borchert, Glen M; Tan, Ming

2016-01-01

Identification of non-coding RNAs (ncRNAs) has been significantly improved over the past decade. On the other hand, semantic annotation of ncRNA data is facing critical challenges due to the lack of a comprehensive ontology to serve as common data elements and data exchange standards in the field. We developed the Non-Coding RNA Ontology (NCRO) to handle this situation. By providing a formally defined ncRNA controlled vocabulary, the NCRO aims to fill a specific and highly needed niche in semantic annotation of large amounts of ncRNA biological and clinical data.

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.

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

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

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

Developing VISO: Vaccine Information Statement Ontology for patient education.

PubMed

Amith, Muhammad; Gong, Yang; Cunningham, Rachel; Boom, Julie; Tao, Cui

2015-01-01

To construct a comprehensive vaccine information ontology that can support personal health information applications using patient-consumer lexicon, and lead to outcomes that can improve patient education. The authors composed the Vaccine Information Statement Ontology (VISO) using the web ontology language (OWL). We started with 6 Vaccine Information Statement (VIS) documents collected from the Centers for Disease Control and Prevention (CDC) website. Important and relevant selections from the documents were recorded, and knowledge triples were derived. Based on the collection of knowledge triples, the meta-level formalization of the vaccine information domain was developed. Relevant instances and their relationships were created to represent vaccine domain knowledge. The initial iteration of the VISO was realized, based on the 6 Vaccine Information Statements and coded into OWL2 with Protégé. The ontology consisted of 132 concepts (classes and subclasses) with 33 types of relationships between the concepts. The total number of instances from classes totaled at 460, along with 429 knowledge triples in total. Semiotic-based metric scoring was applied to evaluate quality of the ontology.

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

33. FOUNDRY WALL SHOWING WOOD PATTERNS OF STEAMER GRATES, WHEELS, ...

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

33. FOUNDRY WALL SHOWING WOOD PATTERNS OF STEAMER GRATES, WHEELS, AND CRANE TRACKS-LOOKING NORTH. - W. A. Young & Sons Foundry & Machine Shop, On Water Street along Monongahela River, Rices Landing, Greene County, PA

Versioning System for Distributed Ontology Development

DTIC Science & Technology

2016-02-02

Semantic   Web   community. For example, the distributed and isolated development requirement may apply to non‐cyber  range communities of public ontology... semantic   web .” However, we observe that the  maintenance of an ontology and its reuse is not a high priority for the majority of the publicly available... Semantic )  Web . AAAI Spring Symposium: Symbiotic Relationships between  Semantic   Web  and  Knowledge Engineering. 2008.  [LHK09] Matthias Loskyll

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.

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

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

Ontology to relational database transformation for web application development and maintenance

NASA Astrophysics Data System (ADS)

Mahmudi, Kamal; Inggriani Liem, M. M.; Akbar, Saiful

2018-03-01

Ontology is used as knowledge representation while database is used as facts recorder in a KMS (Knowledge Management System). In most applications, data are managed in a database system and updated through the application and then they are transformed to knowledge as needed. Once a domain conceptor defines the knowledge in the ontology, application and database can be generated from the ontology. Most existing frameworks generate application from its database. In this research, ontology is used for generating the application. As the data are updated through the application, a mechanism is designed to trigger an update to the ontology so that the application can be rebuilt based on the newest ontology. By this approach, a knowledge engineer has a full flexibility to renew the application based on the latest ontology without dependency to a software developer. In many cases, the concept needs to be updated when the data changed. The framework is built and tested in a spring java environment. A case study was conducted to proof the concepts.

The Ontology of Biological and Clinical Statistics (OBCS) for standardized and reproducible statistical analysis.

PubMed

Zheng, Jie; Harris, Marcelline R; Masci, Anna Maria; Lin, Yu; Hero, Alfred; Smith, Barry; He, Yongqun

2016-09-14

Statistics play a critical role in biological and clinical research. However, most reports of scientific results in the published literature make it difficult for the reader to reproduce the statistical analyses performed in achieving those results because they provide inadequate documentation of the statistical tests and algorithms applied. The Ontology of Biological and Clinical Statistics (OBCS) is put forward here as a step towards solving this problem. The terms in OBCS including 'data collection', 'data transformation in statistics', 'data visualization', 'statistical data analysis', and 'drawing a conclusion based on data', cover the major types of statistical processes used in basic biological research and clinical outcome studies. OBCS is aligned with the Basic Formal Ontology (BFO) and extends the Ontology of Biomedical Investigations (OBI), an OBO (Open Biological and Biomedical Ontologies) Foundry ontology supported by over 20 research communities. Currently, OBCS comprehends 878 terms, representing 20 BFO classes, 403 OBI classes, 229 OBCS specific classes, and 122 classes imported from ten other OBO ontologies. We discuss two examples illustrating how the ontology is being applied. In the first (biological) use case, we describe how OBCS was applied to represent the high throughput microarray data analysis of immunological transcriptional profiles in human subjects vaccinated with an influenza vaccine. In the second (clinical outcomes) use case, we applied OBCS to represent the processing of electronic health care data to determine the associations between hospital staffing levels and patient mortality. Our case studies were designed to show how OBCS can be used for the consistent representation of statistical analysis pipelines under two different research paradigms. Other ongoing projects using OBCS for statistical data processing are also discussed. The OBCS source code and documentation are available at: https://github.com/obcs/obcs . The Ontology

Developing a Domain Ontology: the Case of Water Cycle and Hydrology

NASA Astrophysics Data System (ADS)

Gupta, H.; Pozzi, W.; Piasecki, M.; Imam, B.; Houser, P.; Raskin, R.; Ramachandran, R.; Martinez Baquero, G.

2008-12-01

A semantic web ontology enables semantic data integration and semantic smart searching. Several organizations have attempted to implement smart registration and integration or searching using ontologies. These are the NOESIS (NSF project: LEAD) and HydroSeek (NSF project: CUAHS HIS) data discovery engines and the NSF project GEON. All three applications use ontologies to discover data from multiple sources and projects. The NASA WaterNet project was established to identify creative, innovative ways to bridge NASA research results to real world applications, linking decision support needs to available data, observations, and modeling capability. WaterNet (NASA project) utilized the smart query tool Noesis as a testbed to test whether different ontologies (and different catalog searches) could be combined to match resources with user needs. NOESIS contains the upper level SWEET ontology that accepts plug in domain ontologies to refine user search queries, reducing the burden of multiple keyword searches. Another smart search interface was that developed for CUAHSI, HydroSeek, that uses a multi-layered concept search ontology, tagging variables names from any number of data sources to specific leaf and higher level concepts on which the search is executed. This approach has proven to be quite successful in mitigating semantic heterogeneity as the user does not need to know the semantic specifics of each data source system but just uses a set of common keywords to discover the data for a specific temporal and geospatial domain. This presentation will show tests with Noesis and Hydroseek lead to the conclusion that the construction of a complex, and highly heterogeneous water cycle ontology requires multiple ontology modules. To illustrate the complexity and heterogeneity of a water cycle ontology, Hydroseek successfully utilizes WaterOneFlow to integrate data across multiple different data collections, such as USGS NWIS. However,different methodologies are employed by

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.

Excess Foundry Sand Characterization and Experimental Investigation in Controlled Low-Strength Material and Hot-Mixing Asphalt

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

Tikalsky, Paul J.; Bahia, Hussain U.; Deng, An

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. Notmore » 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.« less

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

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

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

OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.

PubMed

Beauheim, Catherine C; Wymore, Farrell; Nitzberg, Michael; Zachariah, Zachariah K; Jin, Heng; Skene, J H Pate; Ball, Catherine A; Sherlock, Gavin

2007-09-13

Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML) and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD), which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO) website 1. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1) install Apache Tomcat 2 on one's web server, (2) download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3) create an html (HyperText Markup Language) file that refers to the OntologyWidget using a simple, well-defined format. We have developed OntologyWidget, an easy-to-use ontology search and display

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.

Excess Foundry Sand Characterization and Experimental Investigation in Controlled Low-Strength Material and Hot-Mixing Asphalt

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

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 andmore » 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.« less

Foundry Technologies Focused on Environmental and Ecological Applications

NASA Astrophysics Data System (ADS)

Roizin, Ya.; Lisiansky, M.; Pikhay, E.

Solutions allowing fabrication of remote control systems with integrated sensors (motes) were introduced as a part of CMOS foundry production platform and verified on silicon. The integrated features include sensors employing principles previously verified in the development of ultra-low power consuming non-volatile memories (C-Flash, MRAM) and components allowing low-power energy harvesting (low voltage rectifiers, high -voltage solar cells). The developed systems are discussed with emphasis on their environmental and security applications.

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

OntologyWidget – a reusable, embeddable widget for easily locating ontology terms

PubMed Central

Beauheim, Catherine C; Wymore, Farrell; Nitzberg, Michael; Zachariah, Zachariah K; Jin, Heng; Skene, JH Pate; Ball, Catherine A; Sherlock, Gavin

2007-01-01

Background Biomedical ontologies are being widely used to annotate biological data in a computer-accessible, consistent and well-defined manner. However, due to their size and complexity, annotating data with appropriate terms from an ontology is often challenging for experts and non-experts alike, because there exist few tools that allow one to quickly find relevant ontology terms to easily populate a web form. Results We have produced a tool, OntologyWidget, which allows users to rapidly search for and browse ontology terms. OntologyWidget can easily be embedded in other web-based applications. OntologyWidget is written using AJAX (Asynchronous JavaScript and XML) and has two related elements. The first is a dynamic auto-complete ontology search feature. As a user enters characters into the search box, the appropriate ontology is queried remotely for terms that match the typed-in text, and the query results populate a drop-down list with all potential matches. Upon selection of a term from the list, the user can locate this term within a generic and dynamic ontology browser, which comprises the second element of the tool. The ontology browser shows the paths from a selected term to the root as well as parent/child tree hierarchies. We have implemented web services at the Stanford Microarray Database (SMD), which provide the OntologyWidget with access to over 40 ontologies from the Open Biological Ontology (OBO) website [1]. Each ontology is updated weekly. Adopters of the OntologyWidget can either use SMD's web services, or elect to rely on their own. Deploying the OntologyWidget can be accomplished in three simple steps: (1) install Apache Tomcat [2] on one's web server, (2) download and install the OntologyWidget servlet stub that provides access to the SMD ontology web services, and (3) create an html (HyperText Markup Language) file that refers to the OntologyWidget using a simple, well-defined format. Conclusion We have developed OntologyWidget, an easy

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

GPCR ontology: development and application of a G protein-coupled receptor pharmacology knowledge framework.

PubMed

Przydzial, Magdalena J; Bhhatarai, Barun; Koleti, Amar; Vempati, Uma; Schürer, Stephan C

2013-12-15

Novel tools need to be developed to help scientists analyze large amounts of available screening data with the goal to identify entry points for the development of novel chemical probes and drugs. As the largest class of drug targets, G protein-coupled receptors (GPCRs) remain of particular interest and are pursued by numerous academic and industrial research projects. We report the first GPCR ontology to facilitate integration and aggregation of GPCR-targeting drugs and demonstrate its application to classify and analyze a large subset of the PubChem database. The GPCR ontology, based on previously reported BioAssay Ontology, depicts available pharmacological, biochemical and physiological profiles of GPCRs and their ligands. The novelty of the GPCR ontology lies in the use of diverse experimental datasets linked by a model to formally define these concepts. Using a reasoning system, GPCR ontology offers potential for knowledge-based classification of individuals (such as small molecules) as a function of the data. The GPCR ontology is available at http://www.bioassayontology.org/bao_gpcr and the National Center for Biomedical Ontologies Web site.

[Re-analysis of occupational hazards in foundry].

PubMed

Zhang, Min; Qi, Cheng; Chen, Wei-Hong; Lu, Yang; Du, Xie-Yi; Li, Wen-Jie; Meng, Chuan-San

2010-04-01

To analyze systematically the characteristics of occupational hazards in the foundry, and provide precise data for epidemiology studies and control of occupational hazards in the foundry. Data of airborne dust, chemical occupational hazards and physical occupational agents in environment in the foundry from 1978 to 2008 were dynamically collected. Mean concentration and intensity (geometric mean) of occupational hazards were calculated by job in different years. Main occupational hazards in the foundry were silica, metal fume, noise and heat stress. Silica existed in all of main jobs. The mean concentration of silica before 1986 was an extremely high level of 8.6 mg/m(3), and then remarkably dropped after 1986, with the level of 2.4 mg/m(3) from 1986 to 1989, 2.7 mg/m(3) from 1990 to 2002 and 2.7 mg/m(3) from 2003 to 2008. The trend of silica concentrations by job was consistent with that in general. Silica concentrations among jobs were significantly different, with highest level in melting (4.4 mg/m(3)), followed by cast shakeout and finishing (3.4 mg/m(3)), pouring (3.4 mg/m(3)), sand preparation (2.4 mg/m(3)), moulding (2.1 mg/m(3)) and core-making (1.7 mg/m(3)). Concentration of respirable dust in pouring was highest (2.76 mg/m(3)), followed by cast shakeout and finishing (1.14 mg/m(3)). Mean concentration of asbestos dust in melting was a relative high level of 2.0 mg/m(3). In core-making and sand preparation, there existed emission production of adhesive, with mean concentrations as followed, ammonia (5.84 mg/m(3)), formaldehyde (0.60 mg/m(3)), phenol (1.73 mg/m(3)) and phenol formaldehyde resin (1.3 mg/m(3)) also existed. Benzene and its homologues existed in cast shakeout and finishing, and the level of benzene, toluene, xylene was 0.2 mg/m(3), 0.1 mg/m(3) and 1.3 mg/m(3), respectively. In pouring and melting, there existed chemical occupational hazards, including benzo(a) pyrene, metal fume (lead, cadmium, manganese, nickel, chromium) and gas

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.

Ontorat: automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns.

PubMed

Xiang, Zuoshuang; Zheng, Jie; Lin, Yu; He, Yongqun

2015-01-01

It is time-consuming to build an ontology with many terms and axioms. Thus it is desired to automate the process of ontology development. Ontology Design Patterns (ODPs) provide a reusable solution to solve a recurrent modeling problem in the context of ontology engineering. Because ontology terms often follow specific ODPs, the Ontology for Biomedical Investigations (OBI) developers proposed a Quick Term Templates (QTTs) process targeted at generating new ontology classes following the same pattern, using term templates in a spreadsheet format. Inspired by the ODPs and QTTs, the Ontorat web application is developed to automatically generate new ontology terms, annotations of terms, and logical axioms based on a specific ODP(s). The inputs of an Ontorat execution include axiom expression settings, an input data file, ID generation settings, and a target ontology (optional). The axiom expression settings can be saved as a predesigned Ontorat setting format text file for reuse. The input data file is generated based on a template file created by a specific ODP (text or Excel format). Ontorat is an efficient tool for ontology expansion. Different use cases are described. For example, Ontorat was applied to automatically generate over 1,000 Japan RIKEN cell line cell terms with both logical axioms and rich annotation axioms in the Cell Line Ontology (CLO). Approximately 800 licensed animal vaccines were represented and annotated in the Vaccine Ontology (VO) by Ontorat. The OBI team used Ontorat to add assay and device terms required by ENCODE project. Ontorat was also used to add missing annotations to all existing Biobank specific terms in the Biobank Ontology. A collection of ODPs and templates with examples are provided on the Ontorat website and can be reused to facilitate ontology development. With ever increasing ontology development and applications, Ontorat provides a timely platform for generating and annotating a large number of ontology terms by following

Ontology or formal ontology

NASA Astrophysics Data System (ADS)

Žáček, Martin

2017-07-01

Ontology or formal ontology? Which word is correct? The aim of this article is to introduce correct terms and explain their basis. Ontology describes a particular area of interest (domain) in a formal way - defines the classes of objects that are in that area, and relationships that may exist between them. Meaning of ontology consists mainly in facilitating communication between people, improve collaboration of software systems and in the improvement of systems engineering. Ontology in all these areas offer the possibility of unification of view, maintaining consistency and unambiguity.

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

Zinc Chloride Influence on The Resins Furan Polymerization to Foundry Moulds

NASA Astrophysics Data System (ADS)

de Miranda, Leila Figueiredo; Vale, Marcus; Júnior, Antonio Hortêncio Munhoz; Masson, Terezinha Jocelen; de Andrade e Silva, Leonardo Gondin

The resins used in foundry molds developed for the automotive market has led to major changes in the manufacturing method of foundry molds. The polymerization of these resins and a subsequent curing are used to connect to the foundry sand in a rigid structure capable of receiving and holding liquid metal. It is essential to know the process of polymerization of these resins and their impact on the final properties of the obtained molds, especially in the mechanical characteristics. In this work it was studied the influence of the addition of zinc chloride (in solution) in the sand-furan resin mixture, with the aim of reducing the relation between the extraction time intervals and time bench life. The results showed that addition of percentages of the order of 5.0wt% to 7.5wt% zinc chloride solution reduces this ratio between 10% and 17%; this means that the casting model may be extracted from the sand mass in a smaller time interval increasing the productivity of manufacturing molds. It was also observed that there was also an increase of 9% to 18% in bench life intervals.

77 FR 20788 - Foundry Coke Products From the People's Republic of China: Final Results of Expedited Second...

Federal Register 2010, 2011, 2012, 2013, 2014

2012-04-06

... DEPARTMENT OF COMMERCE International Trade Administration [A-570-862] Foundry Coke Products From... (``sunset'') review of the antidumping duty order on foundry coke products (``foundry coke'') from the... Department finds that revocation of the antidumping duty order on foundry coke from the PRC would be likely...

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

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

PubMed Central

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

2010-01-01

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. PMID:21347039

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

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

PubMed

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

2015-05-15

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. © 2015. Published by The Company of Biologists Ltd.

Development of FuGO: An Ontology for Functional Genomics Investigations

PubMed Central

Whetzel, Patricia L.; Brinkman, Ryan R.; Causton, Helen C.; Fan, Liju; Field, Dawn; Fostel, Jennifer; Fragoso, Gilberto; Gray, Tanya; Heiskanen, Mervi; Hernandez-Boussard, Tina; Morrison, Norman; Parkinson, Helen; Rocca-Serra, Philippe; Sansone, Susanna-Assunta; Schober, Daniel; Smith, Barry; Stevens, Robert; Stoeckert, Christian J.; Taylor, Chris; White, Joe; Wood, Andrew

2009-01-01

The development of the Functional Genomics Investigation Ontology (FuGO) is a collaborative, international effort that will provide a resource for annotating functional genomics investigations, including the study design, protocols and instrumentation used, the data generated and the types of analysis performed on the data. FuGO will contain both terms that are universal to all functional genomics investigations and those that are domain specific. In this way, the ontology will serve as the “semantic glue” to provide a common understanding of data from across these disparate data sources. In addition, FuGO will reference out to existing mature ontologies to avoid the need to duplicate these resources, and will do so in such a way as to enable their ease of use in annotation. This project is in the early stages of development; the paper will describe efforts to initiate the project, the scope and organization of the project, the work accomplished to date, and the challenges encountered, as well as future plans. PMID:16901226

Simple Ontology Format (SOFT)

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

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.

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

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. Copyright © 2016 Elsevier Inc. All rights reserved.

NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation.

PubMed

Martínez-Romero, Marcos; Jonquet, Clement; O'Connor, Martin J; Graybeal, John; Pazos, Alejandro; Musen, Mark A

2017-06-07

Ontologies and controlled terminologies have become increasingly important in biomedical research. Researchers use ontologies to annotate their data with ontology terms, enabling better data integration and interoperability across disparate datasets. However, the number, variety and complexity of current biomedical ontologies make it cumbersome for researchers to determine which ones to reuse for their specific needs. To overcome this problem, in 2010 the National Center for Biomedical Ontology (NCBO) released the Ontology Recommender, which is a service that receives a biomedical text corpus or a list of keywords and suggests ontologies appropriate for referencing the indicated terms. We developed a new version of the NCBO Ontology Recommender. Called Ontology Recommender 2.0, it uses a novel recommendation approach that evaluates the relevance of an ontology to biomedical text data according to four different criteria: (1) the extent to which the ontology covers the input data; (2) the acceptance of the ontology in the biomedical community; (3) the level of detail of the ontology classes that cover the input data; and (4) the specialization of the ontology to the domain of the input data. Our evaluation shows that the enhanced recommender provides higher quality suggestions than the original approach, providing better coverage of the input data, more detailed information about their concepts, increased specialization for the domain of the input data, and greater acceptance and use in the community. In addition, it provides users with more explanatory information, along with suggestions of not only individual ontologies but also groups of ontologies to use together. It also can be customized to fit the needs of different ontology recommendation scenarios. Ontology Recommender 2.0 suggests relevant ontologies for annotating biomedical text data. It combines the strengths of its predecessor with a range of adjustments and new features that improve its reliability

[Comparison of color reappearance between metal-ceram restoration and foundry-ceram restoration using crystaleye spectrophotometer].

PubMed

Shi, Tao; Zhang, Ning; Kong, Fan-wen; Zhan, De-song

2010-10-01

To study the color reappearance effect of metal-ceram restoration and foundry-ceram restoration using Crystaleye spectrophotometer. 58 metal-ceram restorations and 58 foundry-ceram restorations according to the result of the Crystaleye spectrophotometer were made respectively. The deltaE between restorations and natural teeth as referenced were analyzed. And satisfaction of dentists and patients were evaluated. The deltaE between metal-ceram restorations and natural teeth was 7.13 +/- 0.74. The deltaE between foundry-ceram restorations and teeth was 1.47 +/- 0.84. There were statistical differences between the deltaE (P < 0.01). The satisnatural faction of dentists and patients to the foundry-ceram restorations were higher than to the metal-ceram restorations (P < 0.05). Crystaleye spectrophotometer can provide accurate reference for foundry-ceram restoration, but for metal-ceram restoration it is not accurate.

The use of concept maps during knowledge elicitation in ontology development processes – the nutrigenomics use case

PubMed Central

Castro, Alexander Garcia; Rocca-Serra, Philippe; Stevens, Robert; Taylor, Chris; Nashar, Karim; Ragan, Mark A; Sansone, Susanna-Assunta

2006-01-01

Background Incorporation of ontologies into annotations has enabled 'semantic integration' of complex data, making explicit the knowledge within a certain field. One of the major bottlenecks in developing bio-ontologies is the lack of a unified methodology. Different methodologies have been proposed for different scenarios, but there is no agreed-upon standard methodology for building ontologies. The involvement of geographically distributed domain experts, the need for domain experts to lead the design process, the application of the ontologies and the life cycles of bio-ontologies are amongst the features not considered by previously proposed methodologies. Results Here, we present a methodology for developing ontologies within the biological domain. We describe our scenario, competency questions, results and milestones for each methodological stage. We introduce the use of concept maps during knowledge acquisition phases as a feasible transition between domain expert and knowledge engineer. Conclusion The contributions of this paper are the thorough description of the steps we suggest when building an ontology, example use of concept maps, consideration of applicability to the development of lower-level ontologies and application to decentralised environments. We have found that within our scenario conceptual maps played an important role in the development process. PMID:16725019

Molecular Foundry Workshop draws overflow crowd to BerkeleyLab

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

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).

Application of the Financial Industry Business Ontology (FIBO) for development of a financial organization ontology

NASA Astrophysics Data System (ADS)

Petrova, G. G.; Tuzovsky, A. F.; Aksenova, N. V.

2017-01-01

The article considers an approach to a formalized description and meaning harmonization for financial terms and means of semantic modeling. Ontologies for the semantic models are described with the help of special languages developed for the Semantic Web. Results of FIBO application to solution of different tasks in the Russian financial sector are given.

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.

Prevalence of job strain among Indian foundry shop floor workers.

PubMed

Mohan, G Madhan; Elangovan, S; Prasad, P S S; Krishna, P Rama; Mokkapati, Anil Kumar

2008-01-01

Global competition in manufacturing sector demand higher productivity levels. In this context, workers in this sector are set with high output targets, leading to job strain. In addition to the strain, hazardous conditions also prevail in some of the manufacturing processes like foundry activities. This paper attempts to appraise the prevalence of job strain among foundry shop floor workers in India with the help of Demands-Control model [8]. In this study, data was collected through a survey using 49-item Job Content Questionnaire (JCQ) [9], a widely used and well-validated test for job strain. Then the data was subjected to statistical analysis after ascertaining the reliability. This survey has revealed that 25% of workers in foundry were experiencing high job strain. Hazardous working conditions, limited decision making authority, etc. appear to be the main contributing factors for the higher levels of strain.

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.

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

PubMed Central

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

Cognitive Foundry v. 3.0 (OSS)

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

Basilico, Justin; Dixon, Kevin; McClain, Jonathan

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 Frameworkmore » components from domain-relevant data.« less

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.

77 FR 34012 - Foundry Coke Products From the People's Republic of China: Continuation of Antidumping Duty Order

Federal Register 2010, 2011, 2012, 2013, 2014

2012-06-08

... DEPARTMENT OF COMMERCE International Trade Administration [A-570-862] Foundry Coke Products From... Commission (``ITC'') that revocation of the antidumping duty order on foundry coke products from the People's... order on foundry coke products from the PRC, pursuant to section 751(c) of the Tariff Act of 1930, as...

An Ontology of Therapies

NASA Astrophysics Data System (ADS)

Eccher, Claudio; Ferro, Antonella; Pisanelli, Domenico M.

Ontologies are the essential glue to build interoperable systems and the talk of the day in the medical community. In this paper we present the ontology of medical therapies developed in the course of the Oncocure project, aimed at building a guideline based decision support integrated with a legacy Electronic Patient Record (EPR). The therapy ontology is based upon the DOLCE top level ontology. It is our opinion that our ontology, besides constituting a model capturing the precise meaning of therapy-related concepts, can serve for several practical purposes: interfacing automatic support systems with a legacy EPR, allowing the automatic data analysis, and controlling possible medical errors made during EPR data input.

A two-staged approach to developing and evaluating an ontology for delivering personalized education to diabetic patients.

PubMed

Quinn, Susan; Bond, Raymond; Nugent, Chris

2018-09-01

Ontologies are often used in biomedical and health domains to provide a concise and consistent means of attributing meaning to medical terminology. While they are novices in terms of ontology engineering, the evaluation of an ontology by domain specialists provides an opportunity to enhance its objectivity, accuracy, and coverage of the domain itself. This paper provides an evaluation of the viability of using ontology engineering novices to evaluate and enrich an ontology that can be used for personalized diabetic patient education. We describe a methodology for engaging healthcare and information technology specialists with a range of ontology engineering tasks. We used 87.8% of the data collected to validate the accuracy of our ontological model. The contributions also enabled a 16% increase in the class size and an 18% increase in object properties. Furthermore, we propose that ontology engineering novices can make valuable contributions to ontology development. Application-specific evaluation of the ontology using a semantic-web-based architecture is also discussed.

Acme Foundry, Inc. - Clean Water Act Public Notice

EPA Pesticide Factsheets

The EPA is providing notice of a proposed Administrative Penalty Assessment against Acme Foundry, Inc., for alleged violations at its facility located at 1502 South Spruce Street, Coffeyville, Kansas 67337

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.

The ACGT Master Ontology and its applications – Towards an ontology-driven cancer research and management system

PubMed Central

Brochhausen, Mathias; Spear, Andrew D.; Cocos, Cristian; Weiler, Gabriele; Martín, Luis; Anguita, Alberto; Stenzhorn, Holger; Daskalaki, Evangelia; Schera, Fatima; Schwarz, Ulf; Sfakianakis, Stelios; Kiefer, Stephan; Dörr, Martin; Graf, Norbert; Tsiknakis, Manolis

2017-01-01

Objective This paper introduces the objectives, methods and results of ontology development in the EU co-funded project Advancing Clinico-genomic Trials on Cancer – Open Grid Services for Improving Medical Knowledge Discovery (ACGT). While the available data in the life sciences has recently grown both in amount and quality, the full exploitation of it is being hindered by the use of different underlying technologies, coding systems, category schemes and reporting methods on the part of different research groups. The goal of the ACGT project is to contribute to the resolution of these problems by developing an ontology-driven, semantic grid services infrastructure that will enable efficient execution of discovery-driven scientific workflows in the context of multi-centric, post-genomic clinical trials. The focus of the present paper is the ACGT Master Ontology (MO). Methods ACGT project researchers undertook a systematic review of existing domain and upper-level ontologies, as well as of existing ontology design software, implementation methods, and end-user interfaces. This included the careful study of best practices, design principles and evaluation methods for ontology design, maintenance, implementation, and versioning, as well as for use on the part of domain experts and clinicians. Results To date, the results of the ACGT project include (i) the development of a master ontology (the ACGT-MO) based on clearly defined principles of ontology development and evaluation; (ii) the development of a technical infra-structure (the ACGT Platform) that implements the ACGT-MO utilizing independent tools, components and resources that have been developed based on open architectural standards, and which includes an application updating and evolving the ontology efficiently in response to end-user needs; and (iii) the development of an Ontology-based Trial Management Application (ObTiMA) that integrates the ACGT-MO into the design process of clinical trials in order to

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.

Developing and Validating the Socio-Technical Model in Ontology Engineering

NASA Astrophysics Data System (ADS)

Silalahi, Mesnan; Indra Sensuse, Dana; Giri Sucahyo, Yudho; Fadhilah Akmaliah, Izzah; Rahayu, Puji; Cahyaningsih, Elin

2018-03-01

This paper describes results from an attempt to develop a model in ontology engineering methodology and a way to validate the model. The approach to methodology in ontology engineering is from the point view of socio-technical system theory. Qualitative research synthesis is used to build the model using meta-ethnography. In order to ensure the objectivity of the measurement, inter-rater reliability method was applied using a multi-rater Fleiss Kappa. The results show the accordance of the research output with the diamond model in the socio-technical system theory by evidence of the interdependency of the four socio-technical variables namely people, technology, structure and task.

Towards an Interoperability Ontology for Software Development Tools

DTIC Science & Technology

2003-03-01

The description of feature models was tied to the introduction of the Feature-Oriented Domain Analysis ( FODA *) [KANG90] approach in the late eighties...Feature-oriented domain analysis ( FODA ) is a domain analysis method developed at the Software...ese obstacles was to construct a “pilot” ontology that is extensible. We applied the Feature-Oriented Domain Analysis approach to capture the

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.

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.

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

PubMed Central

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

2013-01-01

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. PMID:24311994

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

Evaluating the Good Ontology Design Guideline (GoodOD) with the ontology quality requirements and evaluation method and metrics (OQuaRE).

PubMed

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

2014-01-01

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. 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. 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. 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. 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.

77 FR 15123 - Foundry Coke From China; Scheduling of an Expedited Five-Year Review

Federal Register 2010, 2011, 2012, 2013, 2014

2012-03-14

... INTERNATIONAL TRADE COMMISSION [Investigation No. 731-TA-891 (Second Review)] Foundry Coke From... whether revocation of the antidumping duty order on foundry coke from China would be likely to lead to... submitted by ABC Coke, Erie Coke, Tonawanda Coke Corporation, and Walter Coke Co. to be individually...

Matching disease and phenotype ontologies in the ontology alignment evaluation initiative.

PubMed

Harrow, Ian; Jiménez-Ruiz, Ernesto; Splendiani, Andrea; Romacker, Martin; Woollard, Peter; Markel, Scott; Alam-Faruque, Yasmin; Koch, Martin; Malone, James; Waaler, Arild

2017-12-02

The disease and phenotype track was designed to evaluate the relative performance of ontology matching systems that generate mappings between source ontologies. Disease and phenotype ontologies are important for applications such as data mining, data integration and knowledge management to support translational science in drug discovery and understanding the genetics of disease. Eleven systems (out of 21 OAEI participating systems) were able to cope with at least one of the tasks in the Disease and Phenotype track. AML, FCA-Map, LogMap(Bio) and PhenoMF systems produced the top results for ontology matching in comparison to consensus alignments. The results against manually curated mappings proved to be more difficult most likely because these mapping sets comprised mostly subsumption relationships rather than equivalence. Manual assessment of unique equivalence mappings showed that AML, LogMap(Bio) and PhenoMF systems have the highest precision results. Four systems gave the highest performance for matching disease and phenotype ontologies. These systems coped well with the detection of equivalence matches, but struggled to detect semantic similarity. This deserves more attention in the future development of ontology matching systems. The findings of this evaluation show that such systems could help to automate equivalence matching in the workflow of curators, who maintain ontology mapping services in numerous domains such as disease and phenotype.

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.

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

Inferring ontology graph structures using OWL reasoning.

PubMed

Rodríguez-García, Miguel Ángel; Hoehndorf, Robert

2018-01-05

Ontologies are representations of a conceptualization of a domain. Traditionally, ontologies in biology were represented as directed acyclic graphs (DAG) which represent the backbone taxonomy and additional relations between classes. These graphs are widely exploited for data analysis in the form of ontology enrichment or computation of semantic similarity. More recently, ontologies are developed in a formal language such as the Web Ontology Language (OWL) and consist of a set of axioms through which classes are defined or constrained. While the taxonomy of an ontology can be inferred directly from the axioms of an ontology as one of the standard OWL reasoning tasks, creating general graph structures from OWL ontologies that exploit the ontologies' semantic content remains a challenge. We developed a method to transform ontologies into graphs using an automated reasoner while taking into account all relations between classes. Searching for (existential) patterns in the deductive closure of ontologies, we can identify relations between classes that are implied but not asserted and generate graph structures that encode for a large part of the ontologies' semantic content. We demonstrate the advantages of our method by applying it to inference of protein-protein interactions through semantic similarity over the Gene Ontology and demonstrate that performance is increased when graph structures are inferred using deductive inference according to our method. Our software and experiment results are available at http://github.com/bio-ontology-research-group/Onto2Graph . Onto2Graph is a method to generate graph structures from OWL ontologies using automated reasoning. The resulting graphs can be used for improved ontology visualization and ontology-based data analysis.

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…

Materials and processing approaches for foundry-compatible transient electronics

PubMed Central

Chang, Jan-Kai; Fang, Hui; Bower, Christopher A.; Song, Enming; Yu, Xinge; Rogers, John A.

2017-01-01

Foundry-based routes to transient silicon electronic devices have the potential to serve as the manufacturing basis for “green” electronic devices, biodegradable implants, hardware secure data storage systems, and unrecoverable remote devices. This article introduces materials and processing approaches that enable state-of-the-art silicon complementary metal-oxide-semiconductor (CMOS) foundries to be leveraged for high-performance, water-soluble forms of electronics. The key elements are (i) collections of biodegradable electronic materials (e.g., silicon, tungsten, silicon nitride, silicon dioxide) and device architectures that are compatible with manufacturing procedures currently used in the integrated circuit industry, (ii) release schemes and transfer printing methods for integration of multiple ultrathin components formed in this way onto biodegradable polymer substrates, and (iii) planarization and metallization techniques to yield interconnected and fully functional systems. Various CMOS devices and circuit elements created in this fashion and detailed measurements of their electrical characteristics highlight the capabilities. Accelerated dissolution studies in aqueous environments reveal the chemical kinetics associated with the underlying transient behaviors. The results demonstrate the technical feasibility for using foundry-based routes to sophisticated forms of transient electronic devices, with functional capabilities and cost structures that could support diverse applications in the biomedical, military, industrial, and consumer industries. PMID:28652373

Materials and processing approaches for foundry-compatible transient electronics.

PubMed

Chang, Jan-Kai; Fang, Hui; Bower, Christopher A; Song, Enming; Yu, Xinge; Rogers, John A

2017-07-11

Foundry-based routes to transient silicon electronic devices have the potential to serve as the manufacturing basis for "green" electronic devices, biodegradable implants, hardware secure data storage systems, and unrecoverable remote devices. This article introduces materials and processing approaches that enable state-of-the-art silicon complementary metal-oxide-semiconductor (CMOS) foundries to be leveraged for high-performance, water-soluble forms of electronics. The key elements are ( i ) collections of biodegradable electronic materials (e.g., silicon, tungsten, silicon nitride, silicon dioxide) and device architectures that are compatible with manufacturing procedures currently used in the integrated circuit industry, ( ii ) release schemes and transfer printing methods for integration of multiple ultrathin components formed in this way onto biodegradable polymer substrates, and ( iii ) planarization and metallization techniques to yield interconnected and fully functional systems. Various CMOS devices and circuit elements created in this fashion and detailed measurements of their electrical characteristics highlight the capabilities. Accelerated dissolution studies in aqueous environments reveal the chemical kinetics associated with the underlying transient behaviors. The results demonstrate the technical feasibility for using foundry-based routes to sophisticated forms of transient electronic devices, with functional capabilities and cost structures that could support diverse applications in the biomedical, military, industrial, and consumer industries.

Materials and processing approaches for foundry-compatible transient electronics

NASA Astrophysics Data System (ADS)

Chang, Jan-Kai; Fang, Hui; Bower, Christopher A.; Song, Enming; Yu, Xinge; Rogers, John A.

2017-07-01

Foundry-based routes to transient silicon electronic devices have the potential to serve as the manufacturing basis for “green” electronic devices, biodegradable implants, hardware secure data storage systems, and unrecoverable remote devices. This article introduces materials and processing approaches that enable state-of-the-art silicon complementary metal-oxide-semiconductor (CMOS) foundries to be leveraged for high-performance, water-soluble forms of electronics. The key elements are (i) collections of biodegradable electronic materials (e.g., silicon, tungsten, silicon nitride, silicon dioxide) and device architectures that are compatible with manufacturing procedures currently used in the integrated circuit industry, (ii) release schemes and transfer printing methods for integration of multiple ultrathin components formed in this way onto biodegradable polymer substrates, and (iii) planarization and metallization techniques to yield interconnected and fully functional systems. Various CMOS devices and circuit elements created in this fashion and detailed measurements of their electrical characteristics highlight the capabilities. Accelerated dissolution studies in aqueous environments reveal the chemical kinetics associated with the underlying transient behaviors. The results demonstrate the technical feasibility for using foundry-based routes to sophisticated forms of transient electronic devices, with functional capabilities and cost structures that could support diverse applications in the biomedical, military, industrial, and consumer industries.

Building a developmental toxicity ontology.

PubMed

Baker, Nancy; Boobis, Alan; Burgoon, Lyle; Carney, Edward; Currie, Richard; Fritsche, Ellen; Knudsen, Thomas; Laffont, Madeleine; Piersma, Aldert H; Poole, Alan; Schneider, Steffen; Daston, George

2018-04-03

As more information is generated about modes of action for developmental toxicity and more data are generated using high-throughput and high-content technologies, it is becoming necessary to organize that information. This report discussed the need for a systematic representation of knowledge about developmental toxicity (i.e., an ontology) and proposes a method to build one based on knowledge of developmental biology and mode of action/ adverse outcome pathways in developmental toxicity. This report is the result of a consensus working group developing a plan to create an ontology for developmental toxicity that spans multiple levels of biological organization. This report provide a description of some of the challenges in building a developmental toxicity ontology and outlines a proposed methodology to meet those challenges. As the ontology is built on currently available web-based resources, a review of these resources is provided. Case studies on one of the most well-understood morphogens and developmental toxicants, retinoic acid, are presented as examples of how such an ontology might be developed. This report outlines an approach to construct a developmental toxicity ontology. Such an ontology will facilitate computer-based prediction of substances likely to induce human developmental toxicity. © 2018 Wiley Periodicals, Inc.

The Apollo Structured Vocabulary: an OWL2 ontology of phenomena in infectious disease epidemiology and population biology for use in epidemic simulation.

PubMed

Hogan, William R; Wagner, Michael M; Brochhausen, Mathias; Levander, John; Brown, Shawn T; Millett, Nicholas; DePasse, Jay; Hanna, Josh

2016-08-18

We developed the Apollo Structured Vocabulary (Apollo-SV)-an OWL2 ontology of phenomena in infectious disease epidemiology and population biology-as part of a project whose goal is to increase the use of epidemic simulators in public health practice. Apollo-SV defines a terminology for use in simulator configuration. Apollo-SV is the product of an ontological analysis of the domain of infectious disease epidemiology, with particular attention to the inputs and outputs of nine simulators. Apollo-SV contains 802 classes for representing the inputs and outputs of simulators, of which approximately half are new and half are imported from existing ontologies. The most important Apollo-SV class for users of simulators is infectious disease scenario, which is a representation of an ecosystem at simulator time zero that has at least one infection process (a class) affecting at least one population (also a class). Other important classes represent ecosystem elements (e.g., households), ecosystem processes (e.g., infection acquisition and infectious disease), censuses of ecosystem elements (e.g., censuses of populations), and infectious disease control measures. In the larger project, which created an end-user application that can send the same infectious disease scenario to multiple simulators, Apollo-SV serves as the controlled terminology and strongly influences the design of the message syntax used to represent an infectious disease scenario. As we added simulators for different pathogens (e.g., malaria and dengue), the core classes of Apollo-SV have remained stable, suggesting that our conceptualization of the information required by simulators is sound. Despite adhering to the OBO Foundry principle of orthogonality, we could not reuse Infectious Disease Ontology classes as the basis for infectious disease scenarios. We thus defined new classes in Apollo-SV for host, pathogen, infection, infectious disease, colonization, and infection acquisition. Unlike IDO, our

XML, Ontologies, and Their Clinical Applications.

PubMed

Yu, Chunjiang; Shen, Bairong

2016-01-01

The development of information technology has resulted in its penetration into every area of clinical research. Various clinical systems have been developed, which produce increasing volumes of clinical data. However, saving, exchanging, querying, and exploiting these data are challenging issues. The development of Extensible Markup Language (XML) has allowed the generation of flexible information formats to facilitate the electronic sharing of structured data via networks, and it has been used widely for clinical data processing. In particular, XML is very useful in the fields of data standardization, data exchange, and data integration. Moreover, ontologies have been attracting increased attention in various clinical fields in recent years. An ontology is the basic level of a knowledge representation scheme, and various ontology repositories have been developed, such as Gene Ontology and BioPortal. The creation of these standardized repositories greatly facilitates clinical research in related fields. In this chapter, we discuss the basic concepts of XML and ontologies, as well as their clinical applications.

NanoParticle Ontology for Cancer Nanotechnology Research

PubMed Central

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

2010-01-01

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. PMID:20211274

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

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.

The National Center for Biomedical Ontology

PubMed Central

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

2011-01-01

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. PMID:22081220

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

Wafer-shape metrics based foundry lithography

NASA Astrophysics Data System (ADS)

Kim, Sungtae; Liang, Frida; Mileham, Jeffrey; Tsai, Damon; Bouche, Eric; Lee, Sean; Huang, Albert; Hua, C. F.; Wei, Ming Sheng

2017-03-01

As device shrink, there are many difficulties with process integration and device yield. Lithography process control is expected to be a major challenge due to tighter overlay and focus control requirement. The understanding and control of stresses accumulated during device fabrication has becoming more critical at advanced technology nodes. Within-wafer stress variations cause local wafer distortions which in turn present challenges for managing overlay and depth of focus during lithography. A novel technique for measuring distortion is Coherent Gradient Sensing (CGS) interferometry, which is capable of generating a high-density distortion data set of the full wafer within a time frame suitable for a high volume manufacturing (HVM) environment. In this paper, we describe the adoption of CGS (Coherent Gradient Sensing) interferometry into high volume foundry manufacturing to overcome these challenges. Leveraging this high density 3D metrology, we characterized its In-plane distortion as well as its topography capabilities applied to the full flow of an advanced foundry manufacturing. Case studies are presented that summarize the use of CGS data to reveal correlations between in-plane distortion and overlay variation as well as between topography and device yield.

The Causes of Death in Iron and Steel Workers (Non-foundry)

PubMed Central

McLaughlin, A. I. G.; Harding, H. E.

1961-01-01

Few studies have been made of the pathology associated with the iron and steel trades other than foundries. We review here the clinical, occupational, and pathological (post-mortem) findings in 10 grinders and 16 other non-foundry workers in iron and steel. Grinding is evidently a less dangerous trade than it was 100 or even 50 years ago, but silicosis and/or mixed dust fibrosis is still found amongst them. The risk of the onset of pneumoconiosis in other workers in these trades is small, but not absent. Images PMID:13774071

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

NASA Astrophysics Data System (ADS)

Fu, Linyun; Ma, Xiaogang; Zheng, Jin; Goldstein, Justin; Duggan, Brian; West, Patrick; Aulenbach, Steve; Tilmes, Curt; Fox, Peter

2014-05-01

This poster will show how we used a case-driven iterative methodology to develop an ontology to represent the content structure and the associated provenance information in a National Climate Assessment (NCA) report of the US Global Change Research Program (USGCRP). We applied the W3C PROV-O ontology to implement a formal representation of provenance. We argue that the use case-driven, iterative development process and the application of a formal provenance ontology help efficiently incorporate domain knowledge from earth and environmental scientists in a well-structured model interoperable in the context of the Web of Data.

A histological ontology of the human cardiovascular system.

PubMed

Mazo, Claudia; Salazar, Liliana; Corcho, Oscar; Trujillo, Maria; Alegre, Enrique

2017-10-02

In this paper, we describe a histological ontology of the human cardiovascular system developed in collaboration among histology experts and computer scientists. The histological ontology is developed following an existing methodology using Conceptual Models (CMs) and validated using OOPS!, expert evaluation with CMs, and how accurately the ontology can answer the Competency Questions (CQ). It is publicly available at http://bioportal.bioontology.org/ontologies/HO and https://w3id.org/def/System . The histological ontology is developed to support complex tasks, such as supporting teaching activities, medical practices, and bio-medical research or having natural language interactions.

Knowledge Management Framework for Emerging Infectious Diseases Preparedness and Response: Design and Development of Public Health Document Ontology

PubMed Central

Zhang, Zhizun; Gonzalez, Mila C; Morse, Stephen S

2017-01-01

Background There are increasing concerns about our preparedness and timely coordinated response across the globe to cope with emerging infectious diseases (EIDs). This poses practical challenges that require exploiting novel knowledge management approaches effectively. Objective This work aims to develop an ontology-driven knowledge management framework that addresses the existing challenges in sharing and reusing public health knowledge. Methods We propose a systems engineering-inspired ontology-driven knowledge management approach. It decomposes public health knowledge into concepts and relations and organizes the elements of knowledge based on the teleological functions. Both knowledge and semantic rules are stored in an ontology and retrieved to answer queries regarding EID preparedness and response. Results A hybrid concept extraction was implemented in this work. The quality of the ontology was evaluated using the formal evaluation method Ontology Quality Evaluation Framework. Conclusions Our approach is a potentially effective methodology for managing public health knowledge. Accuracy and comprehensiveness of the ontology can be improved as more knowledge is stored. In the future, a survey will be conducted to collect queries from public health practitioners. The reasoning capacity of the ontology will be evaluated using the queries and hypothetical outbreaks. We suggest the importance of developing a knowledge sharing standard like the Gene Ontology for the public health domain. PMID:29021130

Owlready: Ontology-oriented programming in Python with automatic classification and high level constructs for biomedical ontologies.

PubMed

Lamy, Jean-Baptiste

2017-07-01

Ontologies are widely used in the biomedical domain. While many tools exist for the edition, alignment or evaluation of ontologies, few solutions have been proposed for ontology programming interface, i.e. for accessing and modifying an ontology within a programming language. Existing query languages (such as SPARQL) and APIs (such as OWLAPI) are not as easy-to-use as object programming languages are. Moreover, they provide few solutions to difficulties encountered with biomedical ontologies. Our objective was to design a tool for accessing easily the entities of an OWL ontology, with high-level constructs helping with biomedical ontologies. From our experience on medical ontologies, we identified two difficulties: (1) many entities are represented by classes (rather than individuals), but the existing tools do not permit manipulating classes as easily as individuals, (2) ontologies rely on the open-world assumption, whereas the medical reasoning must consider only evidence-based medical knowledge as true. We designed a Python module for ontology-oriented programming. It allows access to the entities of an OWL ontology as if they were objects in the programming language. We propose a simple high-level syntax for managing classes and the associated "role-filler" constraints. We also propose an algorithm for performing local closed world reasoning in simple situations. We developed Owlready, a Python module for a high-level access to OWL ontologies. The paper describes the architecture and the syntax of the module version 2. It details how we integrated the OWL ontology model with the Python object model. The paper provides examples based on Gene Ontology (GO). We also demonstrate the interest of Owlready in a use case focused on the automatic comparison of the contraindications of several drugs. This use case illustrates the use of the specific syntax proposed for manipulating classes and for performing local closed world reasoning. Owlready has been successfully

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. © 2014 American Academy of Forensic Sciences.

Ontology-aided Data Fusion (Invited)

NASA Astrophysics Data System (ADS)

Raskin, R.

2009-12-01

An ontology provides semantic descriptions that are analogous to those in a dictionary, but are readable by both computers and humans. A data or service is semantically annotated when it is formally associated with elements of an ontology. The ESIP Federation Semantic Web Cluster has developed a set of ontologies to describe datatypes and data services that can be used to support automated data fusion. The service ontology includes descriptors of the service function, its inputs/outputs, and its invocation method. The datatype descriptors resemble typical metadata fields (data format, data model, data structure, originator, etc.) augmented with descriptions of the meaning of the data. These ontologies, in combination with the SWEET science ontology, enable a registered data fusion service to be chained together and implemented that is scientifically meaningful based on machine understanding of the associated data and services. This presentation describes initial results and experiences in automated data fusion.

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.

Ontology Design Patterns as Interfaces (invited)

NASA Astrophysics Data System (ADS)

Janowicz, K.

2015-12-01

In recent years ontology design patterns (ODP) have gained popularity among knowledge engineers. ODPs are modular but self-contained building blocks that are reusable and extendible. They minimize the amount of ontological commitments and thereby are easier to integrate than large monolithic ontologies. Typically, patterns are not directly used to annotate data or to model certain domain problems but are combined and extended to form data and purpose-driven local ontologies that serve the needs of specific applications or communities. By relying on a common set of patterns these local ontologies can be aligned to improve interoperability and enable federated queries without enforcing a top-down model of the domain. In previous work, we introduced ontological views as layer on top of ontology design patterns to ease the reuse, combination, and integration of patterns. While the literature distinguishes multiple types of patterns, e.g., content patterns or logical patterns, we propose to use them as interfaces here to guide the development of ontology-driven systems.

Ontology of fractures

NASA Astrophysics Data System (ADS)

Zhong, Jian; Aydina, Atilla; McGuinness, Deborah L.

2009-03-01

Fractures are fundamental structures in the Earth's crust and they can impact many societal and industrial activities including oil and gas exploration and production, aquifer management, CO 2 sequestration, waste isolation, the stabilization of engineering structures, and assessing natural hazards (earthquakes, volcanoes, and landslides). Therefore, an ontology which organizes the concepts of fractures could help facilitate a sound education within, and communication among, the highly diverse professional and academic community interested in the problems cited above. We developed a process-based ontology that makes explicit specifications about fractures, their properties, and the deformation mechanisms which lead to their formation and evolution. Our ontology emphasizes the relationships among concepts such as the factors that influence the mechanism(s) responsible for the formation and evolution of specific fracture types. Our ontology is a valuable resource with a potential to applications in a number of fields utilizing recent advances in Information Technology, specifically for digital data and information in computers, grids, and Web services.

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

Knowledge Management Framework for Emerging Infectious Diseases Preparedness and Response: Design and Development of Public Health Document Ontology.

PubMed

Zhang, Zhizun; Gonzalez, Mila C; Morse, Stephen S; Venkatasubramanian, Venkat

2017-10-11

There are increasing concerns about our preparedness and timely coordinated response across the globe to cope with emerging infectious diseases (EIDs). This poses practical challenges that require exploiting novel knowledge management approaches effectively. This work aims to develop an ontology-driven knowledge management framework that addresses the existing challenges in sharing and reusing public health knowledge. We propose a systems engineering-inspired ontology-driven knowledge management approach. It decomposes public health knowledge into concepts and relations and organizes the elements of knowledge based on the teleological functions. Both knowledge and semantic rules are stored in an ontology and retrieved to answer queries regarding EID preparedness and response. A hybrid concept extraction was implemented in this work. The quality of the ontology was evaluated using the formal evaluation method Ontology Quality Evaluation Framework. Our approach is a potentially effective methodology for managing public health knowledge. Accuracy and comprehensiveness of the ontology can be improved as more knowledge is stored. In the future, a survey will be conducted to collect queries from public health practitioners. The reasoning capacity of the ontology will be evaluated using the queries and hypothetical outbreaks. We suggest the importance of developing a knowledge sharing standard like the Gene Ontology for the public health domain. ©Zhizun Zhang, Mila C Gonzalez, Stephen S Morse, Venkat Venkatasubramanian. Originally published in JMIR Research Protocols (http://www.researchprotocols.org), 11.10.2017.

Ontology Development for Patient Education Documents Using a Professional- and Patient-Oriented Delphi Method.

PubMed

Heimonen, Juho; Danielsson-Ojala, Riitta; Salakoski, Tapio; Lundgrén-Laine, Heljä; Salanterä, Sanna

2018-04-12

Written patient education materials are essential to motivate and help patients to participate in their own care, but the production and management of a large collection of high-quality and easily accessible patient education documents can be challenging. Ontologies can aid in these tasks, but the existing resources are not directly applicable to patient education. An ontology that models patient education documents and their readers was constructed. The Delphi method was used to identify a compact but sufficient set of entities with which the topics of documents may be described. The preferred terms of the entities were also considered to ensure their understandability. In the ontology, readers may be characterized by gender, age group, language, and role (patient or professional), whereas documents may be characterized by audience, topic(s), and content, as well as the time and place of use. The Delphi method yielded 265 unique document topics that are organized into seven hierarchies. Advantages and disadvantages of the ontology design, as well as possibilities for improvements, were identified. The patient education material ontology can enhance many applications, but further development is needed to reach its full potential.

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.

A Foundational Approach to Designing Geoscience Ontologies

NASA Astrophysics Data System (ADS)

Brodaric, B.

2009-05-01

E-science systems are increasingly deploying ontologies to aid online geoscience research. Geoscience ontologies are typically constructed independently by isolated individuals or groups who tend to follow few design principles. This limits the usability of the ontologies due to conceptualizations that are vague, conflicting, or narrow. Advances in foundational ontologies and formal engineering approaches offer promising solutions, but these advanced techniques have had limited application in the geosciences. This paper develops a design approach for geoscience ontologies by extending aspects of the DOLCE foundational ontology and the OntoClean method. Geoscience examples will be presented to demonstrate the feasibility of the approach.

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.

[Dynamic monitoring and analysis of occupational hazards in working environment of foundry plant from 1987 to 2010].

PubMed

Lu, Yang; Zhang, Min; Chen, Wei-hong; Qi, Cheng

2013-08-01

To investigate the characteristics and changing trend of occupational hazards in the working environment of a foundry plant from 1987 to 2010. The foundry plant of a large-scale automobile company in Hubei Province, China was chosen as the study site. The data on occupational hazards in the working environment of the foundry plant in the past years were collected, and additional measurements were performed. The means and geometric means of the concentrations of occupational hazards were calculated. The characteristics and changing trend of occupational hazards from 1987 to 2010 were presented. There were dust, chemical, and physical occupational hazards in the working environment of the foundry plant, with silica dust, noise, and heat stress as the main ones. Dust, mainly silica dust, is found in all aspects of foundry. The mean concentration of silica dust was high (3.2∼8.2 mg/m(3)), exceeding the national occupational exposure limit (1 mg/m(3)). The mean concentrations of silica dust varied across different types of work, with higher levels in cast shakeout and finishing, overhead crane operation, and sand preparation. The mean concentration of respirable dust in the foundry plant was low (0.38 mg/m(3)), not exceeding the national occupational exposure limit (0.7 mg/m(3)). There were high concentrations of grinding wheel dust (10.6 mg/m(3)) and welding fume (5.7 mg/m(3)) in cast shakeout and finishing, exceeding the national occupational exposure limit (8 and 4 mg/m(3)). Coal dust was mainly found in melting as well as cast shakeout and finishing, with higher concentration in the former (4.7 mg/m(3). The main chemical occupational hazard in the environment of the foundry plant was formaldehyde (1.23 mg/m(3)), exceeding the national occupational exposure limit (0.5 mg/m(3)). The concentrations of ammonia, phenol, metal fume, sulfur dioxide, hydrogen sulfide, and phosphine in the foundry plant were low. The mean concentration of polycyclic aromatic hydrocarbons

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.

Predicting the Extension of Biomedical Ontologies

PubMed Central

Pesquita, Catia; Couto, Francisco M.

2012-01-01

Developing and extending a biomedical ontology is a very demanding task that can never be considered complete given our ever-evolving understanding of the life sciences. Extension in particular can benefit from the automation of some of its steps, thus releasing experts to focus on harder tasks. Here we present a strategy to support the automation of change capturing within ontology extension where the need for new concepts or relations is identified. Our strategy is based on predicting areas of an ontology that will undergo extension in a future version by applying supervised learning over features of previous ontology versions. We used the Gene Ontology as our test bed and obtained encouraging results with average f-measure reaching 0.79 for a subset of biological process terms. Our strategy was also able to outperform state of the art change capturing methods. In addition we have identified several issues concerning prediction of ontology evolution, and have delineated a general framework for ontology extension prediction. Our strategy can be applied to any biomedical ontology with versioning, to help focus either manual or semi-automated extension methods on areas of the ontology that need extension. PMID:23028267

Learning Resources Organization Using Ontological Framework

NASA Astrophysics Data System (ADS)

Gavrilova, Tatiana; Gorovoy, Vladimir; Petrashen, Elena

The paper describes the ontological approach to the knowledge structuring for the e-learning portal design as it turns out to be efficient and relevant to current domain conditions. It is primarily based on the visual ontology-based description of the content of the learning materials and this helps to provide productive and personalized access to these materials. The experience of ontology developing for Knowledge Engineering coursetersburg State University is discussed and “OntolingeWiki” tool for creating ontology-based e-learning portals is described.

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

ontologyX: a suite of R packages for working with ontological data.

PubMed

Greene, Daniel; Richardson, Sylvia; Turro, Ernest

2017-04-01

Ontologies are widely used constructs for encoding and analyzing biomedical data, but the absence of simple and consistent tools has made exploratory and systematic analysis of such data unnecessarily difficult. Here we present three packages which aim to simplify such procedures. The ontologyIndex package enables arbitrary ontologies to be read into R, supports representation of ontological objects by native R types, and provides a parsimonius set of performant functions for querying ontologies. ontologySimilarity and ontologyPlot extend ontologyIndex with functionality for straightforward visualization and semantic similarity calculations, including statistical routines. ontologyIndex , ontologyPlot and ontologySimilarity are all available on the Comprehensive R Archive Network website under https://cran.r-project.org/web/packages/ . Daniel Greene dg333@cam.ac.uk. Supplementary data are available at Bioinformatics online. © The Author 2016. Published by Oxford University Press.

The MMI Device Ontology: Enabling Sensor Integration

NASA Astrophysics Data System (ADS)

Rueda, C.; Galbraith, N.; Morris, R. A.; Bermudez, L. E.; Graybeal, J.; Arko, R. A.; Mmi Device Ontology Working Group

2010-12-01

The Marine Metadata Interoperability (MMI) project has developed an ontology for devices to describe sensors and sensor networks. This ontology is implemented in the W3C Web Ontology Language (OWL) and provides an extensible conceptual model and controlled vocabularies for describing heterogeneous instrument types, with different data characteristics, and their attributes. It can help users populate metadata records for sensors; associate devices with their platforms, deployments, measurement capabilities and restrictions; aid in discovery of sensor data, both historic and real-time; and improve the interoperability of observational oceanographic data sets. We developed the MMI Device Ontology following a community-based approach. By building on and integrating other models and ontologies from related disciplines, we sought to facilitate semantic interoperability while avoiding duplication. Key concepts and insights from various communities, including the Open Geospatial Consortium (eg., SensorML and Observations and Measurements specifications), Semantic Web for Earth and Environmental Terminology (SWEET), and W3C Semantic Sensor Network Incubator Group, have significantly enriched the development of the ontology. Individuals ranging from instrument designers, science data producers and consumers to ontology specialists and other technologists contributed to the work. Applications of the MMI Device Ontology are underway for several community use cases. These include vessel-mounted multibeam mapping sonars for the Rolling Deck to Repository (R2R) program and description of diverse instruments on deepwater Ocean Reference Stations for the OceanSITES program. These trials involve creation of records completely describing instruments, either by individual instances or by manufacturer and model. Individual terms in the MMI Device Ontology can be referenced with their corresponding Uniform Resource Identifiers (URIs) in sensor-related metadata specifications (e

An Ontology for Insider Threat Indicators Development and Applications

DTIC Science & Technology

2014-11-01

An Ontology for Insider Threat Indicators Development and Applications Daniel L. Costa , Matthew L. Collins, Samuel J. Perl, Michael J. Albrethsen...services, commit fraud against an organization, steal intellectual property, or conduct national security espionage, sabotaging systems and data, as...engineering plans from the victim organization’s computer systems to his new employer.  The insider accessed a web server with an administrator account

4. Overall view of complex. Foundry (MN99B) at center. Main ...

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

4. Overall view of complex. Foundry (MN-99-B) at center. Main section of roundhouse (MN-99-A) at left. Machine shop section of roundhouse in center behind foundry. East end of air brake shop section of roundhouse to right of machine shop. Top of sand tower (MN-99-E) just visible above main section of roundhouse at far left. Photograph taken from second floor of office (MN-99-D). View to south. - Duluth & Iron Range Rail Road Company Shops, Southwest of downtown Two Harbors, northwest of Agate Bay, Two Harbors, Lake County, MN

Metallurgical Examination of a Cast Turret Manufactured by the American Steel Foundries

DTIC Science & Technology

1945-03-28

ferrite and a structure stmlar to tempered bainite tnd fine carb ides. 4. The results of this investigatio l inCicate that the American Steel Foundries...1hirrot No 11Mufac t~redj~ t!Le American~ Steel Poidcries J.J Wil jr;I 4?1 ’JJ No. B171; 11000 Picral Structure simuilar to temnpered bainite Lavsociated wita fine carbides and ferrite patcha.. FIGM I ...examination has been conducted on two samples of the. cast turret to. 3171 for the Hedium Tank II4, maiufactured by the i.meriaan Steel Foundries, which

Semantics and metaphysics in informatics: toward an ontology of tasks.

PubMed

Figdor, Carrie

2011-04-01

This article clarifies three principles that should guide the development of any cognitive ontology. First, that an adequate cognitive ontology depends essentially on an adequate task ontology; second, that the goal of developing a cognitive ontology is independent of the goal of finding neural implementations of the processes referred to in the ontology; and third, that cognitive ontologies are neutral regarding the metaphysical relationship between cognitive and neural processes. Copyright © 2011 Cognitive Science Society, Inc.

An Educational Development Tool Based on Principles of Formal Ontology

ERIC Educational Resources Information Center

Guzzi, Rodolfo; Scarpanti, Stefano; Ballista, Giovanni; Di Nicolantonio, Walter

2005-01-01

Computer science provides with virtual laboratories, places where one can merge real experiments with the formalism of algorithms and mathematics and where, with the advent of multimedia, sounds and movies can also be added. In this paper we present a method, based on principles of formal ontology, allowing one to develop interactive educational…

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

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

EMISSION FACTORS FOR IRON FOUNDRIES - CRITERIA AND TOXIC POLLUTANTS

EPA Science Inventory

The report lists criteria and toxic pollutant emission factors or sources commonly found in gray and ductile iron foundries. Emission factors are identified for process source and process fugitive emissions. he emission factors, representing uncontrolled emissions, may be used to...

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.

Gene Ontology Consortium: going forward.

PubMed

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. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The Proteasix Ontology.

PubMed

Arguello Casteleiro, Mercedes; Klein, Julie; Stevens, Robert

2016-06-04

The Proteasix Ontology (PxO) is an ontology that supports the Proteasix tool; an open-source peptide-centric tool that can be used to predict automatically and in a large-scale fashion in silico the proteases involved in the generation of proteolytic cleavage fragments (peptides) The PxO re-uses parts of the Protein Ontology, the three Gene Ontology sub-ontologies, the Chemical Entities of Biological Interest Ontology, the Sequence Ontology and bespoke extensions to the PxO in support of a series of roles: 1. To describe the known proteases and their target cleaveage sites. 2. To enable the description of proteolytic cleaveage fragments as the outputs of observed and predicted proteolysis. 3. To use knowledge about the function, species and cellular location of a protease and protein substrate to support the prioritisation of proteases in observed and predicted proteolysis. The PxO is designed to describe the biological underpinnings of the generation of peptides. The peptide-centric PxO seeks to support the Proteasix tool by separating domain knowledge from the operational knowledge used in protease prediction by Proteasix and to support the confirmation of its analyses and results. The Proteasix Ontology may be found at: http://bioportal.bioontology.org/ontologies/PXO . This ontology is free and open for use by everyone.

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

PubMed

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

2011-09-01

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.

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

The study of heavy metals leaching from waste foundry sands using a one-step extraction

NASA Astrophysics Data System (ADS)

Bożym, Marta

2017-10-01

There are a number of leaching test which are used to evaluate the effect of foundry waste disposal on the environment (TCLP, SPLP, ASTM at al.). Because the spent foundry sand are usually deposited at the ground level and they have a similar structure to the soil, survey mobility of metals using the same methods seems appropriate. One-step extraction allows for the evaluation of the mobility and bioavailability of metals in soil and waste. Waste foundry sands have been successfully used as a component in manufactured soils in U.S., but concern over metal contamination must be eliminated before considering this direction of use. The study evaluated the leaching of heavy metals (Cd, Pb, Cu, Zn, Cr, Ni) from deposited waste foundry sands. The overall, as well as heavy metals were extracted by different type of extractants: H2O, CH3COOH, HCl, EDTA, MgCl2 and NaCOOH. These extractants are most commonly used to study the mobility and bioavailability of metals in soil and waste. In the present study applicable standards and methodology described in the literature in analysis were used. The results allowed to evaluate the bioavailability of metals leached from those wastes.

Tackling the challenges of matching biomedical ontologies.

PubMed

Faria, Daniel; Pesquita, Catia; Mott, Isabela; Martins, Catarina; Couto, Francisco M; Cruz, Isabel F

2018-01-15

Biomedical ontologies pose several challenges to ontology matching due both to the complexity of the biomedical domain and to the characteristics of the ontologies themselves. The biomedical tracks in the Ontology Matching Evaluation Initiative (OAEI) have spurred the development of matching systems able to tackle these challenges, and benchmarked their general performance. In this study, we dissect the strategies employed by matching systems to tackle the challenges of matching biomedical ontologies and gauge the impact of the challenges themselves on matching performance, using the AgreementMakerLight (AML) system as the platform for this study. We demonstrate that the linear complexity of the hash-based searching strategy implemented by most state-of-the-art ontology matching systems is essential for matching large biomedical ontologies efficiently. We show that accounting for all lexical annotations (e.g., labels and synonyms) in biomedical ontologies leads to a substantial improvement in F-measure over using only the primary name, and that accounting for the reliability of different types of annotations generally also leads to a marked improvement. Finally, we show that cross-references are a reliable source of information and that, when using biomedical ontologies as background knowledge, it is generally more reliable to use them as mediators than to perform lexical expansion. We anticipate that translating traditional matching algorithms to the hash-based searching paradigm will be a critical direction for the future development of the field. Improving the evaluation carried out in the biomedical tracks of the OAEI will also be important, as without proper reference alignments there is only so much that can be ascertained about matching systems or strategies. Nevertheless, it is clear that, to tackle the various challenges posed by biomedical ontologies, ontology matching systems must be able to efficiently combine multiple strategies into a mature matching

SPONGY (SPam ONtoloGY): Email Classification Using Two-Level Dynamic Ontology

PubMed Central

2014-01-01

Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user's background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1) to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2) to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance. PMID:25254240

SPONGY (SPam ONtoloGY): email classification using two-level dynamic ontology.

PubMed

Youn, Seongwook

2014-01-01

Email is one of common communication methods between people on the Internet. However, the increase of email misuse/abuse has resulted in an increasing volume of spam emails over recent years. An experimental system has been designed and implemented with the hypothesis that this method would outperform existing techniques, and the experimental results showed that indeed the proposed ontology-based approach improves spam filtering accuracy significantly. In this paper, two levels of ontology spam filters were implemented: a first level global ontology filter and a second level user-customized ontology filter. The use of the global ontology filter showed about 91% of spam filtered, which is comparable with other methods. The user-customized ontology filter was created based on the specific user's background as well as the filtering mechanism used in the global ontology filter creation. The main contributions of the paper are (1) to introduce an ontology-based multilevel filtering technique that uses both a global ontology and an individual filter for each user to increase spam filtering accuracy and (2) to create a spam filter in the form of ontology, which is user-customized, scalable, and modularized, so that it can be embedded to many other systems for better performance.

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.

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

The Representation of Heart Development in the Gene Ontology

PubMed Central

Khodiyar, Varsha K.; Hill, David P.; Howe, Doug; Berardini, Tanya Z.; Tweedie, Susan; Talmud, Philippa J.; Breckenridge, Ross; Bhattarcharya, Shoumo; Riley, Paul; Scambler, Peter; Lovering, Ruth C.

2012-01-01

An understanding of heart development is critical in any systems biology approach to cardiovascular disease. The interpretation of data generated from high-throughput technologies (such as microarray and proteomics) is also essential to this approach. However, characterizing the role of genes in the processes underlying heart development and cardiovascular disease involves the non-trivial task of data analysis and integration of previous knowledge. The Gene Ontology (GO) Consortium provides structured controlled biological vocabularies that are used to summarize previous functional knowledge for gene products across all species. One aspect of GO describes biological processes, such as development and signaling. In order to support high-throughput cardiovascular research, we have initiated an effort to fully describe heart development in GO; expanding the number of GO terms describing heart development from 12 to over 280. This new ontology describes heart morphogenesis, the differentiation of specific cardiac cell types, and the involvement of signaling pathways in heart development and aligns GO with the current views of the heart development research community and its representation in the literature. This extension of GO allows gene product annotators to comprehensively capture the genetic program leading to the developmental progression of the heart. This will enable users to integrate heart development data across species, resulting in the comprehensive retrieval of information about this subject. The revised GO structure, combined with gene product annotations, should improve the interpretation of data from high-throughput methods in a variety of cardiovascular research areas, including heart development, congenital cardiac disease, and cardiac stem cell research. Additionally, we invite the heart development community to contribute to the expansion of this important dataset for the benefit of future research in this area. PMID:21419760

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.

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

Model Driven Engineering with Ontology Technologies

NASA Astrophysics Data System (ADS)

Staab, Steffen; Walter, Tobias; Gröner, Gerd; Parreiras, Fernando Silva

Ontologies constitute formal models of some aspect of the world that may be used for drawing interesting logical conclusions even for large models. Software models capture relevant characteristics of a software artifact to be developed, yet, most often these software models have limited formal semantics, or the underlying (often graphical) software language varies from case to case in a way that makes it hard if not impossible to fix its semantics. In this contribution, we survey the use of ontology technologies for software modeling in order to carry over advantages from ontology technologies to the software modeling domain. It will turn out that ontology-based metamodels constitute a core means for exploiting expressive ontology reasoning in the software modeling domain while remaining flexible enough to accommodate varying needs of software modelers.

History Matters: Incremental Ontology Reasoning Using Modules

NASA Astrophysics Data System (ADS)

Cuenca Grau, Bernardo; Halaschek-Wiener, Christian; Kazakov, Yevgeny

The development of ontologies involves continuous but relatively small modifications. Existing ontology reasoners, however, do not take advantage of the similarities between different versions of an ontology. In this paper, we propose a technique for incremental reasoning—that is, reasoning that reuses information obtained from previous versions of an ontology—based on the notion of a module. Our technique does not depend on a particular reasoning calculus and thus can be used in combination with any reasoner. We have applied our results to incremental classification of OWL DL ontologies and found significant improvement over regular classification time on a set of real-world ontologies.

Nuclear Nonproliferation Ontology Assessment Team Final Report

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

Strasburg, Jana D.; Hohimer, Ryan E.

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 importancemore » 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.« less

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

Diehl, Alexander D.; Meehan, Terrence F.; Bradford, Yvonne M.

Background: The Cell Ontology (CL) is an OBO Foundry candidate ontology covering the domain of canonical, natural biological cell types. Since its inception in 2005, the CL has undergone multiple rounds of revision and expansion, most notably in its representation of hematopoietic cells. For in vivo cells, the CL focuses on vertebrates but provides general classes that can be used for other metazoans, which can be subtyped in species-specific ontologies. Construction and content: Recent work on the CL has focused on extending the representation of various cell types, and developing new modules in the CL itself, and in related ontologiesmore » in coordination with the CL. For example, the Kidney and Urinary Pathway Ontology was used as a template to populate the CL with additional cell types. In addition, subtypes of the class 'cell in vitro' have received improved definitions and labels to provide for modularity with the representation of cells in the Cell Line Ontology and Reagent Ontology. Recent changes in the ontology development methodology for CL include a switch from OBO to OWL for the primary encoding of the ontology, and an increasing reliance on logical definitions for improved reasoning. Utility and discussion: The CL is now mandated as a metadata standard for large functional genomics and transcriptomics projects, and is used extensively for annotation, querying, and analyses of cell type specific data in sequencing consortia such as FANTOM5 and ENCODE, as well as for the NIAID ImmPort database and the Cell Image Library. The CL is also a vital component used in the modular construction of other biomedical ontologies-for example, the Gene Ontology and the cross-species anatomy ontology, Uberon, use CL to support the consistent representation of cell types across different levels of anatomical granularity, such as tissues and organs. Conclusions: The ongoing improvements to the CL make it a valuable resource to both the OBO Foundry community and the

View towards Foundry and Pattern Storage Room, blocked by 3 ...

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

View towards Foundry and Pattern Storage Room, blocked by 3 bay hopper coal cars in foreground - East Broad Top Railroad & Coal Company, State Route 994, West of U.S. Route 522, Rockhill Furnace, Huntingdon County, PA

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

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

Alignment of ICNP® 2.0 ontology and a proposed INCP® Brazilian ontology.

PubMed

Carvalho, Carina Maris Gaspar; Cubas, Marcia Regina; Malucelli, Andreia; Nóbrega, Maria Miriam Lima da

2014-01-01

to align the International Classification for Nursing Practice (ICNP®) Version 2.0 ontology and a proposed INCP® Brazilian Ontology. document-based, exploratory and descriptive study, the empirical basis of which was provided by the ICNP® 2.0 Ontology and the INCP® Brazilian Ontology. The ontology alignment was performed using a computer tool with algorithms to identify correspondences between concepts, which were organized and analyzed according to their presence or absence, their names, and their sibling, parent, and child classes. there were 2,682 concepts present in the ICNP® 2.0 Ontology that were missing in the Brazilian Ontology; 717 concepts present in the Brazilian Ontology were missing in the ICNP® 2.0 Ontology; and there were 215 pairs of matching concepts. it is believed that the correspondences identified in this study might contribute to the interoperability between the representations of nursing practice elements in ICNP®, thus allowing the standardization of nursing records based on this classification system.

Assessing the practice of biomedical ontology evaluation: Gaps and opportunities.

PubMed

Amith, Muhammad; He, Zhe; Bian, Jiang; Lossio-Ventura, Juan Antonio; Tao, Cui

2018-04-01

With the proliferation of heterogeneous health care data in the last three decades, biomedical ontologies and controlled biomedical terminologies play a more and more important role in knowledge representation and management, data integration, natural language processing, as well as decision support for health information systems and biomedical research. Biomedical ontologies and controlled terminologies are intended to assure interoperability. Nevertheless, the quality of biomedical ontologies has hindered their applicability and subsequent adoption in real-world applications. Ontology evaluation is an integral part of ontology development and maintenance. In the biomedicine domain, ontology evaluation is often conducted by third parties as a quality assurance (or auditing) effort that focuses on identifying modeling errors and inconsistencies. In this work, we first organized four categorical schemes of ontology evaluation methods in the existing literature to create an integrated taxonomy. Further, to understand the ontology evaluation practice in the biomedicine domain, we reviewed a sample of 200 ontologies from the National Center for Biomedical Ontology (NCBO) BioPortal-the largest repository for biomedical ontologies-and observed that only 15 of these ontologies have documented evaluation in their corresponding inception papers. We then surveyed the recent quality assurance approaches for biomedical ontologies and their use. We also mapped these quality assurance approaches to the ontology evaluation criteria. It is our anticipation that ontology evaluation and quality assurance approaches will be more widely adopted in the development life cycle of biomedical ontologies. Copyright © 2018 Elsevier Inc. All rights reserved.

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.

Foundry fabricated photonic integrated circuit optical phase lock loop.

PubMed

Bałakier, Katarzyna; Fice, Martyn J; Ponnampalam, Lalitha; Graham, Chris S; Wonfor, Adrian; Seeds, Alwyn J; Renaud, Cyril C

2017-07-24

This paper describes the first foundry-based InP photonic integrated circuit (PIC) designed to work within a heterodyne optical phase locked loop (OPLL). The PIC and an external electronic circuit were used to phase-lock a single-line semiconductor laser diode to an incoming reference laser, with tuneable frequency offset from 4 GHz to 12 GHz. The PIC contains 33 active and passive components monolithically integrated on a single chip, fully demonstrating the capability of a generic foundry PIC fabrication model. The electronic part of the OPLL consists of commercially available RF components. This semi-packaged system stabilizes the phase and frequency of the integrated laser so that an absolute frequency, high-purity heterodyne signal can be generated when the OPLL is in operation, with phase noise lower than -100 dBc/Hz at 10 kHz offset from the carrier. This is the lowest phase noise level ever demonstrated by monolithically integrated OPLLs.

Developing the Quantitative Histopathology Image Ontology (QHIO): A case study using the hot spot detection problem.

PubMed

Gurcan, Metin N; Tomaszewski, John; Overton, James A; Doyle, Scott; Ruttenberg, Alan; Smith, Barry

2017-02-01

Interoperability across data sets is a key challenge for quantitative histopathological imaging. There is a need for an ontology that can support effective merging of pathological image data with associated clinical and demographic data. To foster organized, cross-disciplinary, information-driven collaborations in the pathological imaging field, we propose to develop an ontology to represent imaging data and methods used in pathological imaging and analysis, and call it Quantitative Histopathological Imaging Ontology - QHIO. We apply QHIO to breast cancer hot-spot detection with the goal of enhancing reliability of detection by promoting the sharing of data between image analysts. Copyright © 2016 Elsevier Inc. All rights reserved.

Respiratory cancer and air pollution from iron foundries in a Scottish town: an epidemiological and environmental study.

PubMed Central

Smith, G H; Williams, F L; Lloyd, O L

1987-01-01

A geographical association between respiratory cancer and air pollution from steel foundries has been shown previously in Scotland and elsewhere. In the present study the iron-founding town of Kirkintilloch was found to have standardised mortality ratios (SMRs) for respiratory cancer in 1959-63, 1964-8, and 1969-73 that were unexceptional in comparison with Scotland. Nevertheless, when SMRs were calculated for respiratory cancer for the period 1966-76 in five zones of the town arranged, a priori, according to probable exposure to fumes from two iron foundries, and in the individual enumeration districts of the 1971 census, higher SMRs were found in the residential areas most exposed to pollution from the foundries. The gradient of the zones' SMRs--high close to the foundries to low at some distance from them--persisted despite standardisation of the SMRs for social class. A survey of the concentrations of several metals in soil cores sampled at 51 sites throughout the town showed a pattern of pollution that probably illustrated the effects of prevailing winds and topography on the pollution plumes from the foundries. The value of sampling soil cores in investigations where historical sources of metallic air pollution are of epidemiological interest was emphasised by the detection of high concentrations of Ni in an area where a nickel refinery had been located many decades previously. PMID:3689714

Study of abrasive resistance of foundries models obtained with use of additive technology

NASA Astrophysics Data System (ADS)

Ol'khovik, Evgeniy

2017-10-01

A problem of determination of resistance of the foundry models and patterns from ABS (PLA) plastic, obtained by the method of 3D printing with using FDM additive technology, to abrasive wear and resistance in the environment of foundry sand mould is considered in the present study. The description of a technique and equipment for tests of castings models and patterns for wear is provided in the article. The manufacturing techniques of models with the use of the 3D printer (additive technology) are described. The scheme with vibration load was applied to samples tests. For the most qualitative research of influence of sandy mix on plastic, models in real conditions of abrasive wear have been organized. The results also examined the application of acrylic paintwork to the plastic model and a two-component coating. The practical offers and recommendation on production of master models with the use of FDM technology allowing one to reach indicators of durability, exceeding 2000 cycles of moulding in foundry sand mix, are described.

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

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.

My Corporis Fabrica Embryo: An ontology-based 3D spatio-temporal modeling of human embryo development.

PubMed

Rabattu, Pierre-Yves; Massé, Benoit; Ulliana, Federico; Rousset, Marie-Christine; Rohmer, Damien; Léon, Jean-Claude; Palombi, Olivier

2015-01-01

Embryology is a complex morphologic discipline involving a set of entangled mechanisms, sometime difficult to understand and to visualize. Recent computer based techniques ranging from geometrical to physically based modeling are used to assist the visualization and the simulation of virtual humans for numerous domains such as surgical simulation and learning. On the other side, the ontology-based approach applied to knowledge representation is more and more successfully adopted in the life-science domains to formalize biological entities and phenomena, thanks to a declarative approach for expressing and reasoning over symbolic information. 3D models and ontologies are two complementary ways to describe biological entities that remain largely separated. Indeed, while many ontologies providing a unified formalization of anatomy and embryology exist, they remain only descriptive and make the access to anatomical content of complex 3D embryology models and simulations difficult. In this work, we present a novel ontology describing the development of the human embryology deforming 3D models. Beyond describing how organs and structures are composed, our ontology integrates a procedural description of their 3D representations, temporal deformation and relations with respect to their developments. We also created inferences rules to express complex connections between entities. It results in a unified description of both the knowledge of the organs deformation and their 3D representations enabling to visualize dynamically the embryo deformation during the Carnegie stages. Through a simplified ontology, containing representative entities which are linked to spatial position and temporal process information, we illustrate the added-value of such a declarative approach for interactive simulation and visualization of 3D embryos. Combining ontologies and 3D models enables a declarative description of different embryological models that capture the complexity of human

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…

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.

Development of an Ontology for Occupational Exposure

EPA Science Inventory

When discussing a scientific domain, the use of a common language is required, particularly when communicating across disciplines. This common language, or ontology, is a prescribed vocabulary and a web of contextual relationships within the vocabulary that describe the given dom...

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

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

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

PubMed

Cui, Licong

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

Measuring the level of activity in community built bio-ontologies.

PubMed

Malone, James; Stevens, Robert

2013-02-01

In this paper we explore the measurement of activity in ontology projects as an aspect of community ontology building. When choosing whether to use an ontology or whether to participate in its development, having some knowledge of how actively that ontology is developed is an important issue. Our knowledge of biology grows and changes and an ontology must adapt to keep pace with those changes and also adapt with respect to other ontologies and organisational principles. In essence, we need to know if there is an 'active' community involved with a project or whether a given ontology is inactive or moribund. We explore the use of additions, deletions and changes to ontology files, the regularity and frequency of releases, and the number of ontology repository updates to an ontology as the basis for measuring activity in an ontology. We present our results of this study, which show a dramatic range of activity across some of the more prominent community ontologies, illustrating very active and mature efforts through to those which appear to have become dormant for a number of possible reasons. We show that global activity within the community has remained at a similar level over the last 2 years. Measuring additions, deletions and changes, together with release frequency, appear to be useful metrics of activity and useful pointers towards future behaviour. Measuring who is making edits to ontologies is harder to capture; this raises issues of record keeping in ontology projects and in micro-credit, although we have identified one ontologist that appears influential across many community efforts; a Super-Ontologist. We also discuss confounding factors in our activity metric and discuss how it can be improved and adopted as an assessment criterion for community ontology development. Overall, we show that it is possible to objectively measure the activity in an ontology and to make some prediction about future activity. Copyright © 2012 Elsevier Inc. All rights reserved.

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

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.

A four stage approach for ontology-based health information system design.

PubMed

Kuziemsky, Craig E; Lau, Francis

2010-11-01

To describe and illustrate a four stage methodological approach to capture user knowledge in a biomedical domain area, use that knowledge to design an ontology, and then implement and evaluate the ontology as a health information system (HIS). A hybrid participatory design-grounded theory (GT-PD) method was used to obtain data and code them for ontology development. Prototyping was used to implement the ontology as a computer-based tool. Usability testing evaluated the computer-based tool. An empirically derived domain ontology and set of three problem-solving approaches were developed as a formalized model of the concepts and categories from the GT coding. The ontology and problem-solving approaches were used to design and implement a HIS that tested favorably in usability testing. The four stage approach illustrated in this paper is useful for designing and implementing an ontology as the basis for a HIS. The approach extends existing ontology development methodologies by providing an empirical basis for theory incorporated into ontology design. Copyright © 2010 Elsevier B.V. All rights reserved.

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…

SOUTHWEST VIEW OF FOUNDRY FROM TOP OF GREY IRON CUPOLA ...

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

SOUTHWEST VIEW OF FOUNDRY FROM TOP OF GREY IRON CUPOLA SHOWING OPENED TOP OF CUPOLA WITH EMISSION RECOVERY DUCT COMING OFF. TO THE RIGHT IS THE STORAGE AND SHIPPING BUILDING. - Stockham Pipe & Fittings Company, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

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

Occupational brain cancer risks in Umbria (Italy), with a particular focus on steel foundry workers.

PubMed

Oddone, Enrico; Scaburri, Alessandra; Bai, Edoardo; Modonesi, Carlo; Stracci, Fabrizio; Marchionna, Giuliano; Crosignani, Paolo; Imbriani, Marcello

2014-01-01

As a part of the Occupational Cancer Monitoring (OCCAM) project, a routine analysis based on Umbria region cancer registry (RTUP) database in 2002-2008 was performed. Among other results, the incidental finding of brain cancer increased risk in steel foundry workers in Terni province (Italy), lead us to deepen the analysis, focusing on this specific industrial sector. A monitoring study, based on Umbria Regional Cancer Registry data, was recently carried out. Brain cancer cases and controls identified within this preliminary study were selected. Therefore, we considered all incident cases (in Umbria region 2002-2008) of brain cancer occurred among workers occupied for at least one year in private companies since 1974 and controls randomly sampled from the same population. Afterwards, taking in to account results from steel foundry in Terni province, we further deepened our analysis, focusing on this productive sector. Odds ratios (ORs) and corresponding 90% confidence intervals (CIs) were calculated using multiple logistic regression models, adjusted by age at diagnosis or sampling, sex and province of residence, when appropriate. Statistical analyses were carried out on 14913 subjects, 56 cases and 14857 controls. Significantly increased ORs were observed for garment, mechanical manufacturing and chemical industries. Moreover, the risk estimates were strongly correlated with exposures in iron and steel foundries and a cluster of 14 cases in the same foundry in Terni was observed (OR 9.59, 90% CI 2.76-33.34). Results of this explorative study showed increased ORs of brain cancer in some productive branches, involving possible exposures to chemical compounds and/or solvents. Moreover, our results pointed out a significantly increased risk in Terni foundry workers, determining an interesting brain cancer cluster (14 cases). Further studies on this industrial sector are needed with improved definitions of tasks and exposures.

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.

Pitfalls of Ontology in Medicine.

PubMed

Aldosari, Bakheet; Alanazi, Abdullah; Househ, Mowafa

2017-01-01

Much research has been done in the last few decades in clinical research, medicine, life sciences, etc. leading to an exponential increase in the generation of data. Managing this vast information not only requires integration of the data, but also a means to analyze, relate, and retrieve it. Ontology, in the field of medicine, describes the concepts of medical terminologies and the relation between them, thus, enabling the sharing of medical knowledge. Ontology-based analyses are associated with a risk that errors in modeling may deteriorate the results' quality. Identifying flawed practices or anomalies in ontologies is a crucial issue to be addressed by researchers. In this paper, we review the negative sides of ontology in the field of medicine. Our study results show that ontologies are perceived as a mere tool to represent medical knowledge, thus relying more on the computer science-based understanding of medical terms. While this approach may be sufficient for data entry systems, in which the users merely need to browse the hierarchy and select relevant terms, it may not suffice the real-world scenario of dealing with complex patient records, which are not only grammatically complex, but also are sometimes documented in many native languages. In conclusion, more research is required in identifying poor practices and anomalies in the development of ontologies by computer scientists within the field of medicine.

Studies on Experimental Ontology and Knowledge Service Development in Bio-Environmental Engineering

NASA Astrophysics Data System (ADS)

Zhang, Yunliang

2018-01-01

The existing domain-related ontology and information service patterns are analyzed, and the main problems faced by the experimental scheme knowledge service were clarified. The ontology framework model for knowledge service of Bio-environmental Engineering was proposed from the aspects of experimental materials, experimental conditions and experimental instruments, and this ontology will be combined with existing knowledge organization systems to organize scientific and technological literatures, data and experimental schemes. With the similarity and priority calculation, it can improve the related domain research.

Methodology to build medical ontology from textual resources.

PubMed

Baneyx, Audrey; Charlet, Jean; Jaulent, Marie-Christine

2006-01-01

In the medical field, it is now established that the maintenance of unambiguous thesauri goes through ontologies. Our research task is to help pneumologists code acts and diagnoses with a software that represents medical knowledge through a domain ontology. In this paper, we describe our general methodology aimed at knowledge engineers in order to build various types of medical ontologies based on terminology extraction from texts. The hypothesis is to apply natural language processing tools to textual patient discharge summaries to develop the resources needed to build an ontology in pneumology. Results indicate that the joint use of distributional analysis and lexico-syntactic patterns performed satisfactorily for building such ontologies.

Improving the interoperability of biomedical ontologies with compound alignments.

PubMed

Oliveira, Daniela; Pesquita, Catia

2018-01-09

Ontologies are commonly used to annotate and help process life sciences data. Although their original goal is to facilitate integration and interoperability among heterogeneous data sources, when these sources are annotated with distinct ontologies, bridging this gap can be challenging. In the last decade, ontology matching systems have been evolving and are now capable of producing high-quality mappings for life sciences ontologies, usually limited to the equivalence between two ontologies. However, life sciences research is becoming increasingly transdisciplinary and integrative, fostering the need to develop matching strategies that are able to handle multiple ontologies and more complex relations between their concepts. We have developed ontology matching algorithms that are able to find compound mappings between multiple biomedical ontologies, in the form of ternary mappings, finding for instance that "aortic valve stenosis"(HP:0001650) is equivalent to the intersection between "aortic valve"(FMA:7236) and "constricted" (PATO:0001847). The algorithms take advantage of search space filtering based on partial mappings between ontology pairs, to be able to handle the increased computational demands. The evaluation of the algorithms has shown that they are able to produce meaningful results, with precision in the range of 60-92% for new mappings. The algorithms were also applied to the potential extension of logical definitions of the OBO and the matching of several plant-related ontologies. This work is a first step towards finding more complex relations between multiple ontologies. The evaluation shows that the results produced are significant and that the algorithms could satisfy specific integration needs.

A Systematic Analysis of Term Reuse and Term Overlap across Biomedical Ontologies

PubMed Central

Kamdar, Maulik R.; Tudorache, Tania; Musen, Mark A.

2016-01-01

Reusing ontologies and their terms is a principle and best practice that most ontology development methodologies strongly encourage. Reuse comes with the promise to support the semantic interoperability and to reduce engineering costs. In this paper, we present a descriptive study of the current extent of term reuse and overlap among biomedical ontologies. We use the corpus of biomedical ontologies stored in the BioPortal repository, and analyze different types of reuse and overlap constructs. While we find an approximate term overlap between 25–31%, the term reuse is only <9%, with most ontologies reusing fewer than 5% of their terms from a small set of popular ontologies. Clustering analysis shows that the terms reused by a common set of ontologies have >90% semantic similarity, hinting that ontology developers tend to reuse terms that are sibling or parent–child nodes. We validate this finding by analysing the logs generated from a Protégé plugin that enables developers to reuse terms from BioPortal. We find most reuse constructs were 2-level subtrees on the higher levels of the class hierarchy. We developed a Web application that visualizes reuse dependencies and overlap among ontologies, and that proposes similar terms from BioPortal for a term of interest. We also identified a set of error patterns that indicate that ontology developers did intend to reuse terms from other ontologies, but that they were using different and sometimes incorrect representations. Our results stipulate the need for semi-automated tools that augment term reuse in the ontology engineering process through personalized recommendations. PMID:28819351

From Patient Discharge Summaries to an Ontology for Psychiatry.

PubMed

Richard, Marion; Aimé, Xavier; Jaulent, Marie-Christine; Krebs, Marie-Odile; Charlet, Jean

2017-01-01

Psychiatry aims at detecting symptoms, providing diagnoses and treating mental disorders. We developed ONTOPSYCHIA, an ontology for psychiatry in three modules: social and environmental factors of mental disorders, mental disorders, and treatments. The use of ONTOPSYCHIA, associated with dedicated tools, will facilitate semantic research in Patient Discharge Summaries (PDS). To develop the first module of the ontology we propose a PDS text analysis in order to explicit psychiatry concepts. We decided to set aside classifications during the construction of the modu le, to focus only on the information contained in PDS (bottom-up approach) and to return to domain classifications solely for the enrichment phase (top-down approach). Then, we focused our work on the development of the LOVMI methodology (Les Ontologies Validées par Méthode Interactive - Ontologies Validated by Interactive Method), which aims to provide a methodological framework to validate the structure and the semantic of an ontology.

The mouse-human anatomy ontology mapping project.

PubMed

Hayamizu, Terry F; de Coronado, Sherri; Fragoso, Gilberto; Sioutos, Nicholas; Kadin, James A; Ringwald, Martin

2012-01-01

The overall objective of the Mouse-Human Anatomy Project (MHAP) was to facilitate the mapping and harmonization of anatomical terms used for mouse and human models by Mouse Genome Informatics (MGI) and the National Cancer Institute (NCI). The anatomy resources designated for this study were the Adult Mouse Anatomy (MA) ontology and the set of anatomy concepts contained in the NCI Thesaurus (NCIt). Several methods and software tools were identified and evaluated, then used to conduct an in-depth comparative analysis of the anatomy ontologies. Matches between mouse and human anatomy terms were determined and validated, resulting in a highly curated set of mappings between the two ontologies that has been used by other resources. These mappings will enable linking of data from mouse and human. As the anatomy ontologies have been expanded and refined, the mappings have been updated accordingly. Insights are presented into the overall process of comparing and mapping between ontologies, which may prove useful for further comparative analyses and ontology mapping efforts, especially those involving anatomy ontologies. Finally, issues concerning further development of the ontologies, updates to the mapping files, and possible additional applications and significance were considered. DATABASE URL: http://obofoundry.org/cgi-bin/detail.cgi?id=ma2ncit.

Data-driven Ontology Development: A Case Study at NASA's Atmospheric Science Data Center

NASA Astrophysics Data System (ADS)

Hertz, J.; Huffer, E.; Kusterer, J.

2012-12-01

Well-founded ontologies are key to enabling transformative semantic technologies and accelerating scientific research. One example is semantically enabled search and discovery, making scientific data accessible and more understandable by accurately modeling a complex domain. The ontology creation process remains a challenge for many anxious to pursue semantic technologies. The key may be that the creation process -- whether formal, community-based, automated or semi-automated -- should encompass not only a foundational core and supplemental resources but also a focus on the purpose or mission the ontology is created to support. Are there tools or processes to de-mystify, assess or enhance the resulting ontology? We suggest that comparison and analysis of a domain-focused ontology can be made using text engineering tools for information extraction, tokenizers, named entity transducers and others. The results are analyzed to ensure the ontology reflects the core purpose of the domain's mission and that the ontology integrates and describes the supporting data in the language of the domain - how the science is analyzed and discussed among all users of the data. Commonalities and relationships among domain resources describing the Clouds and Earth's Radiant Energy (CERES) Bi-Directional Scan (BDS) datasets from NASA's Atmospheric Science Data Center are compared. The domain resources include: a formal ontology created for CERES; scientific works such as papers, conference proceedings and notes; information extracted from the datasets (i.e., header metadata); and BDS scientific documentation (Algorithm Theoretical Basis Documents, collection guides, data quality summaries and others). These resources are analyzed using the open source software General Architecture for Text Engineering, a mature framework for computational tasks involving human language.

Mapping between the OBO and OWL ontology languages.

PubMed

Tirmizi, Syed Hamid; Aitken, Stuart; Moreira, Dilvan A; Mungall, Chris; Sequeda, Juan; Shah, Nigam H; Miranker, Daniel P

2011-03-07

Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. NCBO BioPortal currently hosts about 180 different biomedical ontologies. These ontologies have been mainly expressed in either the Open Biomedical Ontology (OBO) format or the Web Ontology Language (OWL). OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content. In comparison, OWL is a Semantic Web language, and is supported by the World Wide Web consortium together with integral query languages, rule languages and distributed infrastructure for information interchange. These features are highly desirable for the OBO content as well. A convenient method for leveraging these features for OBO ontologies is by transforming OBO ontologies to OWL. We have developed a methodology for translating OBO ontologies to OWL using the organization of the Semantic Web itself to guide the work. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Thus we were able to decompose the problem into two parts. Most OBO constructs have easy and obvious equivalence to a construct in OWL. A small subset of OBO constructs requires deeper consideration. We have defined transformations for all constructs in an effort to foster a standard common mapping between OBO and OWL. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. Our Java implementation of the mapping is part of the official Gene Ontology project source. Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge. In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner.

Mapping between the OBO and OWL ontology languages

PubMed Central

2011-01-01

Background Ontologies are commonly used in biomedicine to organize concepts to describe domains such as anatomies, environments, experiment, taxonomies etc. NCBO BioPortal currently hosts about 180 different biomedical ontologies. These ontologies have been mainly expressed in either the Open Biomedical Ontology (OBO) format or the Web Ontology Language (OWL). OBO emerged from the Gene Ontology, and supports most of the biomedical ontology content. In comparison, OWL is a Semantic Web language, and is supported by the World Wide Web consortium together with integral query languages, rule languages and distributed infrastructure for information interchange. These features are highly desirable for the OBO content as well. A convenient method for leveraging these features for OBO ontologies is by transforming OBO ontologies to OWL. Results We have developed a methodology for translating OBO ontologies to OWL using the organization of the Semantic Web itself to guide the work. The approach reveals that the constructs of OBO can be grouped together to form a similar layer cake. Thus we were able to decompose the problem into two parts. Most OBO constructs have easy and obvious equivalence to a construct in OWL. A small subset of OBO constructs requires deeper consideration. We have defined transformations for all constructs in an effort to foster a standard common mapping between OBO and OWL. Our mapping produces OWL-DL, a Description Logics based subset of OWL with desirable computational properties for efficiency and correctness. Our Java implementation of the mapping is part of the official Gene Ontology project source. Conclusions Our transformation system provides a lossless roundtrip mapping for OBO ontologies, i.e. an OBO ontology may be translated to OWL and back without loss of knowledge. In addition, it provides a roadmap for bridging the gap between the two ontology languages in order to enable the use of ontology content in a language independent manner

Interoperability between biomedical ontologies through relation expansion, upper-level ontologies and automatic reasoning.

PubMed

Hoehndorf, Robert; Dumontier, Michel; Oellrich, Anika; Rebholz-Schuhmann, Dietrich; Schofield, Paul N; Gkoutos, Georgios V

2011-01-01

Researchers design ontologies as a means to accurately annotate and integrate experimental data across heterogeneous and disparate data- and knowledge bases. Formal ontologies make the semantics of terms and relations explicit such that automated reasoning can be used to verify the consistency of knowledge. However, many biomedical ontologies do not sufficiently formalize the semantics of their relations and are therefore limited with respect to automated reasoning for large scale data integration and knowledge discovery. We describe a method to improve automated reasoning over biomedical ontologies and identify several thousand contradictory class definitions. Our approach aligns terms in biomedical ontologies with foundational classes in a top-level ontology and formalizes composite relations as class expressions. We describe the semi-automated repair of contradictions and demonstrate expressive queries over interoperable ontologies. Our work forms an important cornerstone for data integration, automatic inference and knowledge discovery based on formal representations of knowledge. Our results and analysis software are available at http://bioonto.de/pmwiki.php/Main/ReasonableOntologies.

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

Concentrations of PCDD/PCDFs and PCBs in spent foundry sands

USDA-ARS?s Scientific Manuscript database

Approximately 10 million tons of spent foundry sand (SFS) are generated in the U.S. each year, and their beneficial use in agricultural and horticultural applications is being considered. Other studies have demonstrated that trace elements are low enough in sands from iron, steel, and aluminum foun...

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.

Extracting Cross-Ontology Weighted Association Rules from Gene Ontology Annotations.

PubMed

Agapito, Giuseppe; Milano, Marianna; Guzzi, Pietro Hiram; Cannataro, Mario

2016-01-01

Gene Ontology (GO) is a structured repository of concepts (GO Terms) that are associated to one or more gene products through a process referred to as annotation. The analysis of annotated data is an important opportunity for bioinformatics. There are different approaches of analysis, among those, the use of association rules (AR) which provides useful knowledge, discovering biologically relevant associations between terms of GO, not previously known. In a previous work, we introduced GO-WAR (Gene Ontology-based Weighted Association Rules), a methodology for extracting weighted association rules from ontology-based annotated datasets. We here adapt the GO-WAR algorithm to mine cross-ontology association rules, i.e., rules that involve GO terms present in the three sub-ontologies of GO. We conduct a deep performance evaluation of GO-WAR by mining publicly available GO annotated datasets, showing how GO-WAR outperforms current state of the art approaches.

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

Proposed actions are no actions: re-modeling an ontology design pattern with a realist top-level ontology.

PubMed

Seddig-Raufie, Djamila; Jansen, Ludger; Schober, Daniel; Boeker, Martin; Grewe, Niels; Schulz, Stefan

2012-09-21

Ontology Design Patterns (ODPs) are representational artifacts devised to offer solutions for recurring ontology design problems. They promise to enhance the ontology building process in terms of flexibility, re-usability and expansion, and to make the result of ontology engineering more predictable. In this paper, we analyze ODP repositories and investigate their relation with upper-level ontologies. In particular, we compare the BioTop upper ontology to the Action ODP from the NeOn an ODP repository. In view of the differences in the respective approaches, we investigate whether the Action ODP can be embedded into BioTop. We demonstrate that this requires re-interpreting the meaning of classes of the NeOn Action ODP in the light of the precepts of realist ontologies. As a result, the re-design required clarifying the ontological commitment of the ODP classes by assigning them to top-level categories. Thus, ambiguous definitions are avoided. Classes of real entities are clearly distinguished from classes of information artifacts. The proposed approach avoids the commitment to the existence of unclear future entities which underlies the NeOn Action ODP. Our re-design is parsimonious in the sense that existing BioTop content proved to be largely sufficient to define the different types of actions and plans. The proposed model demonstrates that an expressive upper-level ontology provides enough resources and expressivity to represent even complex ODPs, here shown with the different flavors of Action as proposed in the NeOn ODP. The advantage of ODP inclusion into a top-level ontology is the given predetermined dependency of each class, an existing backbone structure and well-defined relations. Our comparison shows that the use of some ODPs is more likely to cause problems for ontology developers, rather than to guide them. Besides the structural properties, the explanation of classification results were particularly hard to grasp for 'self-sufficient' ODPs as

The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics

PubMed Central

Cooper, Laurel; Meier, Austin; Laporte, Marie-Angélique; Elser, Justin L; Mungall, Chris; Sinn, Brandon T; Cavaliere, Dario; Carbon, Seth; Dunn, Nathan A; Smith, Barry; Qu, Botong; Preece, Justin; Zhang, Eugene; Todorovic, Sinisa; Gkoutos, Georgios; Doonan, John H; Stevenson, Dennis W; Arnaud, Elizabeth

2018-01-01

Abstract The Planteome project (http://www.planteome.org) provides a suite of reference and species-specific ontologies for plants and annotations to genes and phenotypes. Ontologies serve as common standards for semantic integration of a large and growing corpus of plant genomics, phenomics and genetics data. The reference ontologies include the Plant Ontology, Plant Trait Ontology and the Plant Experimental Conditions Ontology developed by the Planteome project, along with the Gene Ontology, Chemical Entities of Biological Interest, Phenotype and Attribute Ontology, and others. The project also provides access to species-specific Crop Ontologies developed by various plant breeding and research communities from around the world. We provide integrated data on plant traits, phenotypes, and gene function and expression from 95 plant taxa, annotated with reference ontology terms. The Planteome project is developing a plant gene annotation platform; Planteome Noctua, to facilitate community engagement. All the Planteome ontologies are publicly available and are maintained at the Planteome GitHub site (https://github.com/Planteome) for sharing, tracking revisions and new requests. The annotated data are freely accessible from the ontology browser (http://browser.planteome.org/amigo) and our data repository. PMID:29186578

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

PubMed Central

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. PMID:22737162

Exploring biomedical ontology mappings with graph theory methods.

PubMed

Kocbek, Simon; Kim, Jin-Dong

2017-01-01

In the era of semantic web, life science ontologies play an important role in tasks such as annotating biological objects, linking relevant data pieces, and verifying data consistency. Understanding ontology structures and overlapping ontologies is essential for tasks such as ontology reuse and development. We present an exploratory study where we examine structure and look for patterns in BioPortal, a comprehensive publicly available repository of live science ontologies. We report an analysis of biomedical ontology mapping data over time. We apply graph theory methods such as Modularity Analysis and Betweenness Centrality to analyse data gathered at five different time points. We identify communities, i.e., sets of overlapping ontologies, and define similar and closest communities. We demonstrate evolution of identified communities over time and identify core ontologies of the closest communities. We use BioPortal project and category data to measure community coherence. We also validate identified communities with their mutual mentions in scientific literature. With comparing mapping data gathered at five different time points, we identified similar and closest communities of overlapping ontologies, and demonstrated evolution of communities over time. Results showed that anatomy and health ontologies tend to form more isolated communities compared to other categories. We also showed that communities contain all or the majority of ontologies being used in narrower projects. In addition, we identified major changes in mapping data after migration to BioPortal Version 4.

Biomedical ontologies: toward scientific debate.

PubMed

Maojo, V; Crespo, J; García-Remesal, M; de la Iglesia, D; Perez-Rey, D; Kulikowski, C

2011-01-01

Biomedical ontologies have been very successful in structuring knowledge for many different applications, receiving widespread praise for their utility and potential. Yet, the role of computational ontologies in scientific research, as opposed to knowledge management applications, has not been extensively discussed. We aim to stimulate further discussion on the advantages and challenges presented by biomedical ontologies from a scientific perspective. We review various aspects of biomedical ontologies going beyond their practical successes, and focus on some key scientific questions in two ways. First, we analyze and discuss current approaches to improve biomedical ontologies that are based largely on classical, Aristotelian ontological models of reality. Second, we raise various open questions about biomedical ontologies that require further research, analyzing in more detail those related to visual reasoning and spatial ontologies. We outline significant scientific issues that biomedical ontologies should consider, beyond current efforts of building practical consensus between them. For spatial ontologies, we suggest an approach for building "morphospatial" taxonomies, as an example that could stimulate research on fundamental open issues for biomedical ontologies. Analysis of a large number of problems with biomedical ontologies suggests that the field is very much open to alternative interpretations of current work, and in need of scientific debate and discussion that can lead to new ideas and research directions.

Ontology-Driven Business Modelling: Improving the Conceptual Representation of the REA Ontology

NASA Astrophysics Data System (ADS)

Gailly, Frederik; Poels, Geert

Business modelling research is increasingly interested in exploring how domain ontologies can be used as reference models for business models. The Resource Event Agent (REA) ontology is a primary candidate for ontology-driven modelling of business processes because the REA point of view on business reality is close to the conceptual modelling perspective on business models. In this paper Ontology Engineering principles are employed to reengineer REA in order to make it more suitable for ontology-driven business modelling. The new conceptual representation of REA that we propose uses a single representation formalism, includes a more complete domain axiomatizat-ion (containing definitions of concepts, concept relations and ontological axioms), and is proposed as a generic model that can be instantiated to create valid business models. The effects of these proposed improvements on REA-driven business modelling are demonstrated using a business modelling example.

Development of an Ontology to Model Medical Errors, Information Needs, and the Clinical Communication Space

PubMed Central

Stetson, Peter D.; McKnight, Lawrence K.; Bakken, Suzanne; Curran, Christine; Kubose, Tate T.; Cimino, James J.

2002-01-01

Medical errors are common, costly and often preventable. Work in understanding the proximal causes of medical errors demonstrates that systems failures predispose to adverse clinical events. Most of these systems failures are due to lack of appropriate information at the appropriate time during the course of clinical care. Problems with clinical communication are common proximal causes of medical errors. We have begun a project designed to measure the impact of wireless computing on medical errors. We report here on our efforts to develop an ontology representing the intersection of medical errors, information needs and the communication space. We will use this ontology to support the collection, storage and interpretation of project data. The ontology’s formal representation of the concepts in this novel domain will help guide the rational deployment of our informatics interventions. A real-life scenario is evaluated using the ontology in order to demonstrate its utility.

What Four Million Mappings Can Tell You about Two Hundred Ontologies

NASA Astrophysics Data System (ADS)

Ghazvinian, Amir; Noy, Natalya F.; Jonquet, Clement; Shah, Nigam; Musen, Mark A.

The field of biomedicine has embraced the Semantic Web probably more than any other field. As a result, there is a large number of biomedical ontologies covering overlapping areas of the field. We have developed BioPortal—an open community-based repository of biomedical ontologies. We analyzed ontologies and terminologies in BioPortal and the Unified Medical Language System (UMLS), creating more than 4 million mappings between concepts in these ontologies and terminologies based on the lexical similarity of concept names and synonyms. We then analyzed the mappings and what they tell us about the ontologies themselves, the structure of the ontology repository, and the ways in which the mappings can help in the process of ontology design and evaluation. For example, we can use the mappings to guide users who are new to a field to the most pertinent ontologies in that field, to identify areas of the domain that are not covered sufficiently by the ontologies in the repository, and to identify which ontologies will serve well as background knowledge in domain-specific tools. While we used a specific (but large) ontology repository for the study, we believe that the lessons we learned about the value of a large-scale set of mappings to ontology users and developers are general and apply in many other domains.

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.

A top-level ontology of functions and its application in the Open Biomedical Ontologies.

PubMed

Burek, Patryk; Hoehndorf, Robert; Loebe, Frank; Visagie, Johann; Herre, Heinrich; Kelso, Janet

2006-07-15

A clear understanding of functions in biology is a key component in accurate modelling of molecular, cellular and organismal biology. Using the existing biomedical ontologies it has been impossible to capture the complexity of the community's knowledge about biological functions. We present here a top-level ontological framework for representing knowledge about biological functions. This framework lends greater accuracy, power and expressiveness to biomedical ontologies by providing a means to capture existing functional knowledge in a more formal manner. An initial major application of the ontology of functions is the provision of a principled way in which to curate functional knowledge and annotations in biomedical ontologies. Further potential applications include the facilitation of ontology interoperability and automated reasoning. A major advantage of the proposed implementation is that it is an extension to existing biomedical ontologies, and can be applied without substantial changes to these domain ontologies. The Ontology of Functions (OF) can be downloaded in OWL format from http://onto.eva.mpg.de/. Additionally, a UML profile and supplementary information and guides for using the OF can be accessed from the same website.

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.

An Ontology Based Approach to Information Security

NASA Astrophysics Data System (ADS)

Pereira, Teresa; Santos, Henrique

The semantically structure of knowledge, based on ontology approaches have been increasingly adopted by several expertise from diverse domains. Recently ontologies have been moved from the philosophical and metaphysics disciplines to be used in the construction of models to describe a specific theory of a domain. The development and the use of ontologies promote the creation of a unique standard to represent concepts within a specific knowledge domain. In the scope of information security systems the use of an ontology to formalize and represent the concepts of security information challenge the mechanisms and techniques currently used. This paper intends to present a conceptual implementation model of an ontology defined in the security domain. The model presented contains the semantic concepts based on the information security standard ISO/IEC_JTC1, and their relationships to other concepts, defined in a subset of the information security domain.

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

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

Food for thought ... A toxicology ontology roadmap.

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

Foreign substances can have a dramatic and unpredictable adverse effect on human health. In the development of new therapeutic agents, it is essential that the potential adverse effects of all candidates be identified as early as possible. The field of predictive toxicology strives to profile the potential for adverse effects of novel chemical substances before they occur, both with traditional in vivo experimental approaches and increasingly through the development of in vitro and computational methods which can supplement and reduce the need for animal testing. To be maximally effective, the field needs access to the largest possible knowledge base of previous toxicology findings, and such results need to be made available in such a fashion so as to be interoperable, comparable, and compatible with standard toolkits. This necessitates the development of open, public, computable, and standardized toxicology vocabularies and ontologies so as to support the applications required by in silico, in vitro, and in vivo toxicology methods and related analysis and reporting activities. Such ontology development will support data management, model building, integrated analysis, validation and reporting, including regulatory reporting and alternative testing submission requirements as required by guidelines such as the REACH legislation, leading to new scientific advances in a mechanistically-based predictive toxicology. Numerous existing ontology and standards initiatives can contribute to the creation of a toxicology ontology supporting the needs of predictive toxicology and risk assessment. Additionally, new ontologies are needed to satisfy practical use cases and scenarios where gaps currently exist. Developing and integrating these resources will require a well-coordinated and sustained effort across numerous stakeholders engaged in a public-private partnership. In this communication, we set out a roadmap for the development of an integrated toxicology ontology

Analysis of total metals in waste molding and core sands from ferrous and non-ferrous foundries.

PubMed

Miguel, Roberto E; Ippolito, James A; Leytem, April B; Porta, Atilio A; Banda Noriega, Roxana B; Dungan, Robert S

2012-11-15

Waste molding and core sands from the foundry industry are successfully being used around the world in geotechnical and soil-related applications. Although waste foundry sands (WFSs) are generally not hazardous in nature, relevant data is currently not available in Argentina. This study aimed to quantify metals in waste molding and core sands from foundries using a variety of metal-binder combinations. Metal concentrations in WFSs were compared to those in virgin silica sands (VSSs), surface soils and soil guidance levels. A total analysis for Ag, Al, Ba, Be, Cd, Co, Cr, Cu, Fe, Mg, Mn, Mo, Ni, Pb, Sb, Te, Tl, V, and Zn was conducted on 96 WFSs and 14 VSSs collected from 17 small and medium-sized foundries. The majority of WFSs analyzed, regardless of metal cast and binder type, contained metal concentrations similar to those found in VSSs and native soils. In several cases where alkyd urethane binder was used, Co and Pb concentrations were elevated in the waste sands. Elevated Cr, Mo, Ni, and Tl concentrations associated with VSSs should not be an issue since these metals are bound within the silica sand matrix. Because of the naturally low metal concentrations found in most WFSs examined in this study, they should not be considered hazardous waste, thus making them available for encapsulated and unencapsulated beneficial use applications. Published by Elsevier Ltd.

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

The Porifera Ontology (PORO): enhancing sponge systematics with an anatomy ontology.

PubMed

Thacker, Robert W; Díaz, Maria Cristina; Kerner, Adeline; Vignes-Lebbe, Régine; Segerdell, Erik; Haendel, Melissa A; Mungall, Christopher J

2014-01-01

Porifera (sponges) are ancient basal metazoans that lack organs. They provide insight into key evolutionary transitions, such as the emergence of multicellularity and the nervous system. In addition, their ability to synthesize unusual compounds offers potential biotechnical applications. However, much of the knowledge of these organisms has not previously been codified in a machine-readable way using modern web standards. The Porifera Ontology is intended as a standardized coding system for sponge anatomical features currently used in systematics. The ontology is available from http://purl.obolibrary.org/obo/poro.owl, or from the project homepage http://porifera-ontology.googlecode.com/. The version referred to in this manuscript is permanently available from http://purl.obolibrary.org/obo/poro/releases/2014-03-06/. By standardizing character representations, we hope to facilitate more rapid description and identification of sponge taxa, to allow integration with other evolutionary database systems, and to perform character mapping across the major clades of sponges to better understand the evolution of morphological features. Future applications of the ontology will focus on creating (1) ontology-based species descriptions; (2) taxonomic keys that use the nested terms of the ontology to more quickly facilitate species identifications; and (3) methods to map anatomical characters onto molecular phylogenies of sponges. In addition to modern taxa, the ontology is being extended to include features of fossil taxa.

OntoPop: An Ontology Population System for the Semantic Web

NASA Astrophysics Data System (ADS)

Thongkrau, Theerayut; Lalitrojwong, Pattarachai

The development of ontology at the instance level requires the extraction of the terms defining the instances from various data sources. These instances then are linked to the concepts of the ontology, and relationships are created between these instances for the next step. However, before establishing links among data, ontology engineers must classify terms or instances from a web document into an ontology concept. The tool for help ontology engineer in this task is called ontology population. The present research is not suitable for ontology development applications, such as long time processing or analyzing large or noisy data sets. OntoPop system introduces a methodology to solve these problems, which comprises two parts. First, we select meaningful features from syntactic relations, which can produce more significant features than any other method. Second, we differentiate feature meaning and reduce noise based on latent semantic analysis. Experimental evaluation demonstrates that the OntoPop works well, significantly out-performing the accuracy of 49.64%, a learning accuracy of 76.93%, and executes time of 5.46 second/instance.

Environmental behavior of cement-based stabilized foundry sludge products incorporating additives.

PubMed

Ruiz, M C; Irabien, A

2004-06-18

A series of experiments were conducted to stabilize the inorganic and organic pollutants in a foundry sludge from a cast iron activity using Portland cement as binder and three different types of additives, organophilic bentonite, lime and coal fly ash. Ecotoxicological and chemical behavior of stabilized mixes of foundry sludge were analyzed to assess the feasibility to immobilize both types of contaminants, all determined on the basis of compliance leaching tests. The incorporation of lime reduces the ecotoxicity of stabilized mixes and enhances stabilization of organic pollutants obtaining better results when a 50% of cement is replaced by lime. However, the alkalinity of lime increases slightly the leached zinc up to concentrations above the limit set under neutral conditions by the European regulations. The addition of organophilic bentonite and coal fly ash can immobilize the phenolic compounds but are inefficient to reduce the ecotoxicity and mobility of zinc of final products.

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.

Biomedicine: an ontological dissection.

PubMed

Baronov, David

2008-01-01

Though ubiquitous across the medical social sciences literature, the term "biomedicine" as an analytical concept remains remarkably slippery. It is argued here that this imprecision is due in part to the fact that biomedicine is comprised of three interrelated ontological spheres, each of which frames biomedicine as a distinct subject of investigation. This suggests that, depending upon one's ontological commitment, the meaning of biomedicine will shift. From an empirical perspective, biomedicine takes on the appearance of a scientific enterprise and is defined as a derivative category of Western science more generally. From an interpretive perspective, biomedicine represents a symbolic-cultural expression whose adherence to the principles of scientific objectivity conceals an ideological agenda. From a conceptual perspective, biomedicine represents an expression of social power that reflects structures of power and privilege within capitalist society. No one perspective exists in isolation and so the image of biomedicine from any one presents an incomplete understanding. It is the mutually-conditioning interrelations between these ontological spheres that account for biomedicine's ongoing development. Thus, the ontological dissection of biomedicine that follows, with particular emphasis on the period of its formal crystallization in the latter nineteenth and early twentieth century, is intended to deepen our understanding of biomedicine as an analytical concept across the medical social sciences literature.

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.

A Unified Anatomy Ontology of the Vertebrate Skeletal System

PubMed Central

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. PMID:23251424

Construction of ontology augmented networks for protein complex prediction.

PubMed

Zhang, Yijia; Lin, Hongfei; Yang, Zhihao; Wang, Jian

2013-01-01

Protein complexes are of great importance in understanding the principles of cellular organization and function. The increase in available protein-protein interaction data, gene ontology and other resources make it possible to develop computational methods for protein complex prediction. Most existing methods focus mainly on the topological structure of protein-protein interaction networks, and largely ignore the gene ontology annotation information. In this article, we constructed ontology augmented networks with protein-protein interaction data and gene ontology, which effectively unified the topological structure of protein-protein interaction networks and the similarity of gene ontology annotations into unified distance measures. After constructing ontology augmented networks, a novel method (clustering based on ontology augmented networks) was proposed to predict protein complexes, which was capable of taking into account the topological structure of the protein-protein interaction network, as well as the similarity of gene ontology annotations. Our method was applied to two different yeast protein-protein interaction datasets and predicted many well-known complexes. The experimental results showed that (i) ontology augmented networks and the unified distance measure can effectively combine the structure closeness and gene ontology annotation similarity; (ii) our method is valuable in predicting protein complexes and has higher F1 and accuracy compared to other competing methods.

40 CFR Table 1 to Subpart Zzzzzz... - Applicability of General Provisions to Aluminum, Copper, and Other Nonferrous Foundries Area Sources

Code of Federal Regulations, 2010 CFR

2010-07-01

... Aluminum, Copper, and Other Nonferrous Foundries Area Sources 1 Table 1 to Subpart ZZZZZZ of Part 63... Standards for Hazardous Air Pollutants: Area Source Standards for Aluminum, Copper, and Other Nonferrous... Provisions to Aluminum, Copper, and Other Nonferrous Foundries Area Sources As required in § 63.11555, “What...

40 CFR Table 1 to Subpart Zzzzzz... - Applicability of General Provisions to Aluminum, Copper, and Other Nonferrous Foundries Area Sources

Code of Federal Regulations, 2011 CFR

2011-07-01

... Aluminum, Copper, and Other Nonferrous Foundries Area Sources 1 Table 1 to Subpart ZZZZZZ of Part 63... Standards for Hazardous Air Pollutants: Area Source Standards for Aluminum, Copper, and Other Nonferrous... Provisions to Aluminum, Copper, and Other Nonferrous Foundries Area Sources As required in § 63.11555, “What...

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…

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

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

Ontology for Structural Geology

NASA Astrophysics Data System (ADS)

Zhong, J.; McGuinness, D. L.; Antonellini, M.; Aydin, A.

2005-12-01

We present our comprehensive process-based ontology for Structural Geology. This ontology covers major domain concepts, especially those related to geological structure type, properties of these structures, their deformation mechanisms, and the factors that control which deformation mechanisms may operate under certain conditions. The structure class in our ontology extends the planetary structure class of the SWEET ontology by providing additional information required for use in the structural geology domain. The classification followed the architectures of structures, such as structure element, set, zone, and pattern. Our deformation mechanism class does not have a corresponding class in SWEET. In our ontology, it has two subclasses, Macro- and Micro- mechanisms. The property class and the factor class are both subclasses of the physical property class of SWEET. Relationships among those concepts are also included in our ontology. For example, the class structure element has properties associated with the deformation mechanisms, descriptive properties such as geometry and morphology, and physical properties of rocks such as strength, compressibility, seismic velocity, porosity, and permeability. The subject matter expertise was provided by domain experts. Additionally, we surveyed text books and journal articles with the goal of evaluating the completeness and correctness of the domain terms and we used logical reasoners and validators to eliminate logical problems. We propose that our ontology provides a reusable extension to the SWEET ontology that may be of value to scientists and lay people interested in structural geology issues. We have also implemented prototype services that utilize this ontology for search.

Alpha spectrometric characterization of process-related particle size distributions from active particle sampling at the Los Alamos National Laboratory uranium foundry

NASA Astrophysics Data System (ADS)

Plionis, A. A.; Peterson, D. S.; Tandon, L.; LaMont, S. P.

2010-03-01

Uranium particles within the respirable size range pose a significant hazard to the health and safety of workers. Significant differences in the deposition and incorporation patterns of aerosols within the respirable range can be identified and integrated into sophisticated health physics models. Data characterizing the uranium particle size distribution resulting from specific foundry-related processes are needed. Using personal air sampling cascade impactors, particles collected from several foundry processes were sorted by activity median aerodynamic diameter onto various Marple substrates. After an initial gravimetric assessment of each impactor stage, the substrates were analyzed by alpha spectrometry to determine the uranium content of each stage. Alpha spectrometry provides rapid non-distructive isotopic data that can distinguish process uranium from natural sources and the degree of uranium contribution to the total accumulated particle load. In addition, the particle size bins utilized by the impactors provide adequate resolution to determine if a process particle size distribution is: lognormal, bimodal, or trimodal. Data on process uranium particle size values and distributions facilitate the development of more sophisticated and accurate models for internal dosimetry, resulting in an improved understanding of foundry worker health and safety.

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

An ontology-driven, diagnostic modeling system.

PubMed

Haug, Peter J; Ferraro, Jeffrey P; Holmen, John; Wu, Xinzi; Mynam, Kumar; Ebert, Matthew; Dean, Nathan; Jones, Jason

2013-06-01

To present a system that uses knowledge stored in a medical ontology to automate the development of diagnostic decision support systems. To illustrate its function through an example focused on the development of a tool for diagnosing pneumonia. We developed a system that automates the creation of diagnostic decision-support applications. It relies on a medical ontology to direct the acquisition of clinic data from a clinical data warehouse and uses an automated analytic system to apply a sequence of machine learning algorithms that create applications for diagnostic screening. We refer to this system as the ontology-driven diagnostic modeling system (ODMS). We tested this system using samples of patient data collected in Salt Lake City emergency rooms and stored in Intermountain Healthcare's enterprise data warehouse. The system was used in the preliminary development steps of a tool to identify patients with pneumonia in the emergency department. This tool was compared with a manually created diagnostic tool derived from a curated dataset. The manually created tool is currently in clinical use. The automatically created tool had an area under the receiver operating characteristic curve of 0.920 (95% CI 0.916 to 0.924), compared with 0.944 (95% CI 0.942 to 0.947) for the manually created tool. Initial testing of the ODMS demonstrates promising accuracy for the highly automated results and illustrates the route to model improvement. The use of medical knowledge, embedded in ontologies, to direct the initial development of diagnostic computing systems appears feasible.

Molten metal burns: further evidence of industrial foundries' failure to comply with Occupational Safety and Health Administration regulations.

PubMed

Faulkner, B C; Drake, D B; Gear, A J; Watkins, F H; Edlich, R F

1997-01-01

The purpose of this report is to describe another case of a molten metal burn to the foot of a foundry worker. The foundry in which he worked failed to comply with Occupational Safety and Health Administration regulations with regard to protective apparel. This injury could have been prevented with annual, unscheduled inspections by the Occupational Safety and Health Administration and with enforcement of additional regulations regarding protective apparel.

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.

Matching biomedical ontologies based on formal concept analysis.

PubMed

Zhao, Mengyi; Zhang, Songmao; Li, Weizhuo; Chen, Guowei

2018-03-19

The goal of ontology matching is to identify correspondences between entities from different yet overlapping ontologies so as to facilitate semantic integration, reuse and interoperability. As a well developed mathematical model for analyzing individuals and structuring concepts, Formal Concept Analysis (FCA) has been applied to ontology matching (OM) tasks since the beginning of OM research, whereas ontological knowledge exploited in FCA-based methods is limited. This motivates the study in this paper, i.e., to empower FCA with as much as ontological knowledge as possible for identifying mappings across ontologies. We propose a method based on Formal Concept Analysis to identify and validate mappings across ontologies, including one-to-one mappings, complex mappings and correspondences between object properties. Our method, called FCA-Map, incrementally generates a total of five types of formal contexts and extracts mappings from the lattices derived. First, the token-based formal context describes how class names, labels and synonyms share lexical tokens, leading to lexical mappings (anchors) across ontologies. Second, the relation-based formal context describes how classes are in taxonomic, partonomic and disjoint relationships with the anchors, leading to positive and negative structural evidence for validating the lexical matching. Third, the positive relation-based context can be used to discover structural mappings. Afterwards, the property-based formal context describes how object properties are used in axioms to connect anchor classes across ontologies, leading to property mappings. Last, the restriction-based formal context describes co-occurrence of classes across ontologies in anonymous ancestors of anchors, from which extended structural mappings and complex mappings can be identified. Evaluation on the Anatomy, the Large Biomedical Ontologies, and the Disease and Phenotype track of the 2016 Ontology Alignment Evaluation Initiative campaign

Towards Agile Ontology Maintenance

NASA Astrophysics Data System (ADS)

Luczak-Rösch, Markus

Ontologies are an appropriate means to represent knowledge on the Web. Research on ontology engineering reached practices for an integrative lifecycle support. However, a broader success of ontologies in Web-based information systems remains unreached while the more lightweight semantic approaches are rather successful. We assume, paired with the emerging trend of services and microservices on the Web, new dynamic scenarios gain momentum in which a shared knowledge base is made available to several dynamically changing services with disparate requirements. Our work envisions a step towards such a dynamic scenario in which an ontology adapts to the requirements of the accessing services and applications as well as the user's needs in an agile way and reduces the experts' involvement in ontology maintenance processes.

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

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.

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

Ontology and Knowledgebase of Fractures and Faults

NASA Astrophysics Data System (ADS)

Aydin, A.; Zhong, J.

2007-12-01

Fractures and faults are related to many societal and industrial problems including oil and gas exploration and production, CO2 sequestration, and waste isolation. Therefore, an ontology focusing fractures and faults is desirable to facilitate a sound education and communication among this highly diverse community. We developed an ontology for this field. Some high level classes in our ontology include geological structure, deformation mechanism, and property or factor. Throughout our ontology, we emphasis the relationship among the classes, such as structures formed by mechanisms and properties effect the mechanism that will occur. At this stage, there are about 1,000 classes, referencing about 150 articles or textbook and supplemented by about 350 photographs, diagrams, and illustrations. With limited time and resources, we chose a simple application for our ontology - transforming to a knowledgebase made of a series of web pages. Each web page corresponds to one class in the ontology, having discussion, figures, links to subclass and related concepts, as well as references. We believe that our knowledgebase is a valuable resource for finding information about fractures and faults, to both practicing geologists and students who are interested in the related issues either in application or in education and training.

Assessment Applications of Ontologies.

ERIC Educational Resources Information Center

Chung, Gregory K. W. K.; Niemi, David; Bewley, William L.

This paper discusses the use of ontologies and their applications to assessment. An ontology provides a shared and common understanding of a domain that can be communicated among people and computational systems. The ontology captures one or more experts' conceptual representation of a domain expressed in terms of concepts and the relationships…

Webulous and the Webulous Google Add-On--a web service and application for ontology building from templates.

PubMed

Jupp, Simon; Burdett, Tony; Welter, Danielle; Sarntivijai, Sirarat; Parkinson, Helen; Malone, James

2016-01-01

Authoring bio-ontologies is a task that has traditionally been undertaken by skilled experts trained in understanding complex languages such as the Web Ontology Language (OWL), in tools designed for such experts. As requests for new terms are made, the need for expert ontologists represents a bottleneck in the development process. Furthermore, the ability to rigorously enforce ontology design patterns in large, collaboratively developed ontologies is difficult with existing ontology authoring software. We present Webulous, an application suite for supporting ontology creation by design patterns. Webulous provides infrastructure to specify templates for populating ontology design patterns that get transformed into OWL assertions in a target ontology. Webulous provides programmatic access to the template server and a client application has been developed for Google Sheets that allows templates to be loaded, populated and resubmitted to the Webulous server for processing. The development and delivery of ontologies to the community requires software support that goes beyond the ontology editor. Building ontologies by design patterns and providing simple mechanisms for the addition of new content helps reduce the overall cost and effort required to develop an ontology. The Webulous system provides support for this process and is used as part of the development of several ontologies at the European Bioinformatics Institute.

Ontology for customer centric digital services and analytics

NASA Astrophysics Data System (ADS)

Keat, Ng Wai; Shahrir, Mohammad Shazri

2017-11-01

In computer science research, ontologies are commonly utilised to create a unified abstract across many rich and different fields. In this paper, we apply the concept to the customer centric domain of digital services analytics and present an analytics solution ontology. The essence is based from traditional Entity Relationship Diagram (ERD), which then was abstracted out to cover wider areas on customer centric digital services. The ontology we developed covers both static aspects (customer identifiers) and dynamic aspects (customer's temporal interactions). The structure of the customer scape is modeled with classes that represent different types of customer touch points, ranging from digital and digital-stamps which represent physical analogies. The dynamic aspects of customer centric digital service are modeled with a set of classes, with the importance is represented in different associations involving establishment and termination of the target interaction. The realized ontology can be used in development of frameworks for customer centric applications, and for specification of common data format used by cooperating digital service applications.

Survey on Ontology Mapping

NASA Astrophysics Data System (ADS)

Zhu, Junwu

To create a sharable semantic space in which the terms from different domain ontology or knowledge system, Ontology mapping become a hot research point in Semantic Web Community. In this paper, motivated factors of ontology mapping research are given firstly, and then 5 dominating theories and methods, such as information accessing technology, machine learning, linguistics, structure graph and similarity, are illustrated according their technology class. Before we analyses the new requirements and takes a long view, the contributions of these theories and methods are summarized in details. At last, this paper suggest to design a group of semantic connector with the ability of migration learning for OWL-2 extended with constrains and the ontology mapping theory of axiom, so as to provide a new methodology for ontology mapping.

Ontology Design of Influential People Identification Using Centrality

NASA Astrophysics Data System (ADS)

Maulana Awangga, Rolly; Yusril, Muhammad; Setyawan, Helmi

2018-04-01

Identifying influential people as a node in a graph theory commonly calculated by social network analysis. The social network data has the user as node and edge as relation forming a friend relation graph. This research is conducting different meaning of every nodes relation in the social network. Ontology was perfect match science to describe the social network data as conceptual and domain. Ontology gives essential relationship in a social network more than a current graph. Ontology proposed as a standard for knowledge representation for the semantic web by World Wide Web Consortium. The formal data representation use Resource Description Framework (RDF) and Web Ontology Language (OWL) which is strategic for Open Knowledge-Based website data. Ontology used in the semantic description for a relationship in the social network, it is open to developing semantic based relationship ontology by adding and modifying various and different relationship to have influential people as a conclusion. This research proposes a model using OWL and RDF for influential people identification in the social network. The study use degree centrality, between ness centrality, and closeness centrality measurement for data validation. As a conclusion, influential people identification in Facebook can use proposed Ontology model in the Group, Photos, Photo Tag, Friends, Events and Works data.

Development and application of an interaction network ontology for literature mining of vaccine-associated gene-gene interactions.

PubMed

Hur, Junguk; Özgür, Arzucan; Xiang, Zuoshuang; He, Yongqun

2015-01-01

Literature mining of gene-gene interactions has been enhanced by ontology-based name classifications. However, in biomedical literature mining, interaction keywords have not been carefully studied and used beyond a collection of keywords. In this study, we report the development of a new Interaction Network Ontology (INO) that classifies >800 interaction keywords and incorporates interaction terms from the PSI Molecular Interactions (PSI-MI) and Gene Ontology (GO). Using INO-based literature mining results, a modified Fisher's exact test was established to analyze significantly over- and under-represented enriched gene-gene interaction types within a specific area. Such a strategy was applied to study the vaccine-mediated gene-gene interactions using all PubMed abstracts. The Vaccine Ontology (VO) and INO were used to support the retrieval of vaccine terms and interaction keywords from the literature. INO is aligned with the Basic Formal Ontology (BFO) and imports terms from 10 other existing ontologies. Current INO includes 540 terms. In terms of interaction-related terms, INO imports and aligns PSI-MI and GO interaction terms and includes over 100 newly generated ontology terms with 'INO_' prefix. A new annotation property, 'has literature mining keywords', was generated to allow the listing of different keywords mapping to the interaction types in INO. Using all PubMed documents published as of 12/31/2013, approximately 266,000 vaccine-associated documents were identified, and a total of 6,116 gene-pairs were associated with at least one INO term. Out of 78 INO interaction terms associated with at least five gene-pairs of the vaccine-associated sub-network, 14 terms were significantly over-represented (i.e., more frequently used) and 17 under-represented based on our modified Fisher's exact test. These over-represented and under-represented terms share some common top-level terms but are distinct at the bottom levels of the INO hierarchy. The analysis of these

Querying archetype-based EHRs by search ontology-based XPath engineering.

PubMed

Kropf, Stefan; Uciteli, Alexandr; Schierle, Katrin; Krücken, Peter; Denecke, Kerstin; Herre, Heinrich

2018-05-11

Legacy data and new structured data can be stored in a standardized format as XML-based EHRs on XML databases. Querying documents on these databases is crucial for answering research questions. Instead of using free text searches, that lead to false positive results, the precision can be increased by constraining the search to certain parts of documents. A search ontology-based specification of queries on XML documents defines search concepts and relates them to parts in the XML document structure. Such query specification method is practically introduced and evaluated by applying concrete research questions formulated in natural language on a data collection for information retrieval purposes. The search is performed by search ontology-based XPath engineering that reuses ontologies and XML-related W3C standards. The key result is that the specification of research questions can be supported by the usage of search ontology-based XPath engineering. A deeper recognition of entities and a semantic understanding of the content is necessary for a further improvement of precision and recall. Key limitation is that the application of the introduced process requires skills in ontology and software development. In future, the time consuming ontology development could be overcome by implementing a new clinical role: the clinical ontologist. The introduced Search Ontology XML extension connects Search Terms to certain parts in XML documents and enables an ontology-based definition of queries. Search ontology-based XPath engineering can support research question answering by the specification of complex XPath expressions without deep syntax knowledge about XPaths.

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

PubMed Central

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 PMID:25052702

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…

Gene Ontology-Based Analysis of Zebrafish Omics Data Using the Web Tool Comparative Gene Ontology.

PubMed

Ebrahimie, Esmaeil; Fruzangohar, Mario; Moussavi Nik, Seyyed Hani; Newman, Morgan

2017-10-01

Gene Ontology (GO) analysis is a powerful tool in systems biology, which uses a defined nomenclature to annotate genes/proteins within three categories: "Molecular Function," "Biological Process," and "Cellular Component." GO analysis can assist in revealing functional mechanisms underlying observed patterns in transcriptomic, genomic, and proteomic data. The already extensive and increasing use of zebrafish for modeling genetic and other diseases highlights the need to develop a GO analytical tool for this organism. The web tool Comparative GO was originally developed for GO analysis of bacterial data in 2013 ( www.comparativego.com ). We have now upgraded and elaborated this web tool for analysis of zebrafish genetic data using GOs and annotations from the Gene Ontology Consortium.

iSMART: Ontology-based Semantic Query of CDA Documents

PubMed Central

Liu, Shengping; Ni, Yuan; Mei, Jing; Li, Hanyu; Xie, Guotong; Hu, Gang; Liu, Haifeng; Hou, Xueqiao; Pan, Yue

2009-01-01

The Health Level 7 Clinical Document Architecture (CDA) is widely accepted as the format for electronic clinical document. With the rich ontological references in CDA documents, the ontology-based semantic query could be performed to retrieve CDA documents. In this paper, we present iSMART (interactive Semantic MedicAl Record reTrieval), a prototype system designed for ontology-based semantic query of CDA documents. The clinical information in CDA documents will be extracted into RDF triples by a declarative XML to RDF transformer. An ontology reasoner is developed to infer additional information by combining the background knowledge from SNOMED CT ontology. Then an RDF query engine is leveraged to enable the semantic queries. This system has been evaluated using the real clinical documents collected from a large hospital in southern China. PMID:20351883

Deafblindness, ontological security, and social recognition.

PubMed

Danermark, Berth D; Möller, Kerstin

2008-11-01

Trust, ontological security, and social recognition are discussed in relation to self-identity among people with acquired deafblindness. To date the phenomenon has not been elaborated in the context of deafblindness. When a person with deafblindness interacts with the social and material environment, the reliability, constancy, and predictability of his or her relations is crucial for maintaining or achieving ontological security or a general and fairly persistent feeling of well-being. When these relations fundamentally change, the impact on ontological security will be very negative. The construction of social recognition through the interaction between the self and others is embodied across three dimensions: at the individual level, at the legal systems level, and at the normative or value level. The relationship between trust and ontological security on the one hand and social recognition on the other hand is discussed. It is argued that these basic processes affecting personality development have to be identified and acknowledged in the interactions people with deafblindness experience. Some implications for the rehabilitation of people with acquired deafblindness are presented and illustrated.

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.

Evaluation of research in biomedical ontologies

PubMed Central

Dumontier, Michel; Gkoutos, Georgios V.

2013-01-01

Ontologies are now pervasive in biomedicine, where they serve as a means to standardize terminology, to enable access to domain knowledge, to verify data consistency and to facilitate integrative analyses over heterogeneous biomedical data. For this purpose, research on biomedical ontologies applies theories and methods from diverse disciplines such as information management, knowledge representation, cognitive science, linguistics and philosophy. Depending on the desired applications in which ontologies are being applied, the evaluation of research in biomedical ontologies must follow different strategies. Here, we provide a classification of research problems in which ontologies are being applied, focusing on the use of ontologies in basic and translational research, and we demonstrate how research results in biomedical ontologies can be evaluated. The evaluation strategies depend on the desired application and measure the success of using an ontology for a particular biomedical problem. For many applications, the success can be quantified, thereby facilitating the objective evaluation and comparison of research in biomedical ontology. The objective, quantifiable comparison of research results based on scientific applications opens up the possibility for systematically improving the utility of ontologies in biomedical research. PMID:22962340

Lung function and functional capacity among foundry workers using effective risk control measures.

PubMed

Bernardes, Rosane Andrea Bretas; Chiavegato, Luciana Dias; de Moraes, Mônica Vasconcelos; Negreiros, Alexandher; Padula, Rosimeire Simprini

2015-01-01

Inhaled dust in the environment can trigger specific reactions in the airways and cause various respiratory diseases. Evaluate the lung function and functional capacity of foundry workers who are exposed to metals and use effective control measures. A cross-sectional study was realized with 108 workers at a bronze foundry and machining plant and in maintenance at a private university, both in Brazil. The workers were divided into two groups: the study group exposed to metals but using risk control measues and a control group not exposed to metal work. The Medical Research Council Questionnaire on Respiratory Symptoms and the International Physical Activity Questionnaire were administered, and lung function and functional capacity were evaluated. Comparative statistics were used to identify differences in the outcome measures between the two groups. The groups had similar personal and anthropometric characteristics and time on the job. Spirometry and peak expiratory flow presented no significant differences between the groups. And there was also no statistically significant difference between groups in functional capacity as assessed by performance on the six-minute walk test. Foundry industry workers in Brazil who were exposed to metal but used risk control measures had similar lung function and functional capacity when compared to the control group who were not exposed to metal. This is a positive results and maybe related to age, time exposure and control of occupational hazards. However, these workers need to continue being monitored in longitudinal studies.

Integrating systems biology models and biomedical ontologies

PubMed Central

2011-01-01

Background Systems biology is an approach to biology that emphasizes the structure and dynamic behavior of biological systems and the interactions that occur within them. To succeed, systems biology crucially depends on the accessibility and integration of data across domains and levels of granularity. Biomedical ontologies were developed to facilitate such an integration of data and are often used to annotate biosimulation models in systems biology. Results We provide a framework to integrate representations of in silico systems biology with those of in vivo biology as described by biomedical ontologies and demonstrate this framework using the Systems Biology Markup Language. We developed the SBML Harvester software that automatically converts annotated SBML models into OWL and we apply our software to those biosimulation models that are contained in the BioModels Database. We utilize the resulting knowledge base for complex biological queries that can bridge levels of granularity, verify models based on the biological phenomenon they represent and provide a means to establish a basic qualitative layer on which to express the semantics of biosimulation models. Conclusions We establish an information flow between biomedical ontologies and biosimulation models and we demonstrate that the integration of annotated biosimulation models and biomedical ontologies enables the verification of models as well as expressive queries. Establishing a bi-directional information flow between systems biology and biomedical ontologies has the potential to enable large-scale analyses of biological systems that span levels of granularity from molecules to organisms. PMID:21835028

Ontology-Based Retrieval of Spatially Related Objects for Location Based Services

NASA Astrophysics Data System (ADS)

Haav, Hele-Mai; Kaljuvee, Aivi; Luts, Martin; Vajakas, Toivo

Advanced Location Based Service (LBS) applications have to integrate information stored in GIS, information about users' preferences (profile) as well as contextual information and information about application itself. Ontology engineering provides methods to semantically integrate several data sources. We propose an ontology-driven LBS development framework: the paper describes the architecture of ontologies and their usage for retrieval of spatially related objects relevant to the user. Our main contribution is to enable personalised ontology driven LBS by providing a novel approach for defining personalised semantic spatial relationships by means of ontologies. The approach is illustrated by an industrial case study.

Ontology-based specification, identification and analysis of perioperative risks.

PubMed

Uciteli, Alexandr; Neumann, Juliane; Tahar, Kais; Saleh, Kutaiba; Stucke, Stephan; Faulbrück-Röhr, Sebastian; Kaeding, André; Specht, Martin; Schmidt, Tobias; Neumuth, Thomas; Besting, Andreas; Stegemann, Dominik; Portheine, Frank; Herre, Heinrich

2017-09-06

Medical personnel in hospitals often works under great physical and mental strain. In medical decision-making, errors can never be completely ruled out. Several studies have shown that between 50 and 60% of adverse events could have been avoided through better organization, more attention or more effective security procedures. Critical situations especially arise during interdisciplinary collaboration and the use of complex medical technology, for example during surgical interventions and in perioperative settings (the period of time before, during and after surgical intervention). In this paper, we present an ontology and an ontology-based software system, which can identify risks across medical processes and supports the avoidance of errors in particular in the perioperative setting. We developed a practicable definition of the risk notion, which is easily understandable by the medical staff and is usable for the software tools. Based on this definition, we developed a Risk Identification Ontology (RIO) and used it for the specification and the identification of perioperative risks. An agent system was developed, which gathers risk-relevant data during the whole perioperative treatment process from various sources and provides it for risk identification and analysis in a centralized fashion. The results of such an analysis are provided to the medical personnel in form of context-sensitive hints and alerts. For the identification of the ontologically specified risks, we developed an ontology-based software module, called Ontology-based Risk Detector (OntoRiDe). About 20 risks relating to cochlear implantation (CI) have already been implemented. Comprehensive testing has indicated the correctness of the data acquisition, risk identification and analysis components, as well as the web-based visualization of results.

Supporting ontology adaptation and versioning based on a graph of relevance

NASA Astrophysics Data System (ADS)

Sassi, Najla; Jaziri, Wassim; Alharbi, Saad

2016-11-01

Ontologies recently have become a topic of interest in computer science since they are seen as a semantic support to explicit and enrich data-models as well as to ensure interoperability of data. Moreover, supporting ontology adaptation becomes essential and extremely important, mainly when using ontologies in changing environments. An important issue when dealing with ontology adaptation is the management of several versions. Ontology versioning is a complex and multifaceted problem as it should take into account change management, versions storage and access, consistency issues, etc. The purpose of this paper is to propose an approach and tool for ontology adaptation and versioning. A series of techniques are proposed to 'safely' evolve a given ontology and produce a new consistent version. The ontology versions are ordered in a graph according to their relevance. The relevance is computed based on four criteria: conceptualisation, usage frequency, abstraction and completeness. The techniques to carry out the versioning process are implemented in the Consistology tool, which has been developed to assist users in expressing adaptation requirements and managing ontology versions.

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…

Ontology-supported research on vaccine efficacy, safety and integrative biological networks.

PubMed

He, Yongqun

2014-07-01

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 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.

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

Using ontologies for structuring organizational knowledge in Home Care assistance.

PubMed

Valls, Aida; Gibert, Karina; Sánchez, David; Batet, Montserrat

2010-05-01

-health application running on a real scenario, showed that the ontology design and its exploitation brought several benefits with regards to flexibility, adaptability and work efficiency from the end-user point of view; for the maintenance stage, two software tools are presented, aimed to address the incorporation and modification of healthcare units and the personalization of ontological profiles. The paper shows that the ontological paradigm and the expressiveness of modern ontology languages can be exploited not only to represent terminology in a non-ambiguous way, but also to formalize the interrelations and organizational structures involved in a real and distributed healthcare environment. This kind of ontologies facilitates the adaptation in front of changes in the healthcare organization or Care Units, supports the creation of profile-based interaction models in a transparent and seamless way, and increases the reusability and generality of the developed software components. As a conclusion of the exploitation of the developed ontology in a real medical scenario, we can say that an ontology formalizing organizational interrelations is a key component for building effective distributed knowledge-driven e-health systems. Copyright 2010 Elsevier Ireland Ltd. All rights reserved.

Evaluating Health Information Systems Using Ontologies.

PubMed

Eivazzadeh, Shahryar; Anderberg, Peter; Larsson, Tobias C; Fricker, Samuel A; Berglund, Johan

2016-06-16

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. 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. 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 deployed across European Union

Evolutionary characters, phenotypes and ontologies: curating data from the systematic biology literature.

PubMed

Dahdul, Wasila M; Balhoff, James P; Engeman, Jeffrey; Grande, Terry; Hilton, Eric J; Kothari, Cartik; Lapp, Hilmar; Lundberg, John G; Midford, Peter E; Vision, Todd J; Westerfield, Monte; Mabee, Paula M

2010-05-20

The wealth of phenotypic descriptions documented in the published articles, monographs, and dissertations of phylogenetic systematics is traditionally reported in a free-text format, and it is therefore largely inaccessible for linkage to biological databases for genetics, development, and phenotypes, and difficult to manage for large-scale integrative work. The Phenoscape project aims to represent these complex and detailed descriptions with rich and formal semantics that are amenable to computation and integration with phenotype data from other fields of biology. This entails reconceptualizing the traditional free-text characters into the computable Entity-Quality (EQ) formalism using ontologies. We used ontologies and the EQ formalism to curate a collection of 47 phylogenetic studies on ostariophysan fishes (including catfishes, characins, minnows, knifefishes) and their relatives with the goal of integrating these complex phenotype descriptions with information from an existing model organism database (zebrafish, http://zfin.org). We developed a curation workflow for the collection of character, taxonomic and specimen data from these publications. A total of 4,617 phenotypic characters (10,512 states) for 3,449 taxa, primarily species, were curated into EQ formalism (for a total of 12,861 EQ statements) using anatomical and taxonomic terms from teleost-specific ontologies (Teleost Anatomy Ontology and Teleost Taxonomy Ontology) in combination with terms from a quality ontology (Phenotype and Trait Ontology). Standards and guidelines for consistently and accurately representing phenotypes were developed in response to the challenges that were evident from two annotation experiments and from feedback from curators. The challenges we encountered and many of the curation standards and methods for improving consistency that we developed are generally applicable to any effort to represent phenotypes using ontologies. This is because an ontological representation of

Light-Weighted Automatic Import of Standardized Ontologies into the Content Management System Drupal.

PubMed

Beger, Christoph; Uciteli, Alexandr; Herre, Heinrich

2017-01-01

The amount of ontologies, which are utilizable for widespread domains, is growing steadily. BioPortal alone, embraces over 500 published ontologies with nearly 8 million classes. In contrast, the vast informative content of these ontologies is only directly intelligible by experts. To overcome this deficiency it could be possible to represent ontologies as web portals, which does not require knowledge about ontologies and their semantics, but still carries as much information as possible to the end-user. Furthermore, the conception of a complex web portal is a sophisticated process. Many entities must be analyzed and linked to existing terminologies. Ontologies are a decent solution for gathering and storing this complex data and dependencies. Hence, automated imports of ontologies into web portals could support both mentioned scenarios. The Content Management System (CMS) Drupal 8 is one of many solutions to develop web presentations with less required knowledge about programming languages and it is suitable to represent ontological entities. We developed the Drupal Upper Ontology (DUO), which models concepts of Drupal's architecture, such as nodes, vocabularies and links. DUO can be imported into ontologies to map their entities to Drupal's concepts. Because of Drupal's lack of import capabilities, we implemented the Simple Ontology Loader in Drupal (SOLID), a Drupal 8 module, which allows Drupal administrators to import ontologies based on DUO. Our module generates content in Drupal from existing ontologies and makes it accessible by the general public. Moreover Drupal offers a tagging system which may be amplified with multiple standardized and established terminologies by importing them with SOLID. Our Drupal module shows that ontologies can be used to model content of a CMS and vice versa CMS are suitable to represent ontologies in a user-friendly way. Ontological entities are presented to the user as discrete pages with all appropriate properties, links and

Modulated evaluation metrics for drug-based ontologies.

PubMed

Amith, Muhammad; Tao, Cui

2017-04-24

Research for ontology evaluation is scarce. If biomedical ontological datasets and knowledgebases are to be widely used, there needs to be quality control and evaluation for the content and structure of the ontology. This paper introduces how to effectively utilize a semiotic-inspired approach to ontology evaluation, specifically towards drug-related ontologies hosted on the National Center for Biomedical Ontology BioPortal. Using the semiotic-based evaluation framework for drug-based ontologies, we adjusted the quality metrics based on the semiotic features of drug ontologies. Then, we compared the quality scores before and after tailoring. The scores revealed a more precise measurement and a closer distribution compared to the before-tailoring. The results of this study reveal that a tailored semiotic evaluation produced a more meaningful and accurate assessment of drug-based ontologies, lending to the possible usefulness of semiotics in ontology evaluation.

Effects of an ontology display with history representation on organizational memory information systems.

PubMed

Hwang, Wonil; Salvendy, Gavriel

2005-06-10

Ontologies, as a possible element of organizational memory information systems, appear to support organizational learning. Ontology tools can be used to share knowledge among the members of an organization. However, current ontology-viewing user interfaces of ontology tools do not fully support organizational learning, because most of them lack proper history representation in their display. In this study, a conceptual model was developed that emphasized the role of ontology in the organizational learning cycle and explored the integration of history representation in the ontology display. Based on the experimental results from a split-plot design with 30 participants, two conclusions were derived: first, appropriately selected history representations in the ontology display help users to identify changes in the ontologies; and second, compatibility between types of ontology display and history representation is more important than ontology display and history representation in themselves.

MIRO: guidelines for minimum information for the reporting of an ontology.

PubMed

Matentzoglu, Nicolas; Malone, James; Mungall, Chris; Stevens, Robert

2018-01-18

Creation and use of ontologies has become a mainstream activity in many disciplines, in particular, the biomedical domain. Ontology developers often disseminate information about these ontologies in peer-reviewed ontology description reports. There appears to be, however, a high degree of variability in the content of these reports. Often, important details are omitted such that it is difficult to gain a sufficient understanding of the ontology, its content and method of creation. We propose the Minimum Information for Reporting an Ontology (MIRO) guidelines as a means to facilitate a higher degree of completeness and consistency between ontology documentation, including published papers, and ultimately a higher standard of report quality. A draft of the MIRO guidelines was circulated for public comment in the form of a questionnaire, and we subsequently collected 110 responses from ontology authors, developers, users and reviewers. We report on the feedback of this consultation, including comments on each guideline, and present our analysis on the relative importance of each MIRO information item. These results were used to update the MIRO guidelines, mainly by providing more detailed operational definitions of the individual items and assigning degrees of importance. Based on our revised version of MIRO, we conducted a review of 15 recently published ontology description reports from three important journals in the Semantic Web and Biomedical domain and analysed them for compliance with the MIRO guidelines. We found that only 41.38% of the information items were covered by the majority of the papers (and deemed important by the survey respondents) and a large number of important items are not covered at all, like those related to testing and versioning policies. We believe that the community-reviewed MIRO guidelines can contribute to improving significantly the quality of ontology description reports and other documentation, in particular by increasing consistent

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.

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

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

Drug target ontology to classify and integrate drug discovery data.

PubMed

Lin, Yu; Mehta, Saurabh; Küçük-McGinty, Hande; Turner, John Paul; Vidovic, Dusica; Forlin, Michele; Koleti, Amar; Nguyen, Dac-Trung; Jensen, Lars Juhl; Guha, Rajarshi; Mathias, Stephen L; Ursu, Oleg; Stathias, Vasileios; Duan, Jianbin; Nabizadeh, Nooshin; Chung, Caty; Mader, Christopher; Visser, Ubbo; Yang, Jeremy J; Bologa, Cristian G; Oprea, Tudor I; Schürer, Stephan C

2017-11-09

One of the most successful approaches to develop new small molecule therapeutics has been to start from a validated druggable protein target. However, only a small subset of potentially druggable targets has attracted significant research and development resources. The Illuminating the Druggable Genome (IDG) project develops resources to catalyze the development of likely targetable, yet currently understudied prospective drug targets. A central component of the IDG program is a comprehensive knowledge resource of the druggable genome. As part of that effort, we have developed a framework to integrate, navigate, and analyze drug discovery data based on formalized and standardized classifications and annotations of druggable protein targets, the Drug Target Ontology (DTO). DTO was constructed by extensive curation and consolidation of various resources. DTO classifies the four major drug target protein families, GPCRs, kinases, ion channels and nuclear receptors, based on phylogenecity, function, target development level, disease association, tissue expression, chemical ligand and substrate characteristics, and target-family specific characteristics. The formal ontology was built using a new software tool to auto-generate most axioms from a database while supporting manual knowledge acquisition. A modular, hierarchical implementation facilitate ontology development and maintenance and makes use of various external ontologies, thus integrating the DTO into the ecosystem of biomedical ontologies. As a formal OWL-DL ontology, DTO contains asserted and inferred axioms. Modeling data from the Library of Integrated Network-based Cellular Signatures (LINCS) program illustrates the potential of DTO for contextual data integration and nuanced definition of important drug target characteristics. DTO has been implemented in the IDG user interface Portal, Pharos and the TIN-X explorer of protein target disease relationships. DTO was built based on the need for a formal semantic

Geo-Ontologies Are Scale Dependent

NASA Astrophysics Data System (ADS)

Frank, A. U.

2009-04-01

Philosophers aim at a single ontology that describes "how the world is"; for information systems we aim only at ontologies that describe a conceptualization of reality (Guarino 1995; Gruber 2005). A conceptualization of the world implies a spatial and temporal scale: what are the phenomena, the objects and the speed of their change? Few articles (Reitsma et al. 2003) seem to address that an ontology is scale specific (but many articles indicate that ontologies are scale-free in another sense namely that they are scale free in the link densities between concepts). The scale in the conceptualization can be linked to the observation process. The extent of the support of the physical observation instrument and the sampling theorem indicate what level of detail we find in a dataset. These rules apply for remote sensing or sensor networks alike. An ontology of observations must include scale or level of detail, and concepts derived from observations should carry this relation forward. A simple example: in high resolution remote sensing image agricultural plots and roads between them are shown, at lower resolution, only the plots and not the roads are visible. This gives two ontologies, one with plots and roads, the other with plots only. Note that a neighborhood relation in the two different ontologies also yield different results. References Gruber, T. (2005). "TagOntology - a way to agree on the semantics of tagging data." Retrieved October 29, 2005., from http://tomgruber.org/writing/tagontology-tagcapm-talk.pdf. Guarino, N. (1995). "Formal Ontology, Conceptual Analysis and Knowledge Representation." International Journal of Human and Computer Studies. Special Issue on Formal Ontology, Conceptual Analysis and Knowledge Representation, edited by N. Guarino and R. Poli 43(5/6). Reitsma, F. and T. Bittner (2003). Process, Hierarchy, and Scale. Spatial Information Theory. Cognitive and Computational Foundations of Geographic Information ScienceInternational Conference

78 FR 21123 - Charlotte Pipe and Foundry; Analysis to Aid Public Comment

Federal Register 2010, 2011, 2012, 2013, 2014

2013-04-09

... Agreement'') from Charlotte Pipe and Foundry Company (hereinafter ``CP&F'') and its wholly-owned subsidiary... the following allegations. A. The Respondents CP&F is a privately-held corporation with its principal place of business located at 2109 Randolph Road, Charlotte, NC 28207. CP&F is one of the largest...

Region Evolution eXplorer - A tool for discovering evolution trends in ontology regions.

PubMed

Christen, Victor; Hartung, Michael; Groß, Anika

2015-01-01

A large number of life science ontologies has been developed to support different application scenarios such as gene annotation or functional analysis. The continuous accumulation of new insights and knowledge affects specific portions in ontologies and thus leads to their adaptation. Therefore, it is valuable to study which ontology parts have been extensively modified or remained unchanged. Users can monitor the evolution of an ontology to improve its further development or apply the knowledge in their applications. Here we present REX (Region Evolution eXplorer) a web-based system for exploring the evolution of ontology parts (regions). REX provides an analysis platform for currently about 1,000 versions of 16 well-known life science ontologies. Interactive workflows allow an explorative analysis of changing ontology regions and can be used to study evolution trends for long-term periods. REX is a web application providing an interactive and user-friendly interface to identify (un)stable regions in large life science ontologies. It is available at http://www.izbi.de/rex.

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.

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.

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…

Where to search top-K biomedical ontologies?

PubMed

Oliveira, Daniela; Butt, Anila Sahar; Haller, Armin; Rebholz-Schuhmann, Dietrich; Sahay, Ratnesh

2018-03-20

Searching for precise terms and terminological definitions in the biomedical data space is problematic, as researchers find overlapping, closely related and even equivalent concepts in a single or multiple ontologies. Search engines that retrieve ontological resources often suggest an extensive list of search results for a given input term, which leads to the tedious task of selecting the best-fit ontological resource (class or property) for the input term and reduces user confidence in the retrieval engines. A systematic evaluation of these search engines is necessary to understand their strengths and weaknesses in different search requirements. We have implemented seven comparable Information Retrieval ranking algorithms to search through ontologies and compared them against four search engines for ontologies. Free-text queries have been performed, the outcomes have been judged by experts and the ranking algorithms and search engines have been evaluated against the expert-based ground truth (GT). In addition, we propose a probabilistic GT that is developed automatically to provide deeper insights and confidence to the expert-based GT as well as evaluating a broader range of search queries. The main outcome of this work is the identification of key search factors for biomedical ontologies together with search requirements and a set of recommendations that will help biomedical experts and ontology engineers to select the best-suited retrieval mechanism in their search scenarios. We expect that this evaluation will allow researchers and practitioners to apply the current search techniques more reliably and that it will help them to select the right solution for their daily work. The source code (of seven ranking algorithms), ground truths and experimental results are available at https://github.com/danielapoliveira/bioont-search-benchmark.

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.

Reconciliation of ontology and terminology to cope with linguistics.

PubMed

Baud, Robert H; Ceusters, Werner; Ruch, Patrick; Rassinoux, Anne-Marie; Lovis, Christian; Geissbühler, Antoine

2007-01-01

To discuss the relationships between ontologies, terminologies and language in the context of Natural Language Processing (NLP) applications in order to show the negative consequences of confusing them. The viewpoints of the terminologist and (computational) linguist are developed separately, and then compared, leading to the presentation of reconciliation among these points of view, with consideration of the role of the ontologist. In order to encourage appropriate usage of terminologies, guidelines are presented advocating the simultaneous publication of pragmatic vocabularies supported by terminological material based on adequate ontological analysis. Ontologies, terminologies and natural languages each have their own purpose. Ontologies support machine understanding, natural languages support human communication, and terminologies should form the bridge between them. Therefore, future terminology standards should be based on sound ontology and do justice to the diversities in natural languages. Moreover, they should support local vocabularies, in order to be easily adaptable to local needs and practices.

Building an Ontology for Identity Resolution in Healthcare and Public Health.

PubMed

Duncan, Jeffrey; Eilbeck, Karen; Narus, Scott P; Clyde, Stephen; Thornton, Sidney; Staes, Catherine

2015-01-01

Integration of disparate information from electronic health records, clinical data warehouses, birth certificate registries and other public health information systems offers great potential for clinical care, public health practice, and research. Such integration, however, depends on correctly matching patient-specific records using demographic identifiers. Without standards for these identifiers, record linkage is complicated by issues of structural and semantic heterogeneity. Our objectives were to develop and validate an ontology to: 1) identify components of identity and events subsequent to birth that result in creation, change, or sharing of identity information; 2) develop an ontology to facilitate data integration from multiple healthcare and public health sources; and 3) validate the ontology's ability to model identity-changing events over time. We interviewed domain experts in area hospitals and public health programs and developed process models describing the creation and transmission of identity information among various organizations for activities subsequent to a birth event. We searched for existing relevant ontologies. We validated the content of our ontology with simulated identity information conforming to scenarios identified in our process models. We chose the Simple Event Model (SEM) to describe events in early childhood and integrated the Clinical Element Model (CEM) for demographic information. We demonstrated the ability of the combined SEM-CEM ontology to model identity events over time. The use of an ontology can overcome issues of semantic and syntactic heterogeneity to facilitate record linkage.

BioPortal: An Open-Source Community-Based Ontology Repository

NASA Astrophysics Data System (ADS)

Noy, N.; NCBO Team

2011-12-01

Advances in computing power and new computational techniques have changed the way researchers approach science. In many fields, one of the most fruitful approaches has been to use semantically aware software to break down the barriers among disparate domains, systems, data sources, and technologies. Such software facilitates data aggregation, improves search, and ultimately allows the detection of new associations that were previously not detectable. Achieving these analyses requires software systems that take advantage of the semantics and that can intelligently negotiate domains and knowledge sources, identifying commonality across systems that use different and conflicting vocabularies, while understanding apparent differences that may be concealed by the use of superficially similar terms. An ontology, a semantically rich vocabulary for a domain of interest, is the cornerstone of software for bridging systems, domains, and resources. However, as ontologies become the foundation of all semantic technologies in e-science, we must develop an infrastructure for sharing ontologies, finding and evaluating them, integrating and mapping among them, and using ontologies in applications that help scientists process their data. BioPortal [1] is an open-source on-line community-based ontology repository that has been used as a critical component of semantic infrastructure in several domains, including biomedicine and bio-geochemical data. BioPortal, uses the social approaches in the Web 2.0 style to bring structure and order to the collection of biomedical ontologies. It enables users to provide and discuss a wide array of knowledge components, from submitting the ontologies themselves, to commenting on and discussing classes in the ontologies, to reviewing ontologies in the context of their own ontology-based projects, to creating mappings between overlapping ontologies and discussing and critiquing the mappings. Critically, it provides web-service access to all its

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.

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

Information Pre-Processing using Domain Meta-Ontology and Rule Learning System

NASA Astrophysics Data System (ADS)

Ranganathan, Girish R.; Biletskiy, Yevgen

Around the globe, extraordinary amounts of documents are being created by Enterprises and by users outside these Enterprises. The documents created in the Enterprises constitute the main focus of the present chapter. These documents are used to perform numerous amounts of machine processing. While using thesedocuments for machine processing, lack of semantics of the information in these documents may cause misinterpretation of the information, thereby inhibiting the productiveness of computer assisted analytical work. Hence, it would be profitable to the Enterprises if they use well defined domain ontologies which will serve as rich source(s) of semantics for the information in the documents. These domain ontologies can be created manually, semi-automatically or fully automatically. The focus of this chapter is to propose an intermediate solution which will enable relatively easy creation of these domain ontologies. The process of extracting and capturing domain ontologies from these voluminous documents requires extensive involvement of domain experts and application of methods of ontology learning that are substantially labor intensive; therefore, some intermediate solutions which would assist in capturing domain ontologies must be developed. This chapter proposes a solution in this direction which involves building a meta-ontology that will serve as an intermediate information source for the main domain ontology. This chapter proposes a solution in this direction which involves building a meta-ontology as a rapid approach in conceptualizing a domain of interest from huge amount of source documents. This meta-ontology can be populated by ontological concepts, attributes and relations from documents, and then refined in order to form better domain ontology either through automatic ontology learning methods or some other relevant ontology building approach.

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…

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

Ontology matters: a commentary on contribution to cultural historical activity

NASA Astrophysics Data System (ADS)

Martin, Jenny

2017-10-01

This commentary promotes discussion on the imaginary provided by Sanaz Farhangi in her article entitled, Contribution to activity: a lens for understanding students' potential and agency in physics education. The commentary is concerned with aligning ontological assumptions in research accounts of learning and development with transformative aims. A broad definition of ontology as the theory of existence is preferred. Sociocultural approaches share relational ontology as a common foundation. I agree with scholars elaborating Vygotsky's Transformative Activist Stance that a relational ontology does not imply activism. However, I argue that relational ontology provides a necessary and sufficient theoretical grounding for intentional transformation. I draw upon positioning theory to elaborate the moral aspects of language use and to illustrate that a theory of being as relational already eliminates the transcendental position. I draw on Farhangi's article to further the discussion on the necessity and sufficiency of relational ontology and associated grammars in accounting for activism.

Experimental study of optimal self compacting concrete with spent foundry sand as partial replacement for M-sand using Taguchi approach

NASA Astrophysics Data System (ADS)

Nirmala, D. B.; Raviraj, S.

2016-06-01

This paper presents the application of Taguchi approach to obtain optimal mix proportion for Self Compacting Concrete (SCC) containing spent foundry sand and M-sand. Spent foundry sand is used as a partial replacement for M-sand. The SCC mix has seven control factors namely, Coarse aggregate, M-sand with Spent Foundry sand, Cement, Fly ash, Water, Super plasticizer and Viscosity modifying agent. Modified Nan Su method is used to proportion the initial SCC mix. L18 (21×37) Orthogonal Arrays (OA) with the seven control factors having 3 levels is used in Taguchi approach which resulted in 18 SCC mix proportions. All mixtures are extensively tested both in fresh and hardened states to verify whether they meet the practical and technical requirements of SCC. The quality characteristics considering "Nominal the better" situation is applied to the test results to arrive at the optimal SCC mix proportion. Test results indicate that the optimal mix satisfies the requirements of fresh and hardened properties of SCC. The study reveals the feasibility of using spent foundry sand as a partial replacement of M-sand in SCC and also that Taguchi method is a reliable tool to arrive at optimal mix proportion of SCC.

A bibliometric and visual analysis of global geo-ontology research

NASA Astrophysics Data System (ADS)

Li, Lin; Liu, Yu; Zhu, Haihong; Ying, Shen; Luo, Qinyao; Luo, Heng; Kuai, Xi; Xia, Hui; Shen, Hang

2017-02-01

In this paper, the results of a bibliometric and visual analysis of geo-ontology research articles collected from the Web of Science (WOS) database between 1999 and 2014 are presented. The numbers of national institutions and published papers are visualized and a global research heat map is drawn, illustrating an overview of global geo-ontology research. In addition, we present a chord diagram of countries and perform a visual cluster analysis of a knowledge co-citation network of references, disclosing potential academic communities and identifying key points, main research areas, and future research trends. The International Journal of Geographical Information Science, Progress in Human Geography, and Computers & Geosciences are the most active journals. The USA makes the largest contributions to geo-ontology research by virtue of its highest numbers of independent and collaborative papers, and its dominance was also confirmed in the country chord diagram. The majority of institutions are in the USA, Western Europe, and Eastern Asia. Wuhan University, University of Munster, and the Chinese Academy of Sciences are notable geo-ontology institutions. Keywords such as "Semantic Web," "GIS," and "space" have attracted a great deal of attention. "Semantic granularity in ontology-driven geographic information systems, "Ontologies in support of activities in geographical space" and "A translation approach to portable ontology specifications" have the highest cited centrality. Geographical space, computer-human interaction, and ontology cognition are the three main research areas of geo-ontology. The semantic mismatch between the producers and users of ontology data as well as error propagation in interdisciplinary and cross-linguistic data reuse needs to be solved. In addition, the development of geo-ontology modeling primitives based on OWL (Web Ontology Language）and finding methods to automatically rework data in Semantic Web are needed. Furthermore, the topological

TNM-O: ontology support for staging of malignant tumours.

PubMed

Boeker, Martin; França, Fábio; Bronsert, Peter; Schulz, Stefan

2016-11-14

Objectives of this work are to (1) present an ontological framework for the TNM classification system, (2) exemplify this framework by an ontology for colon and rectum tumours, and (3) evaluate this ontology by assigning TNM classes to real world pathology data. The TNM ontology uses the Foundational Model of Anatomy for anatomical entities and BioTopLite 2 as a domain top-level ontology. General rules for the TNM classification system and the specific TNM classification for colorectal tumours were axiomatised in description logic. Case-based information was collected from tumour documentation practice in the Comprehensive Cancer Centre of a large university hospital. Based on the ontology, a module was developed that classifies pathology data. TNM was represented as an information artefact, which consists of single representational units. Corresponding to every representational unit, tumours and tumour aggregates were defined. Tumour aggregates consist of the primary tumour and, if existing, of infiltrated regional lymph nodes and distant metastases. TNM codes depend on the location and certain qualities of the primary tumour (T), the infiltrated regional lymph nodes (N) and the existence of distant metastases (M). Tumour data from clinical and pathological documentation were successfully classified with the ontology. A first version of the TNM Ontology represents the TNM system for the description of the anatomical extent of malignant tumours. The present work demonstrates its representational power and completeness as well as its applicability for classification of instance data.

Sioux City Foundry Company, South Sioux City, Nebraska - Clean Water Act Public Notice

EPA Pesticide Factsheets

The EPA is providing notice of a proposed Administrative Penalty Assessment against the Sioux City Foundry Company, an industry located at 2400 G Street, South Sioux City, NE, for alleged violations of the Clean Water Act, 33 U.S.C. § 1319(g) for discharge

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

Ontological Model of Business Process Management Systems

NASA Astrophysics Data System (ADS)

Manoilov, G.; Deliiska, B.

2008-10-01

The activities which constitute business process management (BPM) can be grouped into five categories: design, modeling, execution, monitoring and optimization. Dedicated software packets for business process management system (BPMS) are available on the market. But the efficiency of its exploitation depends on used ontological model in the development time and run time of the system. In the article an ontological model of BPMS in area of software industry is investigated. The model building is preceded by conceptualization of the domain and taxonomy of BPMS development. On the base of the taxonomy an simple online thesaurus is created.

OAE: The Ontology of Adverse Events.

PubMed

He, Yongqun; Sarntivijai, Sirarat; Lin, Yu; Xiang, Zuoshuang; Guo, Abra; Zhang, Shelley; Jagannathan, Desikan; Toldo, Luca; Tao, Cui; Smith, Barry

2014-01-01

A medical intervention is a medical procedure or application intended to relieve or prevent illness or injury. Examples of medical interventions include vaccination and drug administration. After a medical intervention, adverse events (AEs) may occur which lie outside the intended consequences of the intervention. The representation and analysis of AEs are critical to the improvement of public health. The Ontology of Adverse Events (OAE), previously named Adverse Event Ontology (AEO), is a community-driven ontology developed to standardize and integrate data relating to AEs arising subsequent to medical interventions, as well as to support computer-assisted reasoning. OAE has over 3,000 terms with unique identifiers, including terms imported from existing ontologies and more than 1,800 OAE-specific terms. In OAE, the term 'adverse event' denotes a pathological bodily process in a patient that occurs after a medical intervention. Causal adverse events are defined by OAE as those events that are causal consequences of a medical intervention. OAE represents various adverse events based on patient anatomic regions and clinical outcomes, including symptoms, signs, and abnormal processes. OAE has been used in the analysis of several different sorts of vaccine and drug adverse event data. For example, using the data extracted from the Vaccine Adverse Event Reporting System (VAERS), OAE was used to analyse vaccine adverse events associated with the administrations of different types of influenza vaccines. OAE has also been used to represent and classify the vaccine adverse events cited in package inserts of FDA-licensed human vaccines in the USA. OAE is a biomedical ontology that logically defines and classifies various adverse events occurring after medical interventions. OAE has successfully been applied in several adverse event studies. The OAE ontological framework provides a platform for systematic representation and analysis of adverse events and of the factors (e

TermGenie - a web-application for pattern-based ontology class generation.

PubMed

Dietze, Heiko; Berardini, Tanya Z; Foulger, Rebecca E; Hill, David P; Lomax, Jane; Osumi-Sutherland, David; Roncaglia, Paola; Mungall, Christopher J

2014-01-01

Biological ontologies are continually growing and improving from requests for new classes (terms) by biocurators. These ontology requests can frequently create bottlenecks in the biocuration process, as ontology developers struggle to keep up, while manually processing these requests and create classes. TermGenie allows biocurators to generate new classes based on formally specified design patterns or templates. The system is web-based and can be accessed by any authorized curator through a web browser. Automated rules and reasoning engines are used to ensure validity, uniqueness and relationship to pre-existing classes. In the last 4 years the Gene Ontology TermGenie generated 4715 new classes, about 51.4% of all new classes created. The immediate generation of permanent identifiers proved not to be an issue with only 70 (1.4%) obsoleted classes. TermGenie is a web-based class-generation system that complements traditional ontology development tools. All classes added through pre-defined templates are guaranteed to have OWL equivalence axioms that are used for automatic classification and in some cases inter-ontology linkage. At the same time, the system is simple and intuitive and can be used by most biocurators without extensive training.

Dovetailing biology and chemistry: integrating the Gene Ontology with the ChEBI chemical ontology

PubMed Central

2013-01-01

Background The Gene Ontology (GO) facilitates the description of the action of gene products in a biological context. Many GO terms refer to chemical entities that participate in biological processes. To facilitate accurate and consistent systems-wide biological representation, it is necessary to integrate the chemical view of these entities with the biological view of GO functions and processes. We describe a collaborative effort between the GO and the Chemical Entities of Biological Interest (ChEBI) ontology developers to ensure that the representation of chemicals in the GO is both internally consistent and in alignment with the chemical expertise captured in ChEBI. Results We have examined and integrated the ChEBI structural hierarchy into the GO resource through computationally-assisted manual curation of both GO and ChEBI. Our work has resulted in the creation of computable definitions of GO terms that contain fully defined semantic relationships to corresponding chemical terms in ChEBI. Conclusions The set of logical definitions using both the GO and ChEBI has already been used to automate aspects of GO development and has the potential to allow the integration of data across the domains of biology and chemistry. These logical definitions are available as an extended version of the ontology from http://purl.obolibrary.org/obo/go/extensions/go-plus.owl. PMID:23895341

Comparison of workers’ perceptions toward work climate and health symptoms between ceramic and iron foundry workers

PubMed Central

Majumder, Joydeep; Bagepally, Bhavani S.; Shah, Priyanka; Kotadiya, Sanjay; Yadav, Suresh; Naha, Nibedita

2016-01-01

Background: Workers exposed to heavy manual material handling (MMH) in a hot working environment succumb to severe physical stress and psychological stress. Aims: (1) Recognize the heat load at workplaces of ceramic industry and iron industry, and (2) comparatively examine the characteristics of self-reported physiological responses and heat-health perception among these workers. Settings and Design: Cross-sectional prospective study. Materials and Methods: Workplace microclimate in the ceramic industry and iron industry was monitored. An ergonomic checklist and a questionnaire was used to record self-reported workers’ perceptions toward heat stress at workplace (ceramic workers N = 321, iron foundry workers N = 253). The prevalence rates of subjective symptoms among workers of both the industries were compared. Statistical Analysis: Chi-square test was used to examine the association between stressors and health complaints at a significance level set at P < 0.05. Results: Iron foundries recorded higher mean ambient temperature (43.4 ± 3.7°C) and wet-bulb globe temperature (WGBT) index (31.5 ± 0.7°C) as compared to ceramic industries (39.9 ± 3.3°C and 28 ± 1.5°C, respectively). Heavy sweating, elevated body temperature, sleeplessness, excessive thirst, muscular discomforts, and fatigue were prime symptoms recorded among workers of both industries. Skin-related disorders (red face, dry skin, bumps, itching) were significantly higher among iron foundry workers, whereas sleeplessness, high blood pressure, heavy sweating, kidney stone, decreased urination, muscular discomforts, and fatigue were significantly more among ceramic workers. Young workers reported more sweating and fatigue than older workers. Conclusions: A hot work climate and heavy manual labor designate ceramic and iron industries as arduous. Direct contact with hot surface and continuous MMH in tandem with the mechanical pace of production process makes work in ceramic industries more difficult

Comparison of workers' perceptions toward work climate and health symptoms between ceramic and iron foundry workers.

PubMed

Majumder, Joydeep; Bagepally, Bhavani S; Shah, Priyanka; Kotadiya, Sanjay; Yadav, Suresh; Naha, Nibedita

2016-01-01

Workers exposed to heavy manual material handling (MMH) in a hot working environment succumb to severe physical stress and psychological stress. (1) Recognize the heat load at workplaces of ceramic industry and iron industry, and (2) comparatively examine the characteristics of self-reported physiological responses and heat-health perception among these workers. Cross-sectional prospective study. Workplace microclimate in the ceramic industry and iron industry was monitored. An ergonomic checklist and a questionnaire was used to record self-reported workers' perceptions toward heat stress at workplace (ceramic workers N = 321, iron foundry workers N = 253). The prevalence rates of subjective symptoms among workers of both the industries were compared. Chi-square test was used to examine the association between stressors and health complaints at a significance level set at P < 0.05. Iron foundries recorded higher mean ambient temperature (43.4 ± 3.7°C) and wet-bulb globe temperature (WGBT) index (31.5 ± 0.7°C) as compared to ceramic industries (39.9 ± 3.3°C and 28 ± 1.5°C, respectively). Heavy sweating, elevated body temperature, sleeplessness, excessive thirst, muscular discomforts, and fatigue were prime symptoms recorded among workers of both industries. Skin-related disorders (red face, dry skin, bumps, itching) were significantly higher among iron foundry workers, whereas sleeplessness, high blood pressure, heavy sweating, kidney stone, decreased urination, muscular discomforts, and fatigue were significantly more among ceramic workers. Young workers reported more sweating and fatigue than older workers. A hot work climate and heavy manual labor designate ceramic and iron industries as arduous. Direct contact with hot surface and continuous MMH in tandem with the mechanical pace of production process makes work in ceramic industries more difficult than iron foundries.

Ontology for assessment studies of human-computer-interaction in surgery.

PubMed

Machno, Andrej; Jannin, Pierre; Dameron, Olivier; Korb, Werner; Scheuermann, Gerik; Meixensberger, Jürgen

2015-02-01

New technologies improve modern medicine, but may result in unwanted consequences. Some occur due to inadequate human-computer-interactions (HCI). To assess these consequences, an investigation model was developed to facilitate the planning, implementation and documentation of studies for HCI in surgery. The investigation model was formalized in Unified Modeling Language and implemented as an ontology. Four different top-level ontologies were compared: Object-Centered High-level Reference, Basic Formal Ontology, General Formal Ontology (GFO) and Descriptive Ontology for Linguistic and Cognitive Engineering, according to the three major requirements of the investigation model: the domain-specific view, the experimental scenario and the representation of fundamental relations. Furthermore, this article emphasizes the distinction of "information model" and "model of meaning" and shows the advantages of implementing the model in an ontology rather than in a database. The results of the comparison show that GFO fits the defined requirements adequately: the domain-specific view and the fundamental relations can be implemented directly, only the representation of the experimental scenario requires minor extensions. The other candidates require wide-ranging extensions, concerning at least one of the major implementation requirements. Therefore, the GFO was selected to realize an appropriate implementation of the developed investigation model. The ensuing development considered the concrete implementation of further model aspects and entities: sub-domains, space and time, processes, properties, relations and functions. The investigation model and its ontological implementation provide a modular guideline for study planning, implementation and documentation within the area of HCI research in surgery. This guideline helps to navigate through the whole study process in the form of a kind of standard or good clinical practice, based on the involved foundational frameworks

Building a semi-automatic ontology learning and construction system for geosciences

NASA Astrophysics Data System (ADS)

Babaie, H. A.; Sunderraman, R.; Zhu, Y.

2013-12-01

We are developing an ontology learning and construction framework that allows continuous, semi-automatic knowledge extraction, verification, validation, and maintenance by potentially a very large group of collaborating domain experts in any geosciences field. The system brings geoscientists from the side-lines to the center stage of ontology building, allowing them to collaboratively construct and enrich new ontologies, and merge, align, and integrate existing ontologies and tools. These constantly evolving ontologies can more effectively address community's interests, purposes, tools, and change. The goal is to minimize the cost and time of building ontologies, and maximize the quality, usability, and adoption of ontologies by the community. Our system will be a domain-independent ontology learning framework that applies natural language processing, allowing users to enter their ontology in a semi-structured form, and a combined Semantic Web and Social Web approach that lets direct participation of geoscientists who have no skill in the design and development of their domain ontologies. A controlled natural language (CNL) interface and an integrated authoring and editing tool automatically convert syntactically correct CNL text into formal OWL constructs. The WebProtege-based system will allow a potentially large group of geoscientists, from multiple domains, to crowd source and participate in the structuring of their knowledge model by sharing their knowledge through critiquing, testing, verifying, adopting, and updating of the concept models (ontologies). We will use cloud storage for all data and knowledge base components of the system, such as users, domain ontologies, discussion forums, and semantic wikis that can be accessed and queried by geoscientists in each domain. We will use NoSQL databases such as MongoDB as a service in the cloud environment. MongoDB uses the lightweight JSON format, which makes it convenient and easy to build Web applications using

TrhOnt: building an ontology to assist rehabilitation processes.

PubMed

Berges, Idoia; Antón, David; Bermúdez, Jesús; Goñi, Alfredo; Illarramendi, Arantza

2016-10-04

One of the current research efforts in the area of biomedicine is the representation of knowledge in a structured way so that reasoning can be performed on it. More precisely, in the field of physiotherapy, information such as the physiotherapy record of a patient or treatment protocols for specific disorders must be adequately modeled, because they play a relevant role in the management of the evolutionary recovery process of a patient. In this scenario, we introduce TRHONT, an application ontology that can assist physiotherapists in the management of the patients' evolution via reasoning supported by semantic technology. The ontology was developed following the NeOn Methodology. It integrates knowledge from ontological (e.g. FMA ontology) and non-ontological resources (e.g. a database of movements, exercises and treatment protocols) as well as additional physiotherapy-related knowledge. We demonstrate how the ontology fulfills the purpose of providing a reference model for the representation of the physiotherapy-related information that is needed for the whole physiotherapy treatment of patients, since they step for the first time into the physiotherapist's office, until they are discharged. More specifically, we present the results for each of the intended uses of the ontology listed in the document that specifies its requirements, and show how TRHONT can answer the competency questions defined within that document. Moreover, we detail the main steps of the process followed to build the TRHONT ontology in order to facilitate its reproducibility in a similar context. Finally, we show an evaluation of the ontology from different perspectives. TRHONT has achieved the purpose of allowing for a reasoning process that changes over time according to the patient's state and performance.

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

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.

Ontology construction and application in practice case study of health tourism in Thailand.

PubMed

Chantrapornchai, Chantana; Choksuchat, Chidchanok

2016-01-01

Ontology is one of the key components in semantic webs. It contains the core knowledge for an effective search. However, building ontology requires the carefully-collected knowledge which is very domain-sensitive. In this work, we present the practice of ontology construction for a case study of health tourism in Thailand. The whole process follows the METHONTOLOGY approach, which consists of phases: information gathering, corpus study, ontology engineering, evaluation, publishing, and the application construction. Different sources of data such as structure web documents like HTML and other documents are acquired in the information gathering process. The tourism corpora from various tourism texts and standards are explored. The ontology is evaluated in two aspects: automatic reasoning using Pellet, and RacerPro, and the questionnaires, used to evaluate by experts of the domains: tourism domain experts and ontology experts. The ontology usability is demonstrated via the semantic web application and via example axioms. The developed ontology is actually the first health tourism ontology in Thailand with the published application.

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

SOBA: sequence ontology bioinformatics analysis.

PubMed

Moore, Barry; Fan, Guozhen; Eilbeck, Karen

2010-07-01

The advent of cheaper, faster sequencing technologies has pushed the task of sequence annotation from the exclusive domain of large-scale multi-national sequencing projects to that of research laboratories and small consortia. The bioinformatics burden placed on these laboratories, some with very little programming experience can be daunting. Fortunately, there exist software libraries and pipelines designed with these groups in mind, to ease the transition from an assembled genome to an annotated and accessible genome resource. We have developed the Sequence Ontology Bioinformatics Analysis (SOBA) tool to provide a simple statistical and graphical summary of an annotated genome. We envisage its use during annotation jamborees, genome comparison and for use by developers for rapid feedback during annotation software development and testing. SOBA also provides annotation consistency feedback to ensure correct use of terminology within annotations, and guides users to add new terms to the Sequence Ontology when required. SOBA is available at http://www.sequenceontology.org/cgi-bin/soba.cgi.

VuWiki: An Ontology-Based Semantic Wiki for Vulnerability Assessments

NASA Astrophysics Data System (ADS)

Khazai, Bijan; Kunz-Plapp, Tina; Büscher, Christian; Wegner, Antje

2014-05-01

The concept of vulnerability, as well as its implementation in vulnerability assessments, is used in various disciplines and contexts ranging from disaster management and reduction to ecology, public health or climate change and adaptation, and a corresponding multitude of ideas about how to conceptualize and measure vulnerability exists. Three decades of research in vulnerability have generated a complex and growing body of knowledge that challenges newcomers, practitioners and even experienced researchers. To provide a structured representation of the knowledge field "vulnerability assessment", we have set up an ontology-based semantic wiki for reviewing and representing vulnerability assessments: VuWiki, www.vuwiki.org. Based on a survey of 55 vulnerability assessment studies, we first developed an ontology as an explicit reference system for describing vulnerability assessments. We developed the ontology in a theoretically controlled manner based on general systems theory and guided by principles for ontology development in the field of earth and environment (Raskin and Pan 2005). Four key questions form the first level "branches" or categories of the developed ontology: (1) Vulnerability of what? (2) Vulnerability to what? (3) What reference framework was used in the vulnerability assessment?, and (4) What methodological approach was used in the vulnerability assessment? These questions correspond to the basic, abstract structure of the knowledge domain of vulnerability assessments and have been deduced from theories and concepts of various disciplines. The ontology was then implemented in a semantic wiki which allows for the classification and annotation of vulnerability assessments. As a semantic wiki, VuWiki does not aim at "synthesizing" a holistic and overarching model of vulnerability. Instead, it provides both scientists and practitioners with a uniform ontology as a reference system and offers easy and structured access to the knowledge field of

SSDOnt: An Ontology for Representing Single-Subject Design Studies.

PubMed

Berges, Idoia; Bermúdez, Jesus; Illarramendi, Arantza

2018-02-01

Single-Subject Design is used in several areas such as education and biomedicine. However, no suited formal vocabulary exists for annotating the detailed configuration and the results of this type of research studies with the appropriate granularity for looking for information about them. Therefore, the search for those study designs relies heavily on a syntactical search on the abstract, keywords or full text of the publications about the study, which entails some limitations. To present SSDOnt, a specific purpose ontology for describing and annotating single-subject design studies, so that complex questions can be asked about them afterwards. The ontology was developed following the NeOn methodology. Once the requirements of the ontology were defined, a formal model was described in a Description Logic and later implemented in the ontology language OWL 2 DL. We show how the ontology provides a reference model with a suitable terminology for the annotation and searching of single-subject design studies and their main components, such as the phases, the intervention types, the outcomes and the results. Some mappings with terms of related ontologies have been established. We show as proof-of-concept that classes in the ontology can be easily extended to annotate more precise information about specific interventions and outcomes such as those related to autism. Moreover, we provide examples of some types of queries that can be posed to the ontology. SSDOnt has achieved the purpose of covering the descriptions of the domain of single-subject research studies. Schattauer GmbH.

Ontological modelling of knowledge management for human-machine integrated design of ultra-precision grinding machine

NASA Astrophysics Data System (ADS)

Hong, Haibo; Yin, Yuehong; Chen, Xing

2016-11-01

Despite the rapid development of computer science and information technology, an efficient human-machine integrated enterprise information system for designing complex mechatronic products is still not fully accomplished, partly because of the inharmonious communication among collaborators. Therefore, one challenge in human-machine integration is how to establish an appropriate knowledge management (KM) model to support integration and sharing of heterogeneous product knowledge. Aiming at the diversity of design knowledge, this article proposes an ontology-based model to reach an unambiguous and normative representation of knowledge. First, an ontology-based human-machine integrated design framework is described, then corresponding ontologies and sub-ontologies are established according to different purposes and scopes. Second, a similarity calculation-based ontology integration method composed of ontology mapping and ontology merging is introduced. The ontology searching-based knowledge sharing method is then developed. Finally, a case of human-machine integrated design of a large ultra-precision grinding machine is used to demonstrate the effectiveness of the method.

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