Science.gov

Sample records for foundry ontology development

  1. Survey-based naming conventions for use in OBO Foundry ontology development

    PubMed Central

    Schober, Daniel; Smith, Barry; Lewis, Suzanna E; Kusnierczyk, Waclaw; Lomax, Jane; Mungall, Chris; Taylor, Chris F; Rocca-Serra, Philippe; Sansone, Susanna-Assunta

    2009-01-01

    Background A wide variety of ontologies relevant to the biological and medical domains are available through the OBO Foundry portal, and their number is growing rapidly. Integration of these ontologies, while requiring considerable effort, is extremely desirable. However, heterogeneities in format and style pose serious obstacles to such integration. In particular, inconsistencies in naming conventions can impair the readability and navigability of ontology class hierarchies, and hinder their alignment and integration. While other sources of diversity are tremendously complex and challenging, agreeing a set of common naming conventions is an achievable goal, particularly if those conventions are based on lessons drawn from pooled practical experience and surveys of community opinion. Results We summarize a review of existing naming conventions and highlight certain disadvantages with respect to general applicability in the biological domain. We also present the results of a survey carried out to establish which naming conventions are currently employed by OBO Foundry ontologies and to determine what their special requirements regarding the naming of entities might be. Lastly, we propose an initial set of typographic, syntactic and semantic conventions for labelling classes in OBO Foundry ontologies. Conclusion Adherence to common naming conventions is more than just a matter of aesthetics. Such conventions provide guidance to ontology creators, help developers avoid flaws and inaccuracies when editing, and especially when interlinking, ontologies. Common naming conventions will also assist consumers of ontologies to more readily understand what meanings were intended by the authors of ontologies used in annotating bodies of data. PMID:19397794

  2. The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration

    PubMed Central

    Smith, Barry; Ashburner, Michael; Rosse, Cornelius; Bard, Jonathan; Bug, William; Ceusters, Werner; Goldberg, Louis J; Eilbeck, Karen; Ireland, Amelia; Mungall, Christopher J; Leontis, Neocles; Rocca-Serra, Philippe; Ruttenberg, Alan; Sansone, Susanna-Assunta; Scheuermann, Richard H; Shah, Nigam; Whetzel, Patricia L; Lewis, Suzanna

    2010-01-01

    The value of any kind of data is greatly enhanced when it exists in a form that allows it to be integrated with other data. One approach to integration is through the annotation of multiple bodies of data using common controlled vocabularies or ‘ontologies’. Unfortunately, the very success of this approach has led to a proliferation of ontologies, which itself creates obstacles to integration. The Open Biomedical Ontologies (OBO) consortium is pursuing a strategy to overcome this problem. Existing OBO ontologies, including the Gene Ontology, are undergoing coordinated reform, and new ontologies are being created on the basis of an evolving set of shared principles governing ontology development. The result is an expanding family of ontologies designed to be interoperable and logically well formed and to incorporate accurate representations of biological reality. We describe this OBO Foundry initiative and provide guidelines for those who might wish to become involved. PMID:17989687

  3. A Method for Evaluating and Standardizing Ontologies

    ERIC Educational Resources Information Center

    Seyed, Ali Patrice

    2012-01-01

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

  4. Data mining for ontology development.

    SciTech Connect

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

    2010-06-01

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

  5. 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…

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

    PubMed Central

    2013-01-01

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

  7. 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…

  8. A Probabilistic Ontology Development Methodology

    DTIC Science & Technology

    2014-06-01

    to have a tool guiding the user on the steps necessary to create a probabilistic ontology and link this documentation to its implementation … [4...extension that is beyond the scope of this work and includes methods such as ONIONS , FCA-Merge, and PROMPT. The interested reader may find these...construction “It would be interesting to have a tool guiding the user on the steps necessary to create a probabilistic ontology and link this

  9. Ontology for the asexual development and anatomy of the colonial chordate Botryllus schlosseri.

    PubMed

    Manni, Lucia; Gasparini, Fabio; Hotta, Kohji; Ishizuka, Katherine J; Ricci, Lorenzo; Tiozzo, Stefano; Voskoboynik, Ayelet; Dauga, Delphine

    2014-01-01

    Ontologies provide an important resource to integrate information. For developmental biology and comparative anatomy studies, ontologies of a species are used to formalize and annotate data that are related to anatomical structures, their lineage and timing of development. Here, we have constructed the first ontology for anatomy and asexual development (blastogenesis) of a bilaterian, the colonial tunicate Botryllus schlosseri. Tunicates, like Botryllus schlosseri, are non-vertebrates and the only chordate taxon species that reproduce both sexually and asexually. Their tadpole larval stage possesses structures characteristic of all chordates, i.e. a notochord, a dorsal neural tube, and gill slits. Larvae settle and metamorphose into individuals that are either solitary or colonial. The latter reproduce both sexually and asexually and these two reproductive modes lead to essentially the same adult body plan. The Botryllus schlosseri Ontology of Development and Anatomy (BODA) will facilitate the comparison between both types of development. BODA uses the rules defined by the Open Biomedical Ontologies Foundry. It is based on studies that investigate the anatomy, blastogenesis and regeneration of this organism. BODA features allow the users to easily search and identify anatomical structures in the colony, to define the developmental stage, and to follow the morphogenetic events of a tissue and/or organ of interest throughout asexual development. We invite the scientific community to use this resource as a reference for the anatomy and developmental ontology of B. schlosseri and encourage recommendations for updates and improvements.

  10. Ontology for the Asexual Development and Anatomy of the Colonial Chordate Botryllus schlosseri

    PubMed Central

    Manni, Lucia; Gasparini, Fabio; Hotta, Kohji; Ishizuka, Katherine J.; Ricci, Lorenzo; Tiozzo, Stefano; Voskoboynik, Ayelet; Dauga, Delphine

    2014-01-01

    Ontologies provide an important resource to integrate information. For developmental biology and comparative anatomy studies, ontologies of a species are used to formalize and annotate data that are related to anatomical structures, their lineage and timing of development. Here, we have constructed the first ontology for anatomy and asexual development (blastogenesis) of a bilaterian, the colonial tunicate Botryllus schlosseri. Tunicates, like Botryllus schlosseri, are non-vertebrates and the only chordate taxon species that reproduce both sexually and asexually. Their tadpole larval stage possesses structures characteristic of all chordates, i.e. a notochord, a dorsal neural tube, and gill slits. Larvae settle and metamorphose into individuals that are either solitary or colonial. The latter reproduce both sexually and asexually and these two reproductive modes lead to essentially the same adult body plan. The Botryllus schlosseri Ontology of Development and Anatomy (BODA) will facilitate the comparison between both types of development. BODA uses the rules defined by the Open Biomedical Ontologies Foundry. It is based on studies that investigate the anatomy, blastogenesis and regeneration of this organism. BODA features allow the users to easily search and identify anatomical structures in the colony, to define the developmental stage, and to follow the morphogenetic events of a tissue and/or organ of interest throughout asexual development. We invite the scientific community to use this resource as a reference for the anatomy and developmental ontology of B. schlosseri and encourage recommendations for updates and improvements. PMID:24789338

  11. Ontology Driven Piecemeal Development of Smart Spaces

    NASA Astrophysics Data System (ADS)

    Ovaska, Eila

    Software development is facing new challenges due to transformation from product based software engineering towards integration and collaboration based software engineering that embodies high degree of dynamism both at design time and run time. Short time-to-markets require cost reduction by maximizing software reuse; openness for new innovations presumes a flexible innovation platform and agile software development; and user satisfaction assumes high quality in a situation based manner. How to deal with these contradictory requirements in software engineering? The main contribution of this paper is a novel approach that is influenced by business innovation, human centered design, model driven development and ontology oriented design. The approach is called Ontology driven Piecemeal Software Engineering (OPSE). OPSE facilitates incremental software development based on software pieces that follow the design principles defined by means of ontologies. Its key elements are abstraction, aggregation and adaptivity. The approach is intended for and applied to the development of smart spaces.

  12. 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,…

  13. [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.

  14. 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

  15. 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…

  16. 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.

  17. 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.

  18. Ontology for Vector Surveillance and Management

    PubMed Central

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

    2013-01-01

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

  19. Ontology for vector surveillance and management.

    PubMed

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

    2013-01-01

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

  20. 77 FR 32998 - Foundry Coke From China

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-04

    ... COMMISSION Foundry Coke From China Determination On the basis of the record \\1\\ developed in the subject five... order on foundry coke from China would be likely to lead to continuation or recurrence of material... Commission are contained in USITC Publication 4326 (May 2012), entitled Foundry Coke from...

  1. 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…

  2. 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...

  3. 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.

  4. JPL Innovation Foundry

    NASA Astrophysics Data System (ADS)

    Sherwood, Brent; McCleese, Daniel

    2013-08-01

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

  5. Foundry Manual

    DTIC Science & Technology

    1958-01-01

    AD-A956 386 · ~ 111111!1 illl 111111111 11!11 1/ l lllllf II!! llli DTIC SELECllED · APR091992 D t • Best Available Copy NAVSHIPS 250-0334 I...FOUNDRY MANUAL JAN BUREAU OF SHIPS NAVY DEPARTMENT WASHINGTON 25, D. C l’iiiTKlü ’h* Superintendent o( l )o*nmpnR^M^I?viTnmfnt P/lntlng ()fflo...Shipbuilding and Fleet Maintenance * »..•,. »^ ■ - • • i ♦■»■•< I . ,«,: >i > l I « ■. ■ ii » ■ _. — • I PREFACE This Manual is

  6. Developing a Domain Ontology for the Hydrologic Community

    NASA Astrophysics Data System (ADS)

    Piasecki, M.; Beran, B.

    2005-12-01

    The purpose of this study is to develop a domain ontology for hydraulic science and engineering by extending the Semantic Web for Earth and Environmental Terminology (SWEET) ontologies. SWEET provides an extensive list of terms for Earth Sciences expressed in Web Ontology Language (OWL). When compared to SWEET, our proposed ontology is much smaller in scope but more detailed within its domain. Extensions can involve different type of additions such as introduction of new terms (e.g. Hydrologic Unit, Jetty etc.) some of which may depend on other features (e.g. upstream, downstream depends on flow direction), increasing the level of detail for an existing element (e.g. by creating subclasses of EarthRealm:Dams, and adding dam types - Cofferdam, arch dam, embankment dam etc.-) or introducing new phenomena based on existing processes in the SWEET ontologies. Development of this ontology follows the scalability, orthogonality, application-independence and natural language-independence principles. Besides itself being an example of community involvement, contributions and critique from other members of hydrologic community will help further shaping this product to fit the needs of a larger neighboring user community

  7. A UML profile for the OBO relation ontology

    PubMed Central

    2012-01-01

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

  8. 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.

  9. The development of non-coding RNA ontology

    PubMed Central

    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. PMID:27990175

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

    PubMed Central

    Elayavilli, Ravikumar Komandur; Liu, Hongfang

    2016-01-01

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

  11. 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…

  12. Developing Standard Ontological Behavior Representations to Support Composability

    DTIC Science & Technology

    2004-12-01

    technologies for representing domains through formalized ontologies are evolving. Sir Tim Bemers -Lee, in 1999, set forth his Semantic Web vision (Berners...Software Development. Proceedings of the Interservice/ Industry Training, Simulation and Education Conference (IIITSEC) 2002, Orlando, FL. Bemers -Lee

  13. A Gross Anatomy Ontology for Hymenoptera

    PubMed Central

    Yoder, Matthew J.; Mikó, István; Seltmann, Katja C.; Bertone, Matthew A.; Deans, Andrew R.

    2010-01-01

    Hymenoptera is an extraordinarily diverse lineage, both in terms of species numbers and morphotypes, that includes sawflies, bees, wasps, and ants. These organisms serve critical roles as herbivores, predators, parasitoids, and pollinators, with several species functioning as models for agricultural, behavioral, and genomic research. The collective anatomical knowledge of these insects, however, has been described or referred to by labels derived from numerous, partially overlapping lexicons. The resulting corpus of information—millions of statements about hymenopteran phenotypes—remains inaccessible due to language discrepancies. The Hymenoptera Anatomy Ontology (HAO) was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy. The HAO was built using newly developed interfaces within mx, a Web-based, open source software package, that enables collaborators to simultaneously contribute to an ontology. Over twenty people contributed to the development of this ontology by adding terms, genus differentia, references, images, relationships, and annotations. The database interface returns an Open Biomedical Ontology (OBO) formatted version of the ontology and includes mechanisms for extracting candidate data and for publishing a searchable ontology to the Web. The application tools are subject-agnostic and may be used by others initiating and developing ontologies. The present core HAO data constitute 2,111 concepts, 6,977 terms (labels for concepts), 3,152 relations, 4,361 sensus (links between terms, concepts, and references) and over 6,000 text and graphical annotations. The HAO is rooted with the Common Anatomy Reference Ontology (CARO), in order to facilitate interoperability with and future alignment to other anatomy ontologies, and is available through the OBO Foundry ontology repository and BioPortal. The HAO provides a foundation through which connections between genomic, evolutionary developmental biology

  14. A gross anatomy ontology for hymenoptera.

    PubMed

    Yoder, Matthew J; Mikó, István; Seltmann, Katja C; Bertone, Matthew A; Deans, Andrew R

    2010-12-29

    Hymenoptera is an extraordinarily diverse lineage, both in terms of species numbers and morphotypes, that includes sawflies, bees, wasps, and ants. These organisms serve critical roles as herbivores, predators, parasitoids, and pollinators, with several species functioning as models for agricultural, behavioral, and genomic research. The collective anatomical knowledge of these insects, however, has been described or referred to by labels derived from numerous, partially overlapping lexicons. The resulting corpus of information--millions of statements about hymenopteran phenotypes--remains inaccessible due to language discrepancies. The Hymenoptera Anatomy Ontology (HAO) was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy. The HAO was built using newly developed interfaces within mx, a Web-based, open source software package, that enables collaborators to simultaneously contribute to an ontology. Over twenty people contributed to the development of this ontology by adding terms, genus differentia, references, images, relationships, and annotations. The database interface returns an Open Biomedical Ontology (OBO) formatted version of the ontology and includes mechanisms for extracting candidate data and for publishing a searchable ontology to the Web. The application tools are subject-agnostic and may be used by others initiating and developing ontologies. The present core HAO data constitute 2,111 concepts, 6,977 terms (labels for concepts), 3,152 relations, 4,361 sensus (links between terms, concepts, and references) and over 6,000 text and graphical annotations. The HAO is rooted with the Common Anatomy Reference Ontology (CARO), in order to facilitate interoperability with and future alignment to other anatomy ontologies, and is available through the OBO Foundry ontology repository and BioPortal. The HAO provides a foundation through which connections between genomic, evolutionary developmental biology

  15. Development Program for Improving Foundry and Repair Welding Techniques for ZE41-type Magnesium Alloy Castings

    DTIC Science & Technology

    1976-09-01

    48,49,50 XI Tensile properties of test bars machined from areas of test plate containing flow-line tjrpe of segregation 51 XII Summary...TEST PLATES Melting and Pouring; The metal was prepared from alloyed EZ33 or ZE41 ingots , foundry returns (gates, risers and scrap castings) and...No back-up material, mild-steel back-up and carbon back-up. Carbon back-up gave best results. Sequence of welding: The sequence of welding eight

  16. An Ontology for Insider Threat Indicators Development and Applications

    DTIC Science & Technology

    2014-11-01

    ontology using the Web Ontology Language ( OWL ), due to its maturity, wide use, and extensibility [24]. B. Overview of Top-Level Classes The top-level...event logs into the CybOX format, and, using simple scripts, automatically generating the OWL XML code to create individuals for a small subset of our...G. Antoniou and F. Van Harmelen, "Web ontology language: Owl ," in Handbook on ontologies, ed: Springer, 2004, pp. 67-92

  17. 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

  18. Development of an Ontology for Navigating and Discovering Hydrologic Data

    NASA Astrophysics Data System (ADS)

    Piasecki, M.

    2008-12-01

    Ontologies are increasingly emerging as a tool for bridging semantic heterogeneities, a problem that is prevalent in scientific data sets particularly across domains. The problem of semantic or descriptive heterogeneity is the result of historically independent annotation efforts by those that have collected or acted as steward for collected data responding to a specific mission statement without the realization that these data sets need to come together or at least complement each other in the long run. Because of this legacy approiach and the resulting status quo new ways need to be explored to overcome these annotation discrepancies not necessarily through a complete re-annotation but rather through tools that accept heterogeneity but try to mediate between the various existing description conventions. The hydrologic community is seeking to overcome these discrepancies for their constituency (through the Consortium of Universities for the Development of Hydrologic Sciences, CUAHSI, Hydrologic Information Systems, HIS, effort) by developing an information system in which disparate data sources can be accessed through a single search engine in which all data sources appear to be "one". To this end a data-discovery ontology for hydrologic data has been developed that permits registration of data sets to leaf concepts that are sufficiently detailed but one step more generic then what is typically used for data variable descriptions, for example Nitrate for all nitrate data collected. These leaf concepts originate from broader concept trees that can be navigated upwards through branches to more and more general concepts the top one of which is called HydroShpere. The ontology was in its first design meant to prove the concept and incorporated only a limited number of branches and leafs with detailed information only provided for the nutrients branch. Efforts are under way now to i) expose the ontology and its upper structure to wider audience vetting the approach and

  19. The representation of heart development in the gene ontology.

    PubMed

    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

    2011-06-01

    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. This work also 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.

  20. 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.

  1. 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

  2. Human Development Domain of the Ontology of Craniofacial Development and Malformation

    PubMed Central

    Mejino, Jose LV; Travillian, Ravensara S; Cox, Timothy C; Shapiro, Linda G; Brinkley, James F

    2017-01-01

    In this paper we describe an ontological scheme for representing anatomical entities undergoing morphological transformation and changes in phenotype during prenatal development. This is a proposed component of the Anatomical Transformation Abstraction (ATA) of the Foundational Model of Anatomy (FMA) Ontology that was created to provide an ontological framework for capturing knowledge about human development from the zygote to postnatal life. It is designed to initially describe the structural properties of the anatomical entities that participate in human development and then enhance their description with developmental properties, such as temporal attributes and developmental processes. This approach facilitates the correlation and integration of the classical but static representation of embryology with the evolving novel concepts of developmental biology, which primarily deals with the experimental data on the mechanisms of embryogenesis and organogenesis. This is important for describing and understanding the underlying processes involved in structural malformations. In this study we focused on the development of the lips and the palate in conjunction with our work on the pathogenesis and classification of cleft lip and palate (CL/P) in the FaceBase program. Our aim here is to create the Craniofacial Human Development Ontology (CHDO) to support the Ontology of Craniofacial Development and Malformation (OCDM), which provides the infrastructure for integrating multiple and disparate craniofacial data generated by FaceBase researchers.

  3. Foundry energy conservation workbook

    SciTech Connect

    Not Available

    1990-01-01

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

  4. Rheumatism in Foundry Workers

    PubMed Central

    Lawrence, J. S.; Molyneux, M. K.; Dingwall-Fordyce, Ianthe

    1966-01-01

    In order to investigate loss of work from rheumatic diseases in the metal trades, employees in 10 foundries were questioned. Of 325 foundry workers aged 35 to 74 years, who had worked for at least 10 years on the foundry floor, 299 were examined clinically and radiologically for evidence of rheumatic disease. Radiographs of the hands, knees, and dorsal and lumbar spine were taken as a routine, and the pelvis was included in those aged 45 and over. A comparison was made with a control series of radiographs, from men, matched for age, in a random population sample examined earlier in the town of Leigh. Rheumatic complaints in general were less frequent in the foundry workers than in the random sample, and the foundry workers less often gave a history of prolonged incapacity (three months or more) due to this cause. Radiological evidence of disc degeneration in the lumbar spine, however, was more frequent in the foundry workers than in the controls and was of greater severity. Further, the foundry workers more commonly had symptoms and signs of lumbar disc prolapse. On the other hand, the controls had more osteo-arthrosis of the hips and knees and lost more work from pain at these sites. This was associated with a difference of body habitus, obesity being less frequent in the foundry workers. Foundry workers directly exposed to hot conditions did not have less back or leg pain than those not so exposed despite a greater prevalence of disc degeneration. Measurements of air temperature, humidity, and radiant heat were made in a foundry while pouring was in progress. The air temperature rose from 18°C. to 26°C. and the humidity ranged from 70% to 54%. The mean intensity of radiation incident on the clothed surface of a foundry worker was 0·12 watt/cm.2. This was compared with conditions during therapeutic exposure to radiant heat. The radiant heat under conditions of `heat therapy' varied between 0·16 and 0·37 watt/cm.2. The possible influence of radiant heat on the

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

    PubMed Central

    Smith, Barry; Ceusters, Werner

    2011-01-01

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

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

    PubMed Central

    Chambers, Stephen; Kitney, Richard; Freemont, Paul

    2016-01-01

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

  7. Semi-automated ontology generation within OBO-Edit

    PubMed Central

    Wächter, Thomas; Schroeder, Michael

    2010-01-01

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

  8. 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

  9. 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.

  10. 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

  11. 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.

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

    ERIC Educational Resources Information Center

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

    2010-01-01

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

  13. Foundry energy conservation workbook

    SciTech Connect

    1990-10-01

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

  14. Foundry energy conservation workbook

    SciTech Connect

    Not Available

    1990-12-31

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

  15. 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

  16. 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

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

    PubMed Central

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

    2014-01-01

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

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

    PubMed

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

    2015-06-01

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

  19. Development of clinical ontology for mood disorder with combination of psychomedical information.

    PubMed

    Haghighi, Mojgan; Koeda, Michihiko; Takai, Takako; Tanaka, Hiroshi

    2009-03-01

    We have developed a new educational/clinical ontology named the "Haghighi-Koeda Mood Disorder Ontology", which involves both medical and psychological approaches for mood disorders in order to promote the exchange of information between psychiatrists and psychologists. Data was gathered from more than 5000 articles published in journals and websites specialized in life science. We evaluated and selected articles which were related to 4 main categories of mood disorders. Using Protege 3.4 beta, information related to mood disorders was classified by class/subclass tree in an ontological structure. Then we developed a web-based interface system on the internet enabling the implementation of the ontology. In addition, we have designed an online scale for automated diagnosis of mood disorder. For evaluating experiments, we compare this ontology with "Decisionbase" of which content deals with mood disorders. Evaluation was in accordance with our selected criteria via the AHP (Analysis of Hierarchical Processing) method. The results demonstrated the noteworthy superiority of our ontology. We believe that combining knowledge of medical science with that in psychological fields is a key to improving the quality of diagnosis and promoting appropriate treaTMent in all psychiatric disorders.

  20. Simple Ontology Format (SOFT)

    SciTech Connect

    Sorokine, Alexandre

    2011-10-01

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

  1. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration

    PubMed Central

    Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

    2017-01-01

    Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies. PMID:27733503

  2. Ontobee: A linked ontology data server to support ontology term dereferencing, linkage, query and integration.

    PubMed

    Ong, Edison; Xiang, Zuoshuang; Zhao, Bin; Liu, Yue; Lin, Yu; Zheng, Jie; Mungall, Chris; Courtot, Mélanie; Ruttenberg, Alan; He, Yongqun

    2017-01-04

    Linked Data (LD) aims to achieve interconnected data by representing entities using Unified Resource Identifiers (URIs), and sharing information using Resource Description Frameworks (RDFs) and HTTP. Ontologies, which logically represent entities and relations in specific domains, are the basis of LD. Ontobee (http://www.ontobee.org/) is a linked ontology data server that stores ontology information using RDF triple store technology and supports query, visualization and linkage of ontology terms. Ontobee is also the default linked data server for publishing and browsing biomedical ontologies in the Open Biological Ontology (OBO) Foundry (http://obofoundry.org) library. Ontobee currently hosts more than 180 ontologies (including 131 OBO Foundry Library ontologies) with over four million terms. Ontobee provides a user-friendly web interface for querying and visualizing the details and hierarchy of a specific ontology term. Using the eXtensible Stylesheet Language Transformation (XSLT) technology, Ontobee is able to dereference a single ontology term URI, and then output RDF/eXtensible Markup Language (XML) for computer processing or display the HTML information on a web browser for human users. Statistics and detailed information are generated and displayed for each ontology listed in Ontobee. In addition, a SPARQL web interface is provided for custom advanced SPARQL queries of one or multiple ontologies.

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

    NASA Astrophysics Data System (ADS)

    Al-Debei, Mutaz M.; Fitzgerald, Guy

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

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

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

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

  5. 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

  6. 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

  7. Datamining with Ontologies.

    PubMed

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

    2016-01-01

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

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

    ERIC Educational Resources Information Center

    Fellenz, Martin R.

    2016-01-01

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

  9. 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…

  10. 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

  11. 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

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

    PubMed

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

    2013-08-01

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

  13. DEVELOPMENT OF A MANAGEMENT SYSTEM OF ROADSIDE TREES USING RFID AND ONTOLOGY

    NASA Astrophysics Data System (ADS)

    Yabuki, Nobuyoshi; Kikushige, Yuki; Fukuda, Tomohiro; Ebashi, Yumeka

    It is necessary to make scientific and systematic diagnosis for roadside trees, which are essential for comfortable urban environment, in order to keep them in healthy conditions because they may not be planted adequately. Therefore, in this research, a Roadside Tree Diagnosis Support System (RTDSS) was developed using Radio Frequency IDentification (RFID) and Personal Digital Assistants (PDA) to facilitate diagnosis based on the Visual Tree Assessment (VTA) method. The system was used on a trial basis to real roadside trees by tree surgeons and was highly evaluated. Since governmental or municipal agencies, which develop and maintain the databases of roadside trees, tend to use different terminologies, units and tree registration systems, it is difficult to compare or combine two or more roadside tree databases. Thus, the ontology of roadside tree management was developed to compare and analyze various roadside tree databases. Two different databases were developed and testing of the developed ontology system successfully showed proper searching result over different terminologies.

  14. 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.

  15. Configuring and Exploring the Foundry Trade Space

    DTIC Science & Technology

    2012-04-01

    development of a rapid prototyping process using computer numerical controlled machining. PhD, The Pennsylvania State University. Frank, M. C. and R. A. Wysk...2006). "Determining setup orientations from the visibility of slice geometry for rapid computer numerically controlled machining." Journal of...fully enumerate the space of potential foundries, nor derive a simple preference function that can rank order the space. How best, then, to

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

    PubMed Central

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

    2014-01-01

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

  17. Development of a new international classification of health interventions based on an ontology framework.

    PubMed

    Paviot, Béatrice Trombert; Madden, Richard; Moskal, Lori; Zaiss, Albrecht; Bousquet, Cédric; Kumar, Anand; Lewalle, Pierre; Rodrigues, Jean Marie

    2011-01-01

    : The WHO International Classification of Diseases is used in many national applications to plan, manage and fund through case mix health care systems and allows international comparisons of the performance of these systems. There is no such measuring tool for health interventions or procedures. To fulfil this requirement the WHO-FIC Network recommended in 2006 to develop an International Classification of Health Interventions (ICHI). This initiative is aimed to harmonise the existing national classifications and to provide a basic system for the countries which have not developed their own classification systems. It is based on the CEN/ISO ontology framework standard named Categorial Structure defined from a non formal bottom up ontology approach. The process of populating the framework is ongoing to start from a common model structure encompassing the ICD 9CM Volume 3 granularity.

  18. 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.

  19. Towards automated biomedical ontology harmonization.

    PubMed

    Uribe, Gustavo A; Lopez, Diego M; Blobel, Bernd

    2014-01-01

    The use of biomedical ontologies is increasing, especially in the context of health systems interoperability. Ontologies are key pieces to understand the semantics of information exchanged. However, given the diversity of biomedical ontologies, it is essential to develop tools that support harmonization processes amongst them. Several algorithms and tools are proposed by computer scientist for partially supporting ontology harmonization. However, these tools face several problems, especially in the biomedical domain where ontologies are large and complex. In the harmonization process, matching is a basic task. This paper explains the different ontology harmonization processes, analyzes existing matching tools, and proposes a prototype of an ontology harmonization service. The results demonstrate that there are many open issues in the field of biomedical ontology harmonization, such as: overcoming structural discrepancies between ontologies; the lack of semantic algorithms to automate the process; the low matching efficiency of existing algorithms; and the use of domain and top level ontologies in the matching process.

  20. Development of an Ontology-Directed Signal Processing Toolbox

    SciTech Connect

    Stephen W. Lang

    2011-05-27

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

  1. Molecular Foundry, Berkeley, California (Revised)

    SciTech Connect

    Carlisle, N.

    2008-03-01

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

  2. Primer on Ontologies.

    PubMed

    Hastings, Janna

    2017-01-01

    As molecular biology has increasingly become a data-intensive discipline, ontologies have emerged as an essential computational tool to assist in the organisation, description and analysis of data. Ontologies describe and classify the entities of interest in a scientific domain in a computationally accessible fashion such that algorithms and tools can be developed around them. The technology that underlies ontologies has its roots in logic-based artificial intelligence, allowing for sophisticated automated inference and error detection. This chapter presents a general introduction to modern computational ontologies as they are used in biology.

  3. Cognitive Foundry v. 3.0 (OSS)

    SciTech Connect

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

    2009-11-18

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

  4. 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

  5. Performing ontology.

    PubMed

    Aspers, Patrik

    2015-06-01

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

  6. Quantum ontologies

    SciTech Connect

    Stapp, H.P.

    1988-12-01

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

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

    NASA Astrophysics Data System (ADS)

    Stetsenko, Anna

    2008-07-01

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

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

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

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

  9. 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.

  10. Developing a taxonomy and an ontology of nurses' patient clinical summaries.

    PubMed

    McLane, Sharon; Esquivel, Adol; Turley, James P

    2009-01-01

    Nurses prepare a summary of patient information that they consult and update throughout the shift. This document is believed to be integral to cognition, working memory, and decision-making. While serving as a key support to nursing practice, this summary also represents risks to patient safety. Characterized as a PCCAT, or Personally Created Cognitive Artifact, studies of this document in the context of nursing practice have not been reported. The absence of reported research, the importance of the document to nurse cognition and practice, and related safety risks prompted the research that this paper discusses. A taxonomy was developed through the analysis and coding of 151 PCCATs. Further analysis and mapping provided an ontology of the PCCAT. Content differences were noted between nursing units and among nurses. This may reflect differences in unit-based culture and/or differences in the patient complexity. The interaction between culture and perceived complexity of practice is one of the great difficulties in generating automated information systems for clinical practice settings. This paper is part of a larger research protocol that explores meta-level knowledge structures and revision to the understanding of the granularity of nursing knowledge. Development of a taxonomy and ontology of the nurse PCCAT, an important component of the larger research protocol, is described in this paper.

  11. 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…

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

    ERIC Educational Resources Information Center

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

    2012-01-01

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

  13. Overcoming Interoperability Weaknesses in e-Government Processes: Organizing and Sharing Knowledge in Regional Development Programs Using Ontologies

    NASA Astrophysics Data System (ADS)

    Scorza, Francesco; Casas, Giuseppe Las; Murgante, Beniamino

    European Regional Policy produced several generations of programmes at both National and Regional levels. Such a complex framework tends to increase multi-level governance in the period 2007-2013, promoting a wider participation of stakeholders (including Public Administration, Local Communities, Enterprises, etc). This process has been usually accompanied by e-tools for the management of bottom-up processes, with several instances related to common problems of participation processes. Communication between "programmer" and categories of beneficiaries always presented weakness due to the ineffective system of management knowledge within the process. Relevant issues in the framework of regional development programmes are: Do stakeholders understand the meaning of general and sectoral policies? Are citizens aware of technical instruments implementing such policies? Are they conscious of ex-ante comprehensive context analysis and/or can they share possible future scenarios? A way to tackle these problems is the use of ontologies. In this work we present the structural elements of the ontology of regional development programmes analyzing major steps of the ontology design and nodal phases of the ontology building (i.e. consensus on relations and restrictions, switch from glossary to taxonomy). The result of such an application is an ontology of regional development containing more than one hundred classes.

  14. 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.

  15. 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.

  16. Medication Reconciliation: Work Domain Ontology, prototype development, and a predictive model.

    PubMed

    Markowitz, Eliz; Bernstam, Elmer V; Herskovic, Jorge; Zhang, Jiajie; Shneiderman, Ben; Plaisant, Catherine; Johnson, Todd R

    2011-01-01

    Medication errors can result from administration inaccuracies at any point of care and are a major cause for concern. To develop a successful Medication Reconciliation (MR) tool, we believe it necessary to build a Work Domain Ontology (WDO) for the MR process. A WDO defines the explicit, abstract, implementation-independent description of the task by separating the task from work context, application technology, and cognitive architecture. We developed a prototype based upon the WDO and designed to adhere to standard principles of interface design. The prototype was compared to Legacy Health System's and Pre-Admission Medication List Builder MR tools via a Keystroke-Level Model analysis for three MR tasks. The analysis found the prototype requires the fewest mental operations, completes tasks in the fewest steps, and completes tasks in the least amount of time. Accordingly, we believe that developing a MR tool, based upon the WDO and user interface guidelines, improves user efficiency and reduces cognitive load.

  17. Ayurveda research: Ontological challenges

    PubMed Central

    Nayak, Jayakrishna

    2012-01-01

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

  18. Mask cycle time reduction for foundry projects

    NASA Astrophysics Data System (ADS)

    Balasinski, A.

    2011-11-01

    One of key deliverables of foundry based manufacturing is low cycletime. Building new and enhancing existing products by mask changes involves significant logistical effort, which could be reduced by standardizing data management and communication procedures among design house, mask shop, and foundry (fab) [1]. As an example, a typical process of taping out can take up to two weeks in addition to technical effort, for database handling, mask form completion, management approval, PO signoff and JDV review, translating into loss of revenue. In order to reduce this delay, we are proposing to develop a unified online system which should assist with the following functions: database edits, final verifications, document approvals, mask order entries, and JDV review with engineering signoff as required. This would help a growing number of semiconductor products to be flexibly manufactured at different manufacturing sites. We discuss how the data architecture based on a non-relational database management system (NRDMBS) extracted into a relational one (RDMBS) should provide quality information [2], to reduce cycle time significantly beyond 70% for an example 2 week tapeout schedule.

  19. An Ontological Approach to Developing Information Operations Applications for Use on the Semantic Web

    DTIC Science & Technology

    2008-09-01

    Advisor Peter Denning Chairman, Department of Computer Science Dan Boger Chairman, Information Sciences Department iv THIS PAGE...Class......................................................................65 Figure 25. DL Expressivity...standard ontology language OWL DL , and proposes a reasoning architecture for these two ontology languages. The key features of the author’s

  20. 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...

  1. Theory of ontology and land use ontology construction

    NASA Astrophysics Data System (ADS)

    Zhou, Guofeng; Liu, Yongxue; Chao, Junjie; Shen, Chenhua; Yang, Hui

    2007-06-01

    It mainly presents the problems of data share in land use database construction. How to accurately define geographic classification expression and how to quickly and accurately express the user demand are plaguing problems of information system developer. The introduction of ontology and relevant technologies address the problem with a brand new perspective and provide a strong theoretical and methodological support. From the relevant ontology theoretical study, this paper summarizes the essence of the concept of ontology; and explores the type, role, method, formalization expression and tools of ontology. On the basis of existing research, the paper brings forward 5-step method of ontology building and then uses this method to build ontology in land use database construction. It also puts forward the notion model of land use database based on ontology.

  2. 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.

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

    PubMed Central

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

    2015-01-01

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

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

    PubMed

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

    2013-01-01

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

  5. 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.

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

    ERIC Educational Resources Information Center

    Phiakoksong, Somjin; Niwattanakul, Suphakit; Angskun, Thara

    2013-01-01

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

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

    PubMed

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

    2014-12-01

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

  8. How granularity issues concern biomedical ontology integration.

    PubMed

    Schulz, Stefan; Boeker, Martin; Stenzhorn, Holger

    2008-01-01

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

  9. Final Scientific Report Steel Foundry Refractory Lining Optimization

    SciTech Connect

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

    2002-12-02

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

  10. Automatic generation of warehouse mediators using an ontology engine

    SciTech Connect

    Critchlow, T., LLNL

    1998-03-04

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

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

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

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

  12. 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

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

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

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

  14. 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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

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

  20. Perspective view of the easter face of the iron foundry. ...

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

    Perspective view of the easter face of the iron foundry. The original section (with tow capolas) was completed in 1889. Original capola section still visible in center of the eastern facing of the current foundry building. Additional sections to rear and south of the original building completed between 1899 and 1908. Small storage building to sout to of Foundry completed in 1927. - Johnson Steel Street Rail Company, Iron Foundry, 525 Central Avenue, Johnstown, Cambria County, PA

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

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

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

  2. 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.

  3. Use of coal combustion residues and waste foundry sands in flowable fill. Final report

    SciTech Connect

    Bhat, S.T.; Lovell, C.W.

    1996-05-01

    The purpose of the study is to investigate the use of waste foundry sand (WFS) in flowable fill. However, the concepts developed are applicable to flowable fills containing any type of sand. Even though the flowable fill is presently popular as a trenchfilling material, this study addresses a much broader perspective in order to be able to develop uses of this material in geotechnical applications. Since sand is the major component of flowable fill, replacing sand with a waste material may be beneficial from an economical as well as an environmental point of view. One such waste material produced in large quantities is waste foundry sand, which is a by-product of metal casting industries where sand is used for making molds and cores. Green sands from ferrous foundries in which clay and water are used as binder materials, are mostly non-hazardous. In this research, only green sands were taken. The fly ash used was class F type.

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

    PubMed

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

    2015-07-01

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

  5. Use of anthracite in the foundry industry

    SciTech Connect

    Bethray, A.

    1994-12-31

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

  6. Application Specific Electronic Module (ASEM) Merchant Foundry.

    DTIC Science & Technology

    1995-10-30

    The commercial part of Motorola’s ASEM Foundry is the responsibility of GSTG’s Diversified Technologies Division (DTD) and is a joint venture with...including design, part selection, layout and test. A copy of the business plan as presented at the formation of the joint venture is included as

  7. Integration of IC Foundries and MEMS Fabrication

    DTIC Science & Technology

    2009-03-01

    Peterson, 1982) Polysilicon surface micromachining LIGA (Karlsruhe, 1986) Silicon accelerometers commercialized Micromotors MOSIS CMOS MEMS (1991) MUMPS...1992) DRIE (1995) ’80s Surface Micromachining ’90s MEMS Foundries Bulk Si Micromachining ASTM MEMS Test Structures (1998) Future MOSIS (1986) ASIMPS

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

    SciTech Connect

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

    2005-06-30

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

  9. Plasmonic Smart Windows: A New Invention from Berkeley's Molecular Foundry

    NASA Astrophysics Data System (ADS)

    Garcia, Guillermo

    2014-03-01

    In the United States, roughly 20% of the annual energy consumption comes from lighting and thermal management within buildings. By adjusting to the surrounding environment, dynamic ``smart'' window coatings minimize the need for heating and artificial lighting through solar gain optimization. Current dynamic windows can only operate through a visible tint, which reduces natural light during thermal management. This talk will focus on discussing a near infrared plasmonic electrochromic coating developed at Berkeley's Molecular Foundry that dynamically modulate solar heat without affecting visible light. Use of this new class of dynamic coating can improve energy consumption by minimizing artificial lighting during solar gain optimization.

  10. CLASSIFYING PROCESSES: AN ESSAY IN APPLIED ONTOLOGY

    PubMed Central

    Smith, Barry

    2013-01-01

    We begin by describing recent developments in the burgeoning discipline of applied ontology, focusing especially on the ways ontologies are providing a means for the consistent representation of scientific data. We then introduce Basic Formal Ontology (BFO), a top-level ontology that is serving as domain-neutral framework for the development of lower level ontologies in many specialist disciplines, above all in biology and medicine. BFO is a bicategorial ontology, embracing both three-dimensionalist (continuant) and four-dimensionalist (occurrent) perspectives within a single framework. We examine how BFO-conformant domain ontologies can deal with the consistent representation of scientific data deriving from the measurement of processes of different types, and we outline on this basis the first steps of an approach to the classification of such processes within the BFO framework.1 PMID:23888086

  11. 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.

  12. 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

  13. DEDUCE Clinical Text: An Ontology-based Module to Support Self-Service Clinical Notes Exploration and Cohort Development.

    PubMed

    Roth, Christopher; Rusincovitch, Shelley A; Horvath, Monica M; Brinson, Stephanie; Evans, Steve; Shang, Howard C; Ferranti, Jeffrey M

    2013-01-01

    Large amounts of information, as well as opportunities for informing research, education, and operations, are contained within clinical text such as radiology reports and pathology reports. However, this content is less accessible and harder to leverage than structured, discrete data. We report on an extension to the Duke Enterprise Data Unified Content Explorer (DEDUCE), a self-service query tool developed to provide clinicians and researchers with access to data within the Duke Medicine Enterprise Data Warehouse (EDW). The DEDUCE Clinical Text module supports ontology-based text searching, enhanced filtering capabilities based on document attributes, and integration of clinical text with structured data and cohort development. The module is implemented with open-source tools extensible to other institutions, including a Java-based search engine (Apache Solr) with complementary full-text indexing library (Lucene) employed with a negation engine (NegEx) modified by clinical users to include to local domain-specific negation phrases.

  14. 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…

  15. 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

  16. 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.

  17. 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.

  18. 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.

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

    PubMed

    d'Aquin, Mathieu; Noy, Natalya F

    2012-03-01

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

  20. 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

  1. 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.

  2. 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.

  3. 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.

  4. Creating a magnetic resonance imaging ontology

    PubMed Central

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

    2011-01-01

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

  5. Design of Wrapper Integration Within the DataFoundry Bioinformatics Application

    SciTech Connect

    Anderson, J; Critchlow, T

    2002-08-20

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

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

    NASA Astrophysics Data System (ADS)

    Piasecki, M.; Beran, B.

    2007-12-01

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

  7. 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

  8. 1928 MALLEABLE FOUNDRY MOLD CONVEYOR #1 SHOWING CONVEYOR AND TRACK ...

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

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

  9. 28. CORE STORAGE AREA OF THE GREY IRON FOUNDRY SHOWING ...

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

    28. CORE STORAGE AREA OF THE GREY IRON FOUNDRY SHOWING CORES THAT WILL BE USED TO CREATE INTERIOR WALLS OF SMALL BALL VALVES, FOREGROUND, AND LARGE GATE VALVES, BACKGROUND. - Stockham Pipe & Fittings Company, Grey Iron Foundry, 4000 Tenth Avenue North, Birmingham, Jefferson County, AL

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

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

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

  11. 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

  12. 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

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

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

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

  14. 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

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

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

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

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

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

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

  17. 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

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

    ERIC Educational Resources Information Center

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

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

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

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

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

  20. 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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

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

    2012-01-01

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

  3. Using Network Extracted Ontologies to Identify Novel Genes with Roles in Appressorium Development in the Rice Blast Fungus Magnaporthe oryzae

    PubMed Central

    Ames, Ryan M.

    2017-01-01

    Magnaporthe oryzae is the causal agent of rice blast disease, the most important infection of rice worldwide. Half the world’s population depends on rice for its primary caloric intake and, as such, rice blast poses a serious threat to food security. The stages of M. oryzae infection are well defined, with the formation of an appressorium, a cell type that allows penetration of the plant cuticle, particularly well studied. However, many of the key pathways and genes involved in this disease stage are yet to be identified. In this study, I have used network-extracted ontologies (NeXOs), hierarchical structures inferred from RNA-Seq data, to identify pathways involved in appressorium development, which in turn highlights novel genes with potential roles in this process. This study illustrates the use of NeXOs for pathway identification from large-scale genomics data and also identifies novel genes with potential roles in disease. The methods presented here will be useful to study disease processes in other pathogenic species and these data represent predictions of novel targets for intervention in M. oryzae. PMID:28106722

  4. Predicting the extension of biomedical ontologies.

    PubMed

    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.

  5. Recycling of base metals from metal wastes of brass foundries

    SciTech Connect

    Nesbitt, C.C.; Xue, S.

    1995-07-01

    A process has been developed to recover and recycle metals from wastes of brass foundries which contain copper, zinc and lead in various quantities. Tests were conducted to evaluate several leachants, including sulfuric acid, ammonia, hydrochloric acid, cyanide and acetic acid, and to determine the optimum leaching conditions, such as air flow rate, initial copper ion concentration, temperature, and agitation strength. Sulfuric acid containing copper sulfate with dissolved oxygen is the most successful leachant. More than 99% of the copper and zinc originally present in the waste was dissolved, while only 0.5% of the lead entered the solution after 14 hours of leaching. The leaching mechanisms of copper, zinc, and lead are proposed. The copper and zinc can be recovered from the solution by electrolytic processing. The unleached residue may be converted to a lead carbonate which can be converted to litharge at 400--450 C and to massicot at temperature above 500 C by calcination.

  6. 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.

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

    ERIC Educational Resources Information Center

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

    2015-01-01

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

  8. From Relational Ontology to Transformative Activist Stance on Development and Learning: Expanding Vygotsky's (CHAT) Project

    ERIC Educational Resources Information Center

    Stetsenko, Anna

    2008-01-01

    This paper offers steps towards overcoming current fragmentation within sociocultural approaches by expansively reconstructing a broad dialectical view on human development and learning (drawing on Vygotsky's project) underwritten by ideology of social justice. The common foundation for sociocultural approaches is developed by dialectically…

  9. The Plasmodium falciparum Sexual Development Transcriptome: A Microarray Analysis using Ontology-Based Pattern Identification

    DTIC Science & Technology

    2005-06-17

    et al. Implication of a Plas- modium falciparum gene in the switch between asexual reproduction and gametocytogenesis. Mol Biochem Parasitol 2005;140(2...falciparum [4,5]. The switch from an asexual to sexual mode of replication begins in the haploid intraery- throcytic stages, where a sub-population of... asexual parasites begin to develop into male and female gametocytes. This pro- cess of gametocyte development continues in the human host over a period of

  10. Bringing Ontology to the Gene Ontology

    PubMed Central

    Andersen, William

    2003-01-01

    We present an analysis of some considerations involved in expressing the Gene Ontology (GO) as a machine-processible ontology, reflecting principles of formal ontology. GO is a controlled vocabulary that is intended to facilitate communication between biologists by standardizing usage of terms in database annotations. Making such controlled vocabularies maximally useful in support of bioinformatics applications requires explicating in machine-processible form the implicit background information that enables human users to interpret the meaning of the vocabulary terms. In the case of GO, this process would involve rendering the meanings of GO into a formal (logical) language with the help of domain experts, and adding additional information required to support the chosen formalization. A controlled vocabulary augmented in these ways is commonly called an ontology. In this paper, we make a modest exploration to determine the ontological requirements for this extended version of GO. Using the terms within the three GO hierarchies (molecular function, biological process and cellular component), we investigate the facility with which GO concepts can be ontologized, using available tools from the philosophical and ontological engineering literature. PMID:18629099

  11. Hydrologic Ontology for the Web

    NASA Astrophysics Data System (ADS)

    Bermudez, L. E.; Piasecki, M.

    2003-12-01

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

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

    ERIC Educational Resources Information Center

    Yalcinalp, Serpil; Gulbahar, Yasemin

    2010-01-01

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

  13. Development of an ontology-anchored data warehouse meta-model.

    PubMed

    Kamal, Jyoti; Borlawsky, Tara; Payne, Philip R O

    2007-10-11

    Data warehouses must provide a flexible data model that is integrated with knowledge and metadata describing their components and contents. To provide for advanced query functionality at The Ohio State University Medical Center (OSUMC), we have developed an abstraction layer, or meta-model for our existing Information Warehouse (IW) in order to conceptually and semantically describe and classify its structure and contents using the UMLS.

  14. Ontological Annotation with WordNet

    SciTech Connect

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

    2006-06-06

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

  15. Automating Ontological Annotation with WordNet

    SciTech Connect

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

    2006-01-22

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

  16. 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

  17. Ion traps fabricated in a CMOS foundry

    SciTech Connect

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

    2014-07-28

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

  18. 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.

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

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

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

  20. 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

  1. 38. INTERIOR VIEW OF FOUNDRY SHOWING HEAVY TIMBER ROOF TRUSSES ...

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

    38. INTERIOR VIEW OF FOUNDRY SHOWING HEAVY TIMBER ROOF TRUSSES AND TRAVELING CRANE. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  2. 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

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

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

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

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

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

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

  5. 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

  6. 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

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

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

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

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

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

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

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

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

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

  10. 46. VIEW OF CROSSSECTION OF FOUNDRY BUILDING SHOWING ROOF TRUSSING ...

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

    46. VIEW OF CROSS-SECTION OF FOUNDRY BUILDING SHOWING ROOF TRUSSING SYSTEM THAT WAS REVEALED DURING DEMOLITION. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  11. 40. DETAIL VIEW OF FOUNDRY HEAVY TIMBER ROOF TRUSSING SYSTEM. ...

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

    40. DETAIL VIEW OF FOUNDRY HEAVY TIMBER ROOF TRUSSING SYSTEM. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  12. Temporal Ontologies for Geoscience: Alignment Challenges

    NASA Astrophysics Data System (ADS)

    Cox, S. J. D.

    2014-12-01

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

  13. 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.

  14. Ontology for Genome Comparison and Genomic Rearrangements

    PubMed Central

    Flanagan, Keith; Stevens, Robert; Pocock, Matthew; Lee, Pete

    2004-01-01

    We present an ontology for describing genomes, genome comparisons, their evolution and biological function. This ontology will support the development of novel genome comparison algorithms and aid the community in discussing genomic evolution. It provides a framework for communication about comparative genomics, and a basis upon which further automated analysis can be built. The nomenclature defined by the ontology will foster clearer communication between biologists, and also standardize terms used by data publishers in the results of analysis programs. The overriding aim of this ontology is the facilitation of consistent annotation of genomes through computational methods, rather than human annotators. To this end, the ontology includes definitions that support computer analysis and automated transfer of annotations between genomes, rather than relying upon human mediation. PMID:18629137

  15. 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.

  16. 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

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

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

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

  18. An ontology for description of drug discovery investigations.

    PubMed

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

    2010-03-25

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

  19. 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

  20. Kuhn's Ontological Relativism.

    ERIC Educational Resources Information Center

    Sankey, Howard

    2000-01-01

    Discusses Kuhn's model of scientific theory change. Documents Kuhn's move away from conceptual relativism and rational relativism. Provides an analysis of his present ontological form of relativism. (CCM)

  1. 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…

  2. Gene Ontology Annotations and Resources

    PubMed Central

    2013-01-01

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

  3. Gene Ontology annotations and resources.

    PubMed

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

    2013-01-01

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

  4. The Ontology of Disaster.

    ERIC Educational Resources Information Center

    Thompson, Neil

    1995-01-01

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

  5. 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…

  6. 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.

  7. Effects of Guideline-Based Training on the Quality of Formal Ontologies: A Randomized Controlled Trial

    PubMed Central

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

    2013-01-01

    Background The importance of ontologies in the biomedical domain is generally recognized. However, their quality is often too poor for large-scale use in critical applications, at least partially due to insufficient training of ontology developers. Objective To show the efficacy of guideline-based ontology development training on the performance of ontology developers. The hypothesis was that students who received training on top-level ontologies and design patterns perform better than those who only received training in the basic principles of formal ontology engineering. Methods A curriculum was implemented based on a guideline for ontology design. A randomized controlled trial on the efficacy of this curriculum was performed with 24 students from bioinformatics and related fields. After joint training on the fundamentals of ontology development the students were randomly allocated to two groups. During the intervention, each group received training on different topics in ontology development. In the assessment phase, all students were asked to solve modeling problems on topics taught differentially in the intervention phase. Primary outcome was the similarity of the students’ ontology artefacts compared with gold standard ontologies developed by the authors before the experiment; secondary outcome was the intra-group similarity of group members’ ontologies. Results The experiment showed no significant effect of the guideline-based training on the performance of ontology developers (a) the ontologies developed after specific training were only slightly but not significantly closer to the gold standard ontologies than the ontologies developed without prior specific training; (b) although significant differences for certain ontologies were detected, the intra-group similarity was not consistently influenced in one direction by the differential training. Conclusion Methodologically limited, this study cannot be interpreted as a general failure of a guideline

  8. Nuclear Nonproliferation Ontology Assessment Team Final Report

    SciTech Connect

    Strasburg, Jana D.; Hohimer, Ryan E.

    2012-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  10. Exploring biomedical ontology mappings with graph theory methods

    PubMed Central

    2017-01-01

    Background 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. Methods 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. Results 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. PMID:28265499

  11. The Gene Ontology: enhancements for 2011.

    PubMed

    2012-01-01

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

  12. The Gene Ontology: enhancements for 2011

    PubMed Central

    2012-01-01

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

  13. 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.

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

    ERIC Educational Resources Information Center

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

    2016-01-01

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

  15. Natural Language Processing methods and systems for biomedical ontology learning.

    PubMed

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

    2011-02-01

    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.

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

    PubMed Central

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

    2010-01-01

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

  17. Meeting report: advancing practical applications of biodiversity ontologies

    PubMed Central

    2014-01-01

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

  18. NanoParticle Ontology for Cancer Nanotechnology Research

    PubMed 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

  19. 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

  20. Molecular Foundry Workshop draws overflow crowd to BerkeleyLab

    SciTech Connect

    Robinson, Art

    2002-11-27

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

  1. Ontologies for Bioinformatics

    PubMed Central

    Schuurman, Nadine; Leszczynski, Agnieszka

    2008-01-01

    The past twenty years have witnessed an explosion of biological data in diverse database formats governed by heterogeneous infrastructures. Not only are semantics (attribute terms) different in meaning across databases, but their organization varies widely. Ontologies are a concept imported from computing science to describe different conceptual frameworks that guide the collection, organization and publication of biological data. An ontology is similar to a paradigm but has very strict implications for formatting and meaning in a computational context. The use of ontologies is a means of communicating and resolving semantic and organizational differences between biological databases in order to enhance their integration. The purpose of interoperability (or sharing between divergent storage and semantic protocols) is to allow scientists from around the world to share and communicate with each other. This paper describes the rapid accumulation of biological data, its various organizational structures, and the role that ontologies play in interoperability. PMID:19812775

  2. 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.

  3. An Approach to Support Collaborative Ontology Construction.

    PubMed

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

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-04-01

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

  5. 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.

  6. GFVO: the Genomic Feature and Variation Ontology.

    PubMed

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  8. 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

  9. 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

  10. Reuse of Spent Foundry Sands Yields Environmental Benefits

    EPA Pesticide Factsheets

    WASHINGTON - The U.S. Environmental Protection Agency (EPA), in conjunction with the U.S. Department of Agriculture (USDA) and the Ohio State University, today released a risk assessment concluding that silica-based spent foundry sands from iron, st

  11. 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

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

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

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

  13. 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

  14. 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

  15. 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

  16. AmiGO: online access to ontology and annotation data

    SciTech Connect

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

    2009-01-15

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

  17. FMA-RadLex: An Application Ontology of Radiological Anatomy derived from the Foundational Model of Anatomy Reference Ontology

    PubMed Central

    Mejino, Jose L.V.; Rubin, Daniel L.; Brinkley, James F.

    2008-01-01

    Domain reference ontologies are being developed to serve as generalizable and reusable sources designed to support any application specific to the domain. The challenge is how to develop ways to derive or adapt pertinent portions of reference ontologies into application ontologies. In this paper we demonstrate how a subset of anatomy relevant to the domain of radiology can be derived from an anatomy reference ontology, the Foundational Model of Anatomy (FMA) Ontology, to create an application ontology that is robust and expressive enough to incorporate and accommodate all salient anatomical knowledge necessary to support existing and emerging systems for managing anatomical information related to radiology. The principles underlying this work are applicable to domains beyond radiology, so our results could be extended to other areas of biomedicine in the future. PMID:18999035

  18. The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age

    PubMed Central

    Dahdul, Wasila M.; Lundberg, John G.; Midford, Peter E.; Balhoff, James P.; Lapp, Hilmar; Vision, Todd J.; Haendel, Melissa A.; Westerfield, Monte; Mabee, Paula M.

    2010-01-01

    The rich knowledge of morphological variation among organisms reported in the systematic literature has remained in free-text format, impractical for use in large-scale synthetic phylogenetic work. This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases. We have undertaken an effort to prototype a curated, ontology-based evolutionary morphology database that maps to these genetic databases (http://kb.phenoscape.org) to facilitate investigation into the mechanistic basis and evolution of phenotypic diversity. Among the first requirements in establishing this database was the development of a multispecies anatomy ontology with the goal of capturing anatomical data in a systematic and computable manner. An ontology is a formal representation of a set of concepts with defined relationships between those concepts. Multispecies anatomy ontologies in particular are an efficient way to represent the diversity of morphological structures in a clade of organisms, but they present challenges in their development relative to single-species anatomy ontologies. Here, we describe the Teleost Anatomy Ontology (TAO), a multispecies anatomy ontology for teleost fishes derived from the Zebrafish Anatomical Ontology (ZFA) for the purpose of annotating varying morphological features across species. To facilitate interoperability with other anatomy ontologies, TAO uses the Common Anatomy Reference Ontology as a template for its upper level nodes, and TAO and ZFA are synchronized, with zebrafish terms specified as subtypes of teleost terms. We found that the details of ontology architecture have ramifications for querying, and we present general challenges in developing a multispecies anatomy ontology, including refinement of definitions, taxon-specific relationships among terms, and representation of taxonomically variable developmental pathways. PMID:20547776

  19. Enabling Ontology Based Semantic Queries in Biomedical Database Systems

    PubMed Central

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

    2013-01-01

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

  20. 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.

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

    SciTech Connect

    Gourdin, W H; Sze, J

    1999-08-19

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

  2. 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

  3. Ontology-Driven Information Integration

    NASA Technical Reports Server (NTRS)

    Tissot, Florence; Menzel, Chris

    2005-01-01

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

  4. Developing the ontological foundations of a terminological system for end-stage diseases, organ failure, dialysis and transplantation.

    PubMed

    Jacquelinet, Christian; Burgun, Anita; Delamarre, Denis; Strang, Nigel; Djabbour, Sami; Boutin, Bernard; Le Beux, Pierre

    2003-07-01

    The Etablissement français des Greffes (EfG) is a state agency dealing with Public Health issues related to organ, tissue and cell transplantation in France. The evaluation of organ retrieval and transplantation activities, one of its missions, is supported by a national information system (EfG-IS). The EfG-IS is moving towards a new n-tier architecture comprising a terminology server for end-stage diseases, organ failure, dialysis and transplantation (EfG-TS). Following a preliminary audit of the existing coding system and in order to facilitate data recording, to improve the quality of information, to assume compatibility with terminological existing standards and to allow semantic interoperability with other local, national or international registries, a specific work has been conducted on the thesauri to integrate within the EfG-TS. In this paper focusing on the server's content rather than the container, we report first the functional and cognitive requirements that resulted from the preliminary audit. We then describe the methodological approach used to build the terminological server on "sound ontological foundations". We performed the semantic analysis of existing medical terms to set up disease description frame-like structures. These diseases description frames consist of a limited set of nosological discriminating slots such as etiology, semiology, pathology, evolution and associated diseases. Each relevant medical term is thus associated to a concept defined and inserted within a hierarchy according to disease description frame resulting from the semantic analysis. Last, because this terminological server is shared by various transplant and dialysis centers to record patient data at different time point, contextualization of terms appeared as one of the functional requirements. We will also point out various contexts for medical terms and how they have been taken into account.

  5. On the Ontology Based Representation of Cell Lines

    PubMed Central

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

    2012-01-01

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

  6. 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…

  7. GFVO: the Genomic Feature and Variation Ontology

    PubMed Central

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

    2015-01-01

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

  8. 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.

  9. 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

  10. Dahlbeck and Pure Ontology

    ERIC Educational Resources Information Center

    Mackenzie, Jim

    2016-01-01

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

  11. Ontology, Language, and Culture

    ERIC Educational Resources Information Center

    Hyde, Richard Bruce

    The purpose of this essay is to consider some of the practical implications of Martin Heideger's view that "Language is the house of Being," for the academic study of cultural transformation and intercultural communication. The paper describes the ontological basis of Heidegger's work, and the inquiry into Being, and contains sections on…

  12. 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.

  13. 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.

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

    NASA Astrophysics Data System (ADS)

    Pautz, J.

    1980-08-01

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

  15. NOA: a novel Network Ontology Analysis method.

    PubMed

    Wang, Jiguang; Huang, Qiang; Liu, Zhi-Ping; Wang, Yong; Wu, Ling-Yun; Chen, Luonan; Zhang, Xiang-Sun

    2011-07-01

    Gene ontology analysis has become a popular and important tool in bioinformatics study, and current ontology analyses are mainly conducted in individual gene or a gene list. However, recent molecular network analysis reveals that the same list of genes with different interactions may perform different functions. Therefore, it is necessary to consider molecular interactions to correctly and specifically annotate biological networks. Here, we propose a novel Network Ontology Analysis (NOA) method to perform gene ontology enrichment analysis on biological networks. Specifically, NOA first defines link ontology that assigns functions to interactions based on the known annotations of joint genes via optimizing two novel indexes 'Coverage' and 'Diversity'. Then, NOA generates two alternative reference sets to statistically rank the enriched functional terms for a given biological network. We compare NOA with traditional enrichment analysis methods in several biological networks, and find that: (i) NOA can capture the change of functions not only in dynamic transcription regulatory networks but also in rewiring protein interaction networks while the traditional methods cannot and (ii) NOA can find more relevant and specific functions than traditional methods in different types of static networks. Furthermore, a freely accessible web server for NOA has been developed at http://www.aporc.org/noa/.

  16. 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

  17. 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.

  18. Cross-Ontology multi-level association rule mining in the Gene Ontology.

    PubMed

    Manda, Prashanti; Ozkan, Seval; Wang, Hui; McCarthy, Fiona; Bridges, Susan M

    2012-01-01

    The Gene Ontology (GO) has become the internationally accepted standard for representing function, process, and location aspects of gene products. The wealth of GO annotation data provides a valuable source of implicit knowledge of relationships among these aspects. We describe a new method for association rule mining to discover implicit co-occurrence relationships across the GO sub-ontologies at multiple levels of abstraction. Prior work on association rule mining in the GO has concentrated on mining knowledge at a single level of abstraction and/or between terms from the same sub-ontology. We have developed a bottom-up generalization procedure called Cross-Ontology Data Mining-Level by Level (COLL) that takes into account the structure and semantics of the GO, generates generalized transactions from annotation data and mines interesting multi-level cross-ontology association rules. We applied our method on publicly available chicken and mouse GO annotation datasets and mined 5368 and 3959 multi-level cross ontology rules from the two datasets respectively. We show that our approach discovers more and higher quality association rules from the GO as evaluated by biologists in comparison to previously published methods. Biologically interesting rules discovered by our method reveal unknown and surprising knowledge about co-occurring GO terms.

  19. 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.

  20. Primitive Ontology and the Classical World

    NASA Astrophysics Data System (ADS)

    Allori, Valia

    In this chapter, I present the common structure of quantum theories with a primitive ontology (PO), and discuss in what sense the classical world emerges from quantum theories as understood in this framework. In addition, I argue that the PO approach is better at analyzing the classical limit than the rival wave function ontology approach or any other approach in which the classical world is non-reductively "emergent:" even if the classical limit within this framework needs to be fully developed, the difficulties are technical rather than conceptual, while this is not true for the alternatives.

  1. Ontology-Based Model Of Firm Competitiveness

    NASA Astrophysics Data System (ADS)

    Deliyska, Boryana; Stoenchev, Nikolay

    2010-10-01

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

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

    PubMed

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

    2016-08-01

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

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

    PubMed

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

    2016-01-01

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

  4. Mini Ontologies and Metadata Expressions

    NASA Astrophysics Data System (ADS)

    King, T. A.; Ritschel, B.

    2013-12-01

    Ontologies come in many forms and with a wide range of detail and specificity. Of particular interest in the realm of science are classification schemes or taxonomies. Within general science domains there may be multiple taxonomies. Each taxonomy can be represented as a very narrowly defined domain ontology. We call such ontologies "mini ontologies". Since mini ontologies are very modular and portable they can be used in a variety of context. To illustrate the generation and use of mini ontologies we show how enumerations which may part of an existing data model, like SPASE *Region enumerations, can be modeled as a mini ontology. We show how such ontologies can be transformed to generate metadata expressions which can be readily used in different operational context, for example in the tag of a web page. We define a set of context specific transforms for commonly used metadata expressions which can preserve the semantic information in a mini ontology and describe how such expressions are reversible. The sharing and adoption of mini ontologies can significantly enhance the discovery and use of related data resources within a community. We look at several cases where this is true with a special focus on the international ESPAS project.

  5. An evaluation of ontology exchange languages for bioinformatics.

    PubMed

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

    2000-01-01

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

  6. 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.

  7. 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.

  8. OAE: The Ontology of Adverse Events

    PubMed Central

    2014-01-01

    Background 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. Description 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. Conclusion 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

  9. In Defense of Chi's Ontological Incompatibility Hypothesis

    ERIC Educational Resources Information Center

    Slotta, James D.

    2011-01-01

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

  10. 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…

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

    PubMed

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

    2007-02-20

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

  12. The ontology of biological taxa

    PubMed Central

    Schulz, Stefan; Stenzhorn, Holger; Boeker, Martin

    2008-01-01

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

  13. Use of standardized procedures to evaluate metal leaching from waste foundry sands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As part of the casting process, foundries create sand molds and cores to produce ferrous and non-ferrous metal castings. After the process, a portion of the sand is discarded and becomes waste foundry sand (WFS). The aim of this study was to quantify metals (i.e. Ag, Ba, Cd, Cr, Cu, Ni, Pb, and Zn)...

  14. 77 FR 15123 - Foundry Coke From China; Scheduling of an Expedited Five-Year Review

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-14

    ... COMMISSION Foundry Coke From China; Scheduling of an Expedited Five-Year Review AGENCY: United States...)) (the Act) to determine whether revocation of the antidumping duty order on foundry coke from China... submitted by ABC Coke, Erie Coke, Tonawanda Coke Corporation, and Walter Coke Co. to be...

  15. Compressed Air System Improvement Project Saves Foundry Energy and Increases Production

    SciTech Connect

    2002-05-01

    This case study highlights International Truck and Engine Corporation's optimization project on the compressed air system that serves its foundry, Indianapolis Casting Corporation. Due to the project's implementation, the system's efficiency was greatly improved, allowing the foundry to operate with less compressor capacity, which resulted in reduced energy consumption, significant maintenance savings, and more reliable production.

  16. Compressed Air System Retrofitting Project Improves Productivity at a Foundry (Cast Masters, Bowling Green, OH)

    SciTech Connect

    2002-06-01

    This case study highlights International Truck and Engine Corporation's optimization project on the compressed air system that serves its foundry, Indianapolis Casting Corporation. Due to the project's implementation, the system's efficiency was greatly improved, allowing the foundry to operate with less compressor capacity, which resulted in reduced energy consumption, significant maintenance savings, and more reliable production.

  17. 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

    ... International Trade Administration Foundry Coke Products From the People's Republic of China: Continuation of... antidumping duty order on foundry coke products from the People's Republic of China (``PRC'') would likely... notice of initiation of the sunset review of the antidumping duty order on foundry coke products from...

  18. 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

    ... International Trade Administration Foundry Coke Products From the People's Republic of China: Final Results of... coke products (``foundry coke'') from the People's Republic of China (``PRC'') pursuant to section 751... duty order on foundry coke from the PRC would be likely to lead to continuation or recurrence...

  19. Extending ontologies by finding siblings using set expansion techniques

    PubMed Central

    Fabian, Götz; Wächter, Thomas; Schroeder, Michael

    2012-01-01

    Motivation: Ontologies are an everyday tool in biomedicine to capture and represent knowledge. However, many ontologies lack a high degree of coverage in their domain and need to improve their overall quality and maturity. Automatically extending sets of existing terms will enable ontology engineers to systematically improve text-based ontologies level by level. Results: We developed an approach to extend ontologies by discovering new terms which are in a sibling relationship to existing terms of an ontology. For this purpose, we combined two approaches which retrieve new terms from the web. The first approach extracts siblings by exploiting the structure of HTML documents, whereas the second approach uses text mining techniques to extract siblings from unstructured text. Our evaluation against MeSH (Medical Subject Headings) shows that our method for sibling discovery is able to suggest first-class ontology terms and can be used as an initial step towards assessing the completeness of ontologies. The evaluation yields a recall of 80% at a precision of 61% where the two independent approaches are complementing each other. For MeSH in particular, we show that it can be considered complete in its medical focus area. We integrated the work into DOG4DAG, an ontology generation plugin for the editors OBO-Edit and Protégé, making it the first plugin that supports sibling discovery on-the-fly. Availability: Sibling discovery for ontology is available as part of DOG4DAG (www.biotec.tu-dresden.de/research/schroeder/dog4dag) for both Protégé 4.1 and OBO-Edit 2.1. Contact: ms@biotec.tu-dresden.de; goetz.fabian@biotec.tu-dresden.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:22689774

  20. Providing visualisation support for the analysis of anatomy ontology data

    PubMed Central

    Dadzie, Aba-Sah; Burger, Albert

    2005-01-01

    Background Improvements in technology have been accompanied by the generation of large amounts of complex data. This same technology must be harnessed effectively if the knowledge stored within the data is to be retrieved. Storing data in ontologies aids its management; ontologies serve as controlled vocabularies that promote data exchange and re-use, improving analysis. The Edinburgh Mouse Atlas Project stores the developmental stages of the mouse embryo in anatomy ontologies. This project is looking at the use of visual data overviews for intuitive analysis of the ontology data. Results A prototype has been developed that visualises the ontologies using directed acyclic graphs in two dimensions, with the ability to study detail in regions of interest in isolation or within the context of the overview. This is followed by the development of a technique that layers individual anatomy ontologies in three-dimensional space, so that relationships across multiple data sets may be mapped using physical links drawn along the third axis. Conclusion Usability evaluations of the applications confirmed advantages in visual analysis of complex data. This project will look next at data input from multiple sources, and continue to develop the techniques presented to provide intuitive identification of relationships that span multiple ontologies. PMID:15790390

  1. 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.

  2. 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

  3. 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

  4. 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.

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

    PubMed

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

    2014-01-01

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

  6. CSEO – the Cigarette Smoke Exposure Ontology

    PubMed Central

    2014-01-01

    Background In the past years, significant progress has been made to develop and use experimental settings for extensive data collection on tobacco smoke exposure and tobacco smoke exposure-associated diseases. Due to the growing number of such data, there is a need for domain-specific standard ontologies to facilitate the integration of tobacco exposure data. Results The CSEO (version 1.0) is composed of 20091 concepts. The ontology in its current form is able to capture a wide range of cigarette smoke exposure concepts within the knowledge domain of exposure science with a reasonable sensitivity and specificity. Moreover, it showed a promising performance when used to answer domain expert questions. The CSEO complies with standard upper-level ontologies and is freely accessible to the scientific community through a dedicated wiki at https://publicwiki-01.fraunhofer.de/CSEO-Wiki/index.php/Main_Page. Conclusions The CSEO has potential to become a widely used standard within the academic and industrial community. Mainly because of the emerging need of systems toxicology to controlled vocabularies and also the lack of suitable ontologies for this domain, the CSEO prepares the ground for integrative systems-based research in the exposure science. PMID:25093069

  7. An Ontology Representation for Water Bodies

    NASA Astrophysics Data System (ADS)

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

    2015-12-01

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

  8. 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.

  9. 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.

  10. Ontological turns, turnoffs and roundabouts.

    PubMed

    Sismondo, Sergio

    2015-06-01

    There has been much talk of an 'ontological turn' in Science and Technology Studies. This commentary explores some recent work on multiple and historical ontologies, especially articles published in this journal, against a background of constructivism. It can be tempting to read an ontological turn as based and promoting a version of perspectivism, but that is inadequate to the scholarly work and opens multiple ontologies to serious criticisms. Instead, we should read our ontological turn or turns as being about multiplicities of practices and the ways in which these practices shape the material world. Ontologies arise out of practices through which people engage with things; the practices are fundamental and the ontologies derivative. The purchase in this move comes from the elucidating power of the verbs that scholars use to analyze relations of practices and objects--which turn out to be specific cases of constructivist verbs. The difference between this ontological turn and constructivist work in Science and Technology Studies appears to be a matter of emphases found useful for different purposes.

  11. Building Ontologies in DAML + OIL

    PubMed Central

    Wroe, Chris; Bechhofer, Sean; Lord, Phillip; Rector, Alan; Goble, Carole

    2003-01-01

    In this article we describe an approach to representing and building ontologies advocated by the Bioinformatics and Medical Informatics groups at the University of Manchester. The hand-crafting of ontologies offers an easy and rapid avenue to delivering ontologies. Experience has shown that such approaches are unsustainable. Description logic approaches have been shown to offer computational support for building sound, complete and logically consistent ontologies. A new knowledge representation language, DAML + OIL, offers a new standard that is able to support many styles of ontology, from hand-crafted to full logic-based descriptions with reasoning support. We describe this language, the OilEd editing tool, reasoning support and a strategy for the language’s use. We finish with a current example, in the Gene Ontology Next Generation (GONG) project, that uses DAML + OIL as the basis for moving the Gene Ontology from its current hand-crafted, form to one that uses logical descriptions of a concept’s properties to deliver a more complete version of the ontology. PMID:18629114

  12. Ontology through a Mindfulness Process

    ERIC Educational Resources Information Center

    Bearance, Deborah; Holmes, Kimberley

    2015-01-01

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

  13. 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

  14. The Development of Cadastral Domain Model Oriented at Unified Real Estate Registration of China Based on Ontology

    NASA Astrophysics Data System (ADS)

    Li, M.; Zhu, X.; Shen, C.; Chen, D.; Guo, W.

    2012-07-01

    With the certain regulation of unified real estate registration taken by the Property Law and the step-by-step advance of simultaneous development in urban and rural in China, it is the premise and foundation to clearly specify property rights and their relations in promoting the integrated management of urban and rural land. This paper aims at developing a cadastral domain model oriented at unified real estate registration of China from the perspective of legal and spatial, which set up the foundation for unified real estate registration, and facilitates the effective interchange of cadastral information and the administration of land use. The legal cadastral model is provided based on the analysis of gap between current model and the demand of unified real estate registration, which implies the restrictions between different rights. Then the new cadastral domain model is constructed based on the legal cadastral domain model and CCDM (van Oosterom et al., 2006), which integrate real estate rights of urban land and rural land. Finally, the model is validated by a prototype system. The results show that the model is applicable for unified real estate registration in China.

  15. 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

  16. Constructing a Geology Ontology Using a Relational Database

    NASA Astrophysics Data System (ADS)

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

    2013-12-01

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

  17. Laboratory Testing of Foundry Sands as Bulking Agents for Porous Media Filters Used to Treat Agricultural Drainage Waters

    NASA Astrophysics Data System (ADS)

    Allred, B. J.

    2008-12-01

    Foundry sands are industrial byproducts that may have potential application as bulking agents that when mixed with small amounts of more chemically reactive materials (i.e. sulfur modified iron, fly ash, etc.) can be used to produce porous media filters capable of removing contaminants from agricultural drainage waters. Foundry sand bulking agents are attractive primarily as a low cost means to maintain the hydraulic efficiency of a filter. Secondarily, the foundry sands themselves may have some capacity for removal of agricultural nutrients and pesticides from water. Consequently, a laboratory study was initiated to quantify hydraulic efficiency and agricultural contaminant removal abilities of six foundry sands. Of the six foundry sands tested, all were obtained in central Ohio, three from iron casting foundries, two from steel casting foundries, and one from an aluminum casting foundry. Hydraulic efficiencies of the foundry sands were assessed by measuring hydraulic conductivity with twice replicated falling-head permeability tests. Batch tests were employed to evaluate foundry sand potential to treat water containing nitrate and phosphate nutrients, along with the pesticide, atrazine. Five of the six foundry sand samples had measured hydraulic conductivity values from 7.6 x 10-3 cm/s to 3.8 x 10-2 cm/s, which is in the range of hydraulic conductivity values found for clean sand. The one foundry sand that was an exception had much lower measured hydraulic conductivity values of 2.75 x 10-5 cm/s and 5.76 x 10-5 cm/s. For the batch tests conducted, none of the nitrate was removed by any of the six foundry sands; however, conversely, almost all of the phosphate was removed by each foundry sand. Batch test atrazine removal results were much more varied. Compared with baseline batch tests, one foundry sand removed two thirds of the atrazine, one foundry sand removed about one half of the atrazine, three foundry sands removed about a third of the atrazine, and one

  18. DataFoundry: Warehousing techniques for dynamic environments

    SciTech Connect

    Critchlow, T.; Fidelis, K.; Ganesh, M.; Musick, R.; Slezak, T., LLNL

    1998-01-29

    Data warehouses and data marts have been successfully applied to a multitude of commercial business applications as tools for integrating and providing access to data located across an enterprise. Although the need for this capability is as vital in the scientific world as in the business domain, working warehouses in our community are scarce. A primary technical reason for this is that our understanding of the concepts being explored in an evolving scientific domain change constantly, leading to rapid changes in the data representation. When any database providing information to a warehouse changes its format, the warehouse must be updated to reflect these changes, or it will not function properly. The cost of maintaining a warehouse using traditional techniques in this environment is prohibitive. This paper describes ideas for dramatically reducing the amount of work that must be done to keep a warehouse up to date in a dynamic, scientific environment. The ideas are being applied in a prototype warehouse called DataFoundry. DataFoundry, currently in use by structural biologists at LLNL, will eventually support scientists at the Department of Energy`s Joint Genome Institute.

  19. Overlapping ontologies and Indigenous knowledge. From integration to ontological self-determination.

    PubMed

    Ludwig, David

    2016-10-01

    Current controversies about knowledge integration reflect conflicting ideas of what it means to "take Indigenous knowledge seriously". While there is increased interest in integrating Indigenous and Western scientific knowledge in various disciplines such as anthropology and ethnobiology, integration projects are often accused of recognizing Indigenous knowledge only insofar as it is useful for Western scientists. The aim of this article is to use tools from philosophy of science to develop a model of both successful integration and integration failures. On the one hand, I argue that cross-cultural recognition of property clusters leads to an ontological overlap that makes knowledge integration often epistemically productive and socially useful. On the other hand, I argue that knowledge integration is limited by ontological divergence. Adequate models of Indigenous knowledge will therefore have to take integration failures seriously and I argue that integration efforts need to be complemented by a political notion of ontological self-determination.

  20. Relating Science and Religion: An Ontology of Taxonomies and Development of a Research Tool for Identifying Individual Views

    NASA Astrophysics Data System (ADS)

    Yasri, Pratchayapong; Arthur, Shagufta; Smith, Mike U.; Mancy, Rebecca

    2013-10-01

    Understanding how individuals view the relationship between science and religion shows promise for explaining a range of aspects of teaching and learning in science. Several taxonomies, consisting of different views by which people relate science and religion, can be found in the philosophical literature. However, most of the science education literature uses these taxonomies selectively and with limited justification, hindering comparison between existing and future studies. The first aim of this paper is therefore to provide a comprehensive review of the different taxonomies described in the literature and to organise the different views according to their similarities and differences. The second aim of the paper is to present a new research tool developed on the basis of the findings of the literature review. This tool consists of a short questionnaire allowing educational researchers to identify the different viewpoints held by pre-service teachers, undergraduates majoring in biology and school learners. We present the tool itself and demonstrate its usefulness and versatility for future science education research based on three empirical studies covering a range of geographical areas, religious backgrounds, educational levels, age groups and genders.

  1. Enabling Ontology Based Semantic Queries in Biomedical Database Systems

    PubMed Central

    Zheng, Shuai; Lu, James

    2014-01-01

    There is a lack of tools to ease the integration and ontology based semantic queries in biomedical databases, which are often annotated with ontology concepts. We aim to provide a middle layer between ontology repositories and semantically annotated databases to support semantic queries directly in the databases with expressive standard database query languages. We have developed a semantic query engine that provides semantic reasoning and query processing, and translates the queries into ontology repository operations on NCBO BioPortal. Semantic operators are implemented in the database as user defined functions extended to the database engine, thus semantic queries can be directly specified in standard database query languages such as SQL and XQuery. The system provides caching management to boosts query performance. The system is highly adaptable to support different ontologies through easy customizations. We have implemented the system DBOntoLink as an open source software, which supports major ontologies hosted at BioPortal. DBOntoLink supports a set of common ontology based semantic operations and have them fully integrated with a database management system IBM DB2. The system has been deployed and evaluated with an existing biomedical database for managing and querying image annotations and markups (AIM). Our performance study demonstrates the high expressiveness of semantic queries and the high efficiency of the queries. PMID:25541585

  2. Inexact Matching of Ontology Graphs Using Expectation-Maximization

    PubMed Central

    Doshi, Prashant; Kolli, Ravikanth; Thomas, Christopher

    2009-01-01

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

  3. Multiple ontologies in action: composite annotations for biosimulation models.

    PubMed

    Gennari, John H; Neal, Maxwell L; Galdzicki, Michal; Cook, Daniel L

    2011-02-01

    There now exists a rich set of ontologies that provide detailed semantics for biological entities of interest. However, there is not (nor should there be) a single source ontology that provides all the necessary semantics for describing biological phenomena. In the domain of physiological biosimulation models, researchers use annotations to convey semantics, and many of these annotations require the use of multiple reference ontologies. Therefore, we have developed the idea of composite annotations that access multiple ontologies to capture the physics-based meaning of model variables. These composite annotations provide the semantic expressivity needed to disambiguate the often-complex features of biosimulation models, and can be used to assist with model merging and interoperability. In this paper, we demonstrate the utility of composite annotations for model merging by describing their use within SemGen, our semantics-based model composition software. More broadly, if orthogonal reference ontologies are to meet their full potential, users need tools and methods to connect and link these ontologies. Our composite annotations and the SemGen tool provide one mechanism for leveraging multiple reference ontologies.

  4. Foundries Footprint, December 2010 (MECS 2006)

    SciTech Connect

    none,

    2010-06-01

    Manufacturing energy and carbon footprints map fuel energy consumption and losses, as well as greenhouse gas emissions from fuel consumption, for fifteen individual U.S. manufacturing sectors (representing 94% of all manufacturing energy use) and for the entire manufacturing industry sector. By providing energy consumption and emissions figures broken down by end use, the footprints allow for comparisons of energy use and emissions sources both within and across sectors. The footprints portray a large amount of information for each sector, including: * Comparison of the energy generated offsite and transferred to facilities versus that generated onsite * Nature and amount of energy consumed by end use within facilities * Magnitude of the energy lost both outside and inside facility boundaries * Magnitude of the greenhouse gas emissions released due to the combustion of fuel. Energy losses indicate opportunities to improve efficiency by implementing energy management best practices, upgrading energy systems, and developing new technologies. Footprints are available below for each sector. Data is presented in two levels of detail. The first page provides a high-level snapshot of the offsite and onsite energy flow, and the second page shows the detail for onsite generation and end use of energy. The energy data is primarily provided by the U.S. Department of Energy (DOE) Energy Information Administration's (EIA's) Manufacturing Energy Consumption Survey (MECS), and therefore reflects consumption in the year 2006, when the survey was last completed.

  5. Foundries Footprint, October 2012 (MECS 2006)

    SciTech Connect

    2012-10-17

    Manufacturing energy and carbon footprints map energy consumption and losses, as well as greenhouse gas emissions from fuel consumption, for fifteen individual U.S. manufacturing sectors (representing 94% of all manufacturing energy use) and for the entire manufacturing sector. By providing energy consumption and emissions figures broken down by end use, the footprints allow for comparisons of energy use and emissions sources both within and across sectors. The footprints portray a large amount of information for each sector, including: * Comparison of the energy generated offsite and transferred to facilities versus that generated onsite * Nature and amount of energy consumed by end use within facilities * Magnitude of the energy lost both outside and inside facility boundaries * Magnitude of the greenhouse gas emissions released as a result of manufacturing energy use. Energy losses indicate opportunities to improve efficiency by implementing energy management best practices, upgrading energy systems, and developing new technologies. Footprints are available below for each sector. Data is presented in two levels of detail. The first page provides a high- level snapshot of the offsite and onsite energy flow, and the second page shows the detail for onsite generation and end use of energy. The principle energy use data source is the U.S. Department of Energy (DOE) Energy Information Administration's (EIA's) Manufacturing Energy Consumption Survey (MECS), for consumption in the year 2006, when the survey was last completed.

  6. Establishing and harmonizing ontologies in an interdisciplinary health care clinical research environment.

    PubMed

    Smith, Barry; Brochhausen, Mathias

    2008-01-01

    Ontologies are being ever more commonly used in biomedical informatics. The paper provides a survey of some of these uses, and of the relations between ontologies and other terminology resources. In order for ontologies to become truly useful, two objectives must be met. First, ways must be found for the transparent evaluation of ontologies. Second, existing ontologies need to be harmonized. The authors argue that one key foundation for both ontology evaluation and harmonization is the adoption of a realist paradigm in ontology development. For science-based ontologies of the sort which concern us in the eHealth arena, it is reality that provides the common benchmark against which ontologies can be evaluated and aligned within larger frameworks. Given the current multitude of ontologies in the biomedical domain the need for harmonization is becoming ever more urgent. An example of such harmonization within the ACGT project is described, which draws on ontology-based computing as a basis for sharing clinical and laboratory data on cancer research.

  7. Reduction in Energy Consumption & Variability in Steel Foundry Operations

    SciTech Connect

    Frank Peters

    2005-05-04

    This project worked to improve the efficiency of the steel casting industry by reducing the variability that occurs because of process and product variation. The project focused on the post shakeout operations since roughly half of the production costs are in this area. These improvements will reduce the amount of variability, making it easier to manage the operation and improve the competitiveness. The reduction in variability will also reduce the need for many rework operations, which will result in a direct reduction of energy usage, particularly by the reduction of repeated heat treatment operations. Further energy savings will be realized from the reduction of scrap and reduced handling. Field studies were conducted at ten steel foundries that represented the U.S. steel casting industry, for a total of over 100 weeks of production observation. These studies quantified the amount of variability, and looked toward determining the source. A focus of the data collected was the grinding operations since this is a major effort in the cleaning room, and it represents the overall casting quality. The grinding was divided into two categories, expected and unexpected. Expected grinding is that in which the location of the effort is known prior to making the casting, such as smoothing parting lines, gates, and riser contacts. Unexpected grinding, which was approximately 80% of the effort, was done to improve the surfaces at weld repair locations, to rectify burnt on sand, and other surface anomalies at random locations. Unexpected grinding represents about 80% of the grinding effort. By quantifying this effort, the project raised awareness within the industry and the industry is continuing to make improvements. The field studies showed that the amount of variation of grinding operations (normalized because of the diverse set of parts studied) was very consistent across the industry. The field studies identified several specific sources that individually contributed to

  8. The Application of Ontological Methods toward Coastal Restoration

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

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

    SciTech Connect

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

    2004-10-15

    This report provides technical data regarding the reuse of excess foundry sand. The report addresses three topics: a statistically sound evaluation of the characterization of foundry sand, a laboratory investigation to qualify excess foundry sand as a major component in controlled low-strength material (CLSM), and the identification of the best methods for using foundry sand as a replacement for natural aggregates for construction purposes, specifically in asphalt paving materials. The survival analysis statistical technique was used to characterize foundry sand over a full spectrum of general chemical parameters, metallic elements, and organic compounds regarding bulk analysis and leachate characterization. Not limited to characterization and environmental impact, foundry sand was evaluated by factor analyses, which contributes to proper selection of factor and maximization of the reuse marketplace for foundry sand. Regarding the integration of foundry sand into CLSM, excavatable CLSM and structural CLSM containing different types of excess foundry sands were investigated through laboratory experiments. Foundry sand was approved to constitute a major component in CLSM. Regarding the integration of foundry sand into asphalt paving materials, the optimum asphalt content was determined for each mixture, as well as the bulk density, maximum density, asphalt absorption, and air voids at Nini, Ndes, and Nmax. It was found that foundry sands can be used as an aggregate in hot-mix asphalt production, but each sand should be evaluated individually. Foundry sands tend to lower the strength of mixtures and also may make them more susceptible to moisture damage. Finally, traditional anti-stripping additives may decrease the moisture sensitivity of a mixture containing foundry sand, but not to the level allowed by most highway agencies.

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

    SciTech Connect

    Pauul J. Tikalsky

    2004-10-31

    This report provides technical data regarding the reuse of excess foundry sand. The report addresses three topics: (1) a statistically sound evaluation of the characterization of foundry sand, (2) a laboratory investigation to qualify excess foundry sand as a major component in controlled low-strength material (CLSM), and (3) the identification of the best methods for using foundry sand as a replacement for natural aggregates for construction purposes, specifically in asphalt paving materials. The survival analysis statistical technique was used to characterize foundry sand over a full spectrum of general chemical parameters, metallic elements, and organic compounds regarding bulk analysis and leachate characterization. Not limited to characterization and environmental impact, foundry sand was evaluated by factor analyses, which contributes to proper selection of factor and maximization of the reuse marketplace for foundry sand. Regarding the integration of foundry sand into CLSM, excavatable CLSM and structural CLSM containing different types of excess foundry sands were investigated through laboratory experiments. Foundry sand was approved to constitute a major component in CLSM. Regarding the integration of foundry sand into asphalt paving materials, the optimum asphalt content was determined for each mixture, as well as the bulk density, maximum density, asphalt absorption, and air voids at N{sub ini}, N{sub des}, and N{sub max}. It was found that foundry sands can be used as an aggregate in hot-mix asphalt production, but each sand should be evaluated individually. Foundry sands tend to lower the strength of mixtures and also may make them more susceptible to moisture damage. Finally, traditional anti-stripping additives may decrease the moisture sensitivity of a mixture containing foundry sand, but not to the level allowed by most highway agencies.

  11. 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

  12. Ontological analysis of SNOMED CT

    PubMed Central

    Héja, Gergely; Surján, György; Varga, Péter

    2008-01-01

    Background SNOMED CT is the most comprehensive medical terminology. However, its use for intelligent services based on formal reasoning is questionable. Methods The analysis of the structure of SNOMED CT is based on the formal top-level ontology DOLCE. Results The analysis revealed several ontological and knowledge-engineering errors, the most important are errors in the hierarchy (mostly from an ontological point of view, but also regarding medical aspects) and the mixing of subsumption relations with other types (mostly 'part of'). Conclusion The found errors impede formal reasoning. The paper presents a possible way to correct these problems. PMID:19007445

  13. Ontological System for Context Artifacts and Resources

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

  14. Toward the Use of an Upper Ontology for U.S. Government and U.S. Military Domains: An Evaluation

    DTIC Science & Technology

    2004-09-01

    Object-Centered High Level Reference Ontology (OCHRE) [57], and Bunge -Wand-Weber (BWW) [78]. 5-7 5 Ontological Choices: Military and Government...Wand, R. Weber, Mario Bunge’s Ontology as a formal foundation for information systems concepts, in: P. Weingartner, G.J.W. Dorn (Eds.), Studies on... Mario Bunge’s Treatise, Rodopi, Atlanta, 1990, pp. 123-149. [79] Pease, A., (2003). The Sigma Ontology Development Environment, in Working Notes of the

  15. Temperature influence on structural changes of foundry bentonites

    NASA Astrophysics Data System (ADS)

    Holtzer, Mariusz; Bobrowski, Artur; Żymankowska-Kumon, Sylwia

    2011-10-01

    The results of investigations of three calcium bentonites, activated by sodium carbonate, applied in the foundry industry as binding material for moulding sands, subjected to the influence of high temperatures - are presented in the paper. Investigations were performed by the thermal analysis (TG) method, the infrared spectroscopy (FTIR) method and the modern Cu(II)-TET complex method (used for the determination of the montmorillonite content in bentonite samples). The occurrence of the dehydration process and two-stage dehydroxylation process was confirmed only for bentonite no. 2. This probably indicates that cis- and trans-isomers are present in the octahedric bentonite structure. Tests were performed at temperatures: 500, 550, 700, 900, 1000, 1100, 1200 °C.

  16. CLOnE: Controlled Language for Ontology Editing

    NASA Astrophysics Data System (ADS)

    Funk, Adam; Tablan, Valentin; Bontcheva, Kalina; Cunningham, Hamish; Davis, Brian; Handschuh, Siegfried

    This paper presents a controlled language for ontology editing and a software implementation, based partly on standard NLP tools, for processing that language and manipulating an ontology. The input sentences are analysed deterministically and compositionally with respect to a given ontology, which the software consults in order to interpret the input's semantics; this allows the user to learn fewer syntactic structures since some of them can be used to refer to either classes or instances, for example. A repeated-measures, task-based evaluation has been carried out in comparison with a well-known ontology editor; our software received favourable results for basic tasks. The paper also discusses work in progress and future plans for developing this language and tool.

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

    PubMed

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

    2016-01-01

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

  18. Laboratories for the 21st Century: Case Studies, Molecular Foundry, Berkeley, California

    SciTech Connect

    Not Available

    2010-11-01

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

  19. 40 CFR 63.10900 - What parts of the General Provisions apply to my large foundry?

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... SOURCE CATEGORIES (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Iron and Steel Foundries Area Sources Requirements for New and Existing Affected Sources Classified As Large Iron and...

  20. 40 CFR 63.10900 - What parts of the General Provisions apply to my large foundry?

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... SOURCE CATEGORIES (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Iron and Steel Foundries Area Sources Requirements for New and Existing Affected Sources Classified As Large Iron and...

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

    SciTech Connect

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

    2006-01-23

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

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

    NASA Astrophysics Data System (ADS)

    Brookes, David T.; Etkina, Eugenia

    2009-06-01

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

  3. Cancer mortality in a cohort of United Kingdom steel foundry workers: 1946-85.

    PubMed Central

    Sorahan, T; Cooke, M A

    1989-01-01

    The mortality experienced by a cohort of 10,491 United Kingdom steel foundry workers during the period 1946-85 has been investigated. These workers were all male operatives first employed in any one of the 10 participating foundries in 1946-65; all had worked in the industry for a minimum period of one year. Compared with the general population of England and Wales, statistically significant excesses relating to cancer mortality were found for cancer of the stomach (E = 77.4, O = 106, SMR = 137) and cancer of the lung (E = 229.2, O = 441, SMR = 147). A statistically significant deficit was found for cancer of the brain (E = 19.4, O = 10, SMR = 51). Involvement of occupational exposures was assessed by the method of regression models and life tables (RMLT). This method was used to compare the duration of employment in the industry, in "dust exposed" jobs, in "fume exposed" jobs, in foundry area jobs, in fettling shop jobs, and in foundry area or fettling shop jobs, of those dying from cancers of the stomach and lung with those of all matching survivors. The RMLT analyses provided evidence of an occupational involvement in the risk of death from lung cancer from work in the foundry area or fettling shop, and weaker evidence of an occupational involvement in the risk of death from stomach cancer from work in the foundry area. PMID:2923828

  4. 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

  5. Gene function prediction based on the Gene Ontology hierarchical structure.

    PubMed

    Cheng, Liangxi; Lin, Hongfei; Hu, Yuncui; Wang, Jian; Yang, Zhihao

    2014-01-01

    The information of the Gene Ontology annotation is helpful in the explanation of life science phenomena, and can provide great support for the research of the biomedical field. The use of the Gene Ontology is gradually affecting the way people store and understand bioinformatic data. To facilitate the prediction of gene functions with the aid of text mining methods and existing resources, we transform it into a multi-label top-down classification problem and develop a method that uses the hierarchical relationships in the Gene Ontology structure to relieve the quantitative imbalance of positive and negative training samples. Meanwhile the method enhances the discriminating ability of classifiers by retaining and highlighting the key training samples. Additionally, the top-down classifier based on a tree structure takes the relationship of target classes into consideration and thus solves the incompatibility between the classification results and the Gene Ontology structure. Our experiment on the Gene Ontology annotation corpus achieves an F-value performance of 50.7% (precision: 52.7% recall: 48.9%). The experimental results demonstrate that when the size of training set is small, it can be expanded via topological propagation of associated documents between the parent and child nodes in the tree structure. The top-down classification model applies to the set of texts in an ontology structure or with a hierarchical relationship.

  6. Ontological approach to reduce complexity in polypharmacy.

    PubMed

    Farrish, Susan; Grando, Adela

    2013-01-01

    Patients that are on many medications are often non-compliant due to the complexity of the medication regimen; consequently, a patient that is non-compliant can have poor medical outcomes. Providers are not always aware of the complexity of their patient's prescriptions. Methods have been developed to calculate the complexity for a patient's regimen but there are no widely available automated tools that will do this for a provider. Given that ontologies are known to provide well-principled, sharable, setting-independent and machine-interpretable declarative specification frameworks for modeling and reasoning on biomedical problems, we have explored their use in the context of reducing medication complexity. Previously we proposed an Ontology for modeling drug-related knowledge and a repository for complexity scoring. Here we tested the Ontology with patient data from the University of California San Diego Epic database, and we built a decision aide that computes the complexity and recommends changes to reduce the complexity, if needed.

  7. Ontology-Based Search of Genomic Metadata.

    PubMed

    Fernandez, Javier D; Lenzerini, Maurizio; Masseroli, Marco; Venco, Francesco; Ceri, Stefano

    2016-01-01

    The Encyclopedia of DNA Elements (ENCODE) is a huge and still expanding public repository of more than 4,000 experiments and 25,000 data files, assembled by a large international consortium since 2007; unknown biological knowledge can be extracted from these huge and largely unexplored data, leading to data-driven genomic, transcriptomic, and epigenomic discoveries. Yet, search of relevant datasets for knowledge discovery is limitedly supported: metadata describing ENCODE datasets are quite simple and incomplete, and not described by a coherent underlying ontology. Here, we show how to overcome this limitation, by adopting an ENCODE metadata searching approach which uses high-quality ontological knowledge and state-of-the-art indexing technologies. Specifically, we developed S.O.S. GeM (http://www.bioinformatics.deib.polimi.it/SOSGeM/), a system supporting effective semantic search and retrieval of ENCODE datasets. First, we constructed a Semantic Knowledge Base by starting with concepts extracted from ENCODE metadata, matched to and expanded on biomedical ontologies integrated in the well-established Unified Medical Language System. We prove that this inference method is sound and complete. Then, we leveraged the Semantic Knowledge Base to semantically search ENCODE data from arbitrary biologists' queries. This allows correctly finding more datasets than those extracted by a purely syntactic search, as supported by the other available systems. We empirically show the relevance of found datasets to the biologists' queries.

  8. Cyber Forensics Ontology for Cyber Criminal Investigation

    NASA Astrophysics Data System (ADS)

    Park, Heum; Cho, Sunho; Kwon, Hyuk-Chul

    We developed Cyber Forensics Ontology for the criminal investigation in cyber space. Cyber crime is classified into cyber terror and general cyber crime, and those two classes are connected with each other. The investigation of cyber terror requires high technology, system environment and experts, and general cyber crime is connected with general crime by evidence from digital data and cyber space. Accordingly, it is difficult to determine relational crime types and collect evidence. Therefore, we considered the classifications of cyber crime, the collection of evidence in cyber space and the application of laws to cyber crime. In order to efficiently investigate cyber crime, it is necessary to integrate those concepts for each cyber crime-case. Thus, we constructed a cyber forensics domain ontology for criminal investigation in cyber space, according to the categories of cyber crime, laws, evidence and information of criminals. This ontology can be used in the process of investigating of cyber crime-cases, and for data mining of cyber crime; classification, clustering, association and detection of crime types, crime cases, evidences and criminals.

  9. Cleanup under Airlock of an Old Uranium Foundry - 13273

    SciTech Connect

    Thuillier, Daniel; Houee, Jean-Marie; Chambon, Frederic

    2013-07-01

    Since 2004, AREVA's subsidiary SICN has been conducting the cleanup and dismantling of an old uranium foundry located in the town of Annecy (France). The first operations consisted in the removal of the foundry's production equipment, producing more than 300 metric tons (MT) of waste. The second step consisted in performing the radiological characterization of the 1,600 m{sup 2} (17,200 ft{sup 2}) building, including underground trenches and galleries. The building was precisely inventoried, based on operations records and direct measurements. All sub-surfaces, which needed to be cleaned up were characterized, and a determination of the contamination migration was established, in particular with trenches and galleries. The wall thicknesses to be treated were empirically justified, knowing that the maximal migration depth inside concrete is 5 mm for a liquid transfer vector. All singularities such as cracks, anchoring points, etc. were spotted for a complete and systematic treatment. Building structures not laying directly on the soil, such as floor slabs, were not cleaned up but directly deconstructed and disposed of as waste. The facility was located within the town of Annecy. Therefore, in order to avoid the risk of dusts dispersion and public exposure during the building deconstruction and the soil treatment, a third of the building's surface was confined in a sliding airlock built from a metal structure capable of resisting to wind and snow, which are frequent in this area. This particular structure provided a static confinement over the half of the building which was covered and a dynamic confinement using a ventilation and high efficiency air filtration system, sized to provide 2.5 air changes per hour. The enclosure and its metallic structure is 33 m long (108 feet), 25 m wide (82 feet), and 13 m high (42 feet), for a volume of 10,000 m{sup 3} (353,000 ft{sup 3}). It was made up of a double skin envelope, allowing the recycling of its structure and outside

  10. Use of the CIM Ontology

    SciTech Connect

    Neumann, Scott; Britton, Jay; Devos, Arnold N.; Widergren, Steven E.

    2006-02-08

    There are many uses for the Common Information Model (CIM), an ontology that is being standardized through Technical Committee 57 of the International Electrotechnical Commission (IEC TC57). The most common uses to date have included application modeling, information exchanges, information management and systems integration. As one should expect, there are many issues that become apparent when the CIM ontology is applied to any one use. Some of these issues are shortcomings within the current draft of the CIM, and others are a consequence of the different ways in which the CIM can be applied using different technologies. As the CIM ontology will and should evolve, there are several dangers that need to be recognized. One is overall consistency and impact upon applications when extending the CIM for a specific need. Another is that a tight coupling of the CIM to specific technologies could limit the value of the CIM in the longer term as an ontology, which becomes a larger issue over time as new technologies emerge. The integration of systems is one specific area of interest for application of the CIM ontology. This is an area dominated by the use of XML for the definition of messages. While this is certainly true when using Enterprise Application Integration (EAI) products, it is even more true with the movement towards the use of Web Services (WS), Service-Oriented Architectures (SOA) and Enterprise Service Buses (ESB) for integration. This general IT industry trend is consistent with trends seen within the IEC TC57 scope of power system management and associated information exchange. The challenge for TC57 is how to best leverage the CIM ontology using the various XML technologies and standards for integration. This paper will provide examples of how the CIM ontology is used and describe some specific issues that should be addressed within the CIM in order to increase its usefulness as an ontology. It will also describe some of the issues and challenges that will

  11. 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

  12. Theory and ontology for sharing temporal knowledge

    NASA Technical Reports Server (NTRS)

    Loganantharaj, Rasiah

    1996-01-01

    Using current technology, the sharing or re-using of knowledge-bases is very difficult, if not impossible. ARPA has correctly recognized the problem and funded a knowledge sharing initiative. One of the outcomes of this project is a formal language called Knowledge Interchange Format (KIF) for representing knowledge that could be translated into other languages. Capturing and representing design knowledge and reasoning with them have become very important for NASA who is a pioneer of innovative design of unique products. For upgrading an existing design for changing technology, needs, or requirements, it is essential to understand the design rationale, design choices, options and other relevant information associated with the design. Capturing such information and presenting them in the appropriate form are part of the ongoing Design Knowledge Capture project of NASA. The behavior of an object and various other aspects related to time are captured by the appropriate temporal knowledge. The captured design knowledge will be represented in such a way that various groups of NASA who are interested in various aspects of the design cycle should be able to access and use the design knowledge effectively. To facilitate knowledge sharing among these groups, one has to develop a very well defined ontology. Ontology is a specification of conceptualization. In the literature several specific domains were studied and some well defined ontologies were developed for such domains. However, very little, or no work has been done in the area of representing temporal knowledge to facilitate sharing. During the ASEE summer program, I have investigated several temporal models and have proposed a theory for time that is flexible to accommodate the time elements, such as, points and intervals, and is capable of handling the qualitative and quantitative temporal constraints. I have also proposed a primitive temporal ontology using which other relevant temporal ontologies can be built. I

  13. An Ontology Service for Linked Environments for Atmospheric Discovery (LEAD)

    NASA Astrophysics Data System (ADS)

    Ramachandran, R.; Movva, S.

    2005-12-01

    An Ontology encodes concepts and the relationships among them. From a machine learning perspective, it is viewed as a formal, explicit specification of a shared conceptualization. Linked Environments for Atmospheric Discovery (LEAD) is a large NSF Information Technology Research (ITR) initiative to provide scalable, integrated gird framework for use in accessing, preparing, assimilating, predicting, analyzing and managing a broad array of meteorological and related information independent of format and physical location. An ontology that focuses on mesoscale meteorology is currently being designed and developed for LEAD. It uses the Semantic Web for Earth and Environmental Terminology - ontology (SWEET, Rob Raskin - JPL) as a building block and additional concepts for mesoscale meteorology are being added. An Ontology Inference Service (OIS) is also developed to provide querying capabilities on the LEAD Ontology. The drivers for developing such an ontology and inference service specifically for LEAD are many. The LEAD ontology serves as a common vocabulary to allow interoperability for metadata exchange between different LEAD catalogs. Coupled with these LEAD catalogs, the OIS will also provide a 'yellow pages' search capability to the end users. The OIS provides capabilities to search for similar and related concepts for a particular concept. This is essentially, searching with semantic meanings rather than searching with keywords. Thus allowing users to search for datasets without actually having to know and use the specific data parameter names in the catalogs. Finally, the OIS serves as a stand-alone smart search system for the atmospheric domain, specifically mesoscale meteorology. This smart search service collates the definition of a user's search term, useful datasets, related concepts, useful websites and additional related information. It serves as an educational portal for both students and researchers in LEAD.

  14. Binding waste anthracite fines with Si-containing materials as an alternative fuel for foundry cupola furnaces.

    PubMed

    Huang, He; Fox, John T; Cannon, Fred S; Komarneni, Sridhar; Kulik, Joseph; Furness, Jim

    2011-04-01

    An alternative fuel to replace foundry coke in cupolas was developed from waste anthracite fines. Waste anthracite fines were briquetted with Si-containing materials and treated in carbothermal (combination of heat and carbon) conditions that simulated the cupola preheat zone to form silicon carbide nanowires (SCNWs). SCNWs can provide hot crushing strengths, which are important in cupola operations. Lab-scale experiments confirmed that the redox level of the Si-source significantly affected the formation of SiC. With zerovalent silicon, SCNWs were formed within the anthracite pellets. Although amorphous Si (+4) plus anthracite formed SiC, these conditions did not transform the SiC into nanowires. Moreover, under the test conditions, SiC was not formed between crystallized Si (+4) and anthracite. In a full-scale demonstration, bricks made from anthracite fines and zerovalent silicon successfully replaced a part of the foundry coke in a full-scale cupola. In addition to saving in fuel cost, replacing coke by waste anthracite fines can reduce energy consumption and CO2 and other pollution associated with conventional coking.

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

    SciTech Connect

    Plionis, Alexander A; Peterson, Dominic S; Tandon, Lav; Lamont, Stephen P

    2009-01-01

    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 nondestructive 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.

  16. Complex Topographic Feature Ontology Patterns

    USGS Publications Warehouse

    Varanka, Dalia E.; Jerris, Thomas J.

    2015-01-01

    Semantic ontologies are examined as effective data models for the representation of complex topographic feature types. Complex feature types are viewed as integrated relations between basic features for a basic purpose. In the context of topographic science, such component assemblages are supported by resource systems and found on the local landscape. Ontologies are organized within six thematic modules of a domain ontology called Topography that includes within its sphere basic feature types, resource systems, and landscape types. Context is constructed not only as a spatial and temporal setting, but a setting also based on environmental processes. Types of spatial relations that exist between components include location, generative processes, and description. An example is offered in a complex feature type ‘mine.’ The identification and extraction of complex feature types are an area for future research.

  17. Ontology Matching with Semantic Verification

    PubMed Central

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

    2009-01-01

    ASMOV (Automated Semantic Matching of Ontologies with Verification) is a novel algorithm that uses lexical and structural characteristics of two ontologies to iteratively calculate a similarity measure between them, derives an alignment, and then verifies it to ensure that it does not contain semantic inconsistencies. In this paper, we describe the ASMOV algorithm, and then present experimental results that measure its accuracy using the OAEI 2008 tests, and that evaluate its use with two different thesauri: WordNet, and the Unified Medical Language System (UMLS). These results show the increased accuracy obtained by combining lexical, structural and extensional matchers with semantic verification, and demonstrate the advantage of using a domain-specific thesaurus for the alignment of specialized ontologies. PMID:20186256

  18. An Ontology Design Pattern for Surface Water Features

    SciTech Connect

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

    2014-01-01

    Surface water is a primary concept of human experience but concepts are captured in cultures and languages in many different ways. Still, many commonalities can be found due to the physical basis of many of the properties and categories. An abstract ontology of surface water features based only on those physical properties of landscape features has the best potential for serving as a foundational domain ontology. It can then be used to systematically incor-porate concepts that are specific to a culture, language, or scientific domain. The Surface Water ontology design pattern was developed both for domain knowledge distillation and to serve as a conceptual building-block for more complex surface water ontologies. A fundamental distinction is made in this on-tology between landscape features that act as containers (e.g., stream channels, basins) and the bodies of water (e.g., rivers, lakes) that occupy those containers. Concave (container) landforms semantics are specified in a Dry module and the semantics of contained bodies of water in a Wet module. The pattern is imple-mented in OWL, but Description Logic axioms and a detailed explanation is provided. The OWL ontology will be an important contribution to Semantic Web vocabulary for annotating surface water feature datasets. A discussion about why there is a need to complement the pattern with other ontologies, es-pecially the previously developed Surface Network pattern is also provided. Fi-nally, the practical value of the pattern in semantic querying of surface water datasets is illustrated through a few queries and annotated geospatial datasets.

  19. Standards and ontologies in computational systems biology.

    PubMed

    Sauro, Herbert M; Bergmann, Frank T

    2008-01-01

    With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In the present chapter two chief model exchange standards, SBML (Systems Biology Markup Language) and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced, together with a discussion on the future of modelling languages and visualization tools in systems biology.

  20. Standards and Ontologies in Computational Systems Biology

    PubMed Central

    Sauro, Herbert M.; Bergmann, Frank

    2009-01-01

    With the growing importance of computational models in systems biology there has been much interest in recent years to develop standard model interchange languages that permit biologists to easily exchange models between different software tools. In this chapter two chief model exchange standards, SBML and CellML are described. In addition, other related features including visual layout initiatives, ontologies and best practices for model annotation are discussed. Software tools such as developer libraries and basic editing tools are also introduced together with a discussion on the future of modeling languages and visualization tools in systems biology. PMID:18793134

  1. 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

  2. Design of schistosomiasis ontology (IDOSCHISTO) extending the infectious disease ontology.

    PubMed

    Camara, Gaoussou; Despres, Sylvie; Djedidi, Rim; Lo, Moussa

    2013-01-01

    Epidemiological monitoring of the schistosomiasis' spreading brings together many practitioners working at different levels of granularity (biology, host individual, host population), who have different perspectives (biology, clinic and epidemiology) on the same phenomenon. Biological perspective deals with pathogens (e.g. life cycle) or physiopathology while clinical perspective deals with hosts (e.g. healthy or infected host, diagnosis, treatment, etc.). In an epidemiological perspective corresponding to the host population level of granularity, the schistosomiasis disease is characterized according to the way (causes, risk factors, etc.) it spreads in this population over space and time. In this paper we provide an ontological analysis and design for the Schistosomiasis domain knowledge and spreading dynamics. IDOSCHISTO - the schistosomiasis ontology - is designed as an extension of the Infectious Disease Ontology (IDO). This ontology aims at supporting the schistosomiasis monitoring process during a spreading crisis by enabling data integration, semantic interoperability, for collaborative work on one hand and for risk analysis and decision making on the other hand.

  3. A lithography aware design optimization using foundry-certified models and hotspot detection

    NASA Astrophysics Data System (ADS)

    Karklin, L.; Arkhipov, A.; Blakely, D.; Dingenen, M.; Mehrotra, A.; Watson, B.; Zelnik, C.; Cote, M.; Hurat, P.

    2007-10-01

    An automated litho-aware design migration solution has been implemented to enable designers to port existing IP layouts (custom, library, and block) to nanometer technologies while optimizing layout printability and silicon yield. With rapidly shrinking technology nodes, the industry consolidation toward fabless or fab-lite manufacturing, demand for second-sourcing and dramatic increase in cost of IP development, the automation of "vertical" (between nodes) and 'horizontal" (between chip manufacturers) migration becomes a very important task. The challenge comes from the fact that even within the same technology node design and process-induced rules deviate substantially among different IDMs and foundries, which leads to costly, error-prone and time consuming design modifications. At the same time, fast and reliable adjustments to design and ability to switch between processes and chip manufacturers could represent significant improvement to TTM, and respectively improving ROI. Using conservative rules (or restricted design rules) is not always a viable option because of the area, performance and yield penalties. The difficulty of migration is augmented by the fact that design rules are not sufficient to guaranty good printability, maximum process window and high yield. Model-based detection of lithography-induced systematic yield-limiting defects (a.k.a. hotspots) is becoming a vital part of the design-for-manufacturing flow for advanced technology nodes at 65nm and below. Driven by customer demand, a collaborative effort between EDA vendors provides a complete design-for-manufacturing migration solution that allows sub-65 nanometer designers to comprehensively address the impact of manufacturing variations on design yield and performance during layout migration. First, the physical hard IP is migrated from its existing 90nm process to a more advanced 65 and 45 nm processes, resulting in an area-optimized DRC-clean 65nm design retaining the original hierarchy to

  4. Approach for ontological modeling of database schema for the generation of semantic knowledge on the web

    NASA Astrophysics Data System (ADS)

    Rozeva, Anna

    2015-11-01

    Currently there is large quantity of content on web pages that is generated from relational databases. Conceptual domain models provide for the integration of heterogeneous content on semantic level. The use of ontology as conceptual model of a relational data sources makes them available to web agents and services and provides for the employment of ontological techniques for data access, navigation and reasoning. The achievement of interoperability between relational databases and ontologies enriches the web with semantic knowledge. The establishment of semantic database conceptual model based on ontology facilitates the development of data integration systems that use ontology as unified global view. Approach for generation of ontologically based conceptual model is presented. The ontology representing the database schema is obtained by matching schema elements to ontology concepts. Algorithm of the matching process is designed. Infrastructure for the inclusion of mediation between database and ontology for bridging legacy data with formal semantic meaning is presented. Implementation of the knowledge modeling approach on sample database is performed.

  5. 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.

  6. A Gene Ontology Tutorial in Python.

    PubMed

    Vesztrocy, Alex Warwick; Dessimoz, Christophe

    2017-01-01

    This chapter is a tutorial on using Gene Ontology resources in the Python programming language. This entails querying the Gene Ontology graph, retrieving Gene Ontology annotations, performing gene enrichment analyses, and computing basic semantic similarity between GO terms. An interactive version of the tutorial, including solutions, is available at http://gohandbook.org .

  7. Discovering beaten paths in collaborative ontology-engineering projects using Markov chains.

    PubMed

    Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A; Noy, Natalya F

    2014-10-01

    Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50,000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

  8. Discovering Beaten Paths in Collaborative Ontology-Engineering Projects using Markov Chains

    PubMed Central

    Walk, Simon; Singer, Philipp; Strohmaier, Markus; Tudorache, Tania; Musen, Mark A.; Noy, Natalya F.

    2014-01-01

    Biomedical taxonomies, thesauri and ontologies in the form of the International Classification of Diseases as a taxonomy or the National Cancer Institute Thesaurus as an OWL-based ontology, play a critical role in acquiring, representing and processing information about human health. With increasing adoption and relevance, biomedical ontologies have also significantly increased in size. For example, the 11th revision of the International Classification of Diseases, which is currently under active development by the World Health Organization contains nearly 50, 000 classes representing a vast variety of different diseases and causes of death. This evolution in terms of size was accompanied by an evolution in the way ontologies are engineered. Because no single individual has the expertise to develop such large-scale ontologies, ontology-engineering projects have evolved from small-scale efforts involving just a few domain experts to large-scale projects that require effective collaboration between dozens or even hundreds of experts, practitioners and other stakeholders. Understanding the way these different stakeholders collaborate will enable us to improve editing environments that support such collaborations. In this paper, we uncover how large ontology-engineering projects, such as the International Classification of Diseases in its 11th revision, unfold by analyzing usage logs of five different biomedical ontology-engineering projects of varying sizes and scopes using Markov chains. We discover intriguing interaction patterns (e.g., which properties users frequently change after specific given ones) that suggest that large collaborative ontology-engineering projects are governed by a few general principles that determine and drive development. From our analysis, we identify commonalities and differences between different projects that have implications for project managers, ontology editors, developers and contributors working on collaborative ontology

  9. Anatomical reasoning in the informatics age: Principles, ontologies, and agendas.

    PubMed

    Trelease, Robert B

    2006-03-01

    Reasoning about anatomy shares historical scientific roots with formal logic and artificial intelligence. With advances in computer-based intelligent programming, high-level biological structural knowledge may be exploited directly for biomedical research, clinical tasks, and educational applications. We consider the special nature of anatomical domain knowledge, emphasizing the complex concepts and semantics that must be represented in the development of ontologies, formally structured databases of biological information. We review the evolution of the fundamental scientific principles of logic and artificial intelligence needed for building machines that can make use of anatomical knowledge. We look at methods for compiling ontologies and compare the structural designs of the Foundational Model of Anatomy and Open GALEN ontologies. We further consider issues related to mapping developing anatomy resources with other biological ontologies in genomics, proteomics, and physiology. Although early results are promising, considerable resources and continuing effort must be committed to completing and extending anatomical ontologies for the ultimate success of computer-based anatomical reasoning. Anat Rec (Part B: New Anat) 289B:72-84, 2006. (c) 2006 Wiley-Liss, Inc.

  10. 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.

  11. OntoSoft: An Ontology for Capturing Scientific Software Metadata

    NASA Astrophysics Data System (ADS)

    Gil, Y.

    2015-12-01

    We have developed OntoSoft, an ontology to describe metadata for scientific software. The ontology is designed considering how scientists would approach the reuse and sharing of software. This includes supporting a scientist to: 1) identify software, 2) understand and assess software, 3) execute software, 4) get support for the software, 5) do research with the software, and 6) update the software. The ontology is available in OWL and contains more than fifty terms. We have used OntoSoft to structure the OntoSoft software registry for geosciences, and to develop user interfaces to capture its metadata. OntoSoft is part of the NSF EarthCube initiative and contributes to its vision of scientific knowledge sharing, in this case about scientific software.

  12. Grinder Variant System Design and Implementation Based on Ontology

    NASA Astrophysics Data System (ADS)

    Yang, G. H.; Zhang, T. P.

    In order to improve the efficiency of product design and reuse in heterogeneous system of knowledge sharing, this paper introduced the concept of ontology into product variant design, and grinding machine design was as an example. A lot of experience and accumulated knowledge in product design was shared and reused. It is precisely to formulate ontology knowledge such as variant design features and parameter, and applied the software protégé4.3 to construct ontology model, as well as runed resoning on model data information. It developed a set of complete product intelligent system of variant design, which can effectively solve the problem of the repeated design and greatly shorten product development cycle.

  13. An Ontology-Based Framework for Bridging Learning Design and Learning Content

    ERIC Educational Resources Information Center

    Knight, Colin, Gasevic, Dragan; Richards, Griff

    2006-01-01

    The paper describes an ontology-based framework for bridging learning design and learning object content. In present solutions, researchers have proposed conceptual models and developed tools for both of those subjects, but without detailed discussions of how they can be used together. In this paper we advocate the use of ontologies to explicitly…

  14. Towards a reference plant trait ontology for modeling knowledge of plant traits and phenotypes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Ontology engineering and knowledge modeling for the plant sciences is expected to contribute to the understanding of the basis of plant traits that determine phenotypic expression in a given environment. Several crop- or clade-specific plant trait ontologies have been developed to describe plant tr...

  15. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Waste molding and core sands from the foundry industry have been successfully used around the world as byproducts in geotechnical and agricultural applications. Although waste foundry sands (WFSs) are generally not considered hazardous in nature, relevant data are not available in Argentina. This ...

  17. 40 CFR Table 1 to Subpart Zzzzzz... - Applicability of General Provisions to Aluminum, Copper, and Other Nonferrous Foundries Area Sources

    Code of Federal Regulations, 2013 CFR

    2013-07-01

    ... 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,...

  18. 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,...

  19. 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,...

  20. 40 CFR Table 1 to Subpart Zzzzzz... - Applicability of General Provisions to Aluminum, Copper, and Other Nonferrous Foundries Area Sources

    Code of Federal Regulations, 2014 CFR

    2014-07-01

    ... 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,...

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

    Code of Federal Regulations, 2012 CFR

    2012-07-01

    ... 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,...

  2. 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

  3. Quality assurance of the gene ontology using abstraction networks.

    PubMed

    Ochs, Christopher; Perl, Yehoshua; Halper, Michael; Geller, James; Lomax, Jane

    2016-06-01

    The gene ontology (GO) is used extensively in the field of genomics. Like other large and complex ontologies, quality assurance (QA) efforts for GO's content can be laborious and time consuming. Abstraction networks (AbNs) are summarization networks that reveal and highlight high-level structural and hierarchical aggregation patterns in an ontology. They have been shown to successfully support QA work in the context of various ontologies. Two kinds of AbNs, called the area taxonomy and the partial-area taxonomy, are developed for GO hierarchies and derived specifically for the biological process (BP) hierarchy. Within this framework, several QA heuristics, based on the identification of groups of anomalous terms which exhibit certain taxonomy-defined characteristics, are introduced. Such groups are expected to have higher error rates when compared to other terms. Thus, by focusing QA efforts on anomalous terms one would expect to find relatively more erroneous content. By automatically identifying these potential problem areas within an ontology, time and effort will be saved during manual reviews of GO's content. BP is used as a testbed, with samples of three kinds of anomalous BP terms chosen for a taxonomy-based QA review. Additional heuristics for QA are demonstrated. From the results of this QA effort, it is observed that different kinds of inconsistencies in the modeling of GO can be exposed with the use of the proposed heuristics. For comparison, the results of QA work on a sample of terms chosen from GO's general population are presented.

  4. Enabling Enrichment Analysis with the Human Disease Ontology

    PubMed Central

    LePendu, Paea; Musen, Mark A.; Shah, Nigam H.

    2012-01-01

    Advanced statistical methods used to analyze high-throughput data such as gene-expression assays result in long lists of “significant genes.” One way to gain insight into the significance of altered expression levels is to determine whether Gene Ontology (GO) terms associated with a particular biological process, molecular function, or cellular component are over- or under-represented in the set of genes deemed significant. This process, referred to as enrichment analysis, profiles a gene-set, and is widely used to make sense of the results of high-throughput experiments. Our goal is to develop and apply general enrichment analysis methods to profile other sets of interest, such as patient cohorts from the electronic medical record, using a variety of ontologies including SNOMED CT, MedDRA, RxNorm, and others. Although it is possible to perform enrichment analysis using ontologies other than the GO, a key pre-requisite is the availability of a background set of annotations to enable the enrichment calculation. In the case of the GO, this background set is provided by the Gene Ontology Annotations. In the current work, we describe: (i) a general method that uses hand-curated GO annotations as a starting point for creating background datasets for enrichment analysis using other ontologies; and (ii) a gene–disease background annotation set—that enables disease-based enrichment—to demonstrate feasibility of our method. PMID:21550421

  5. An integrated pharmacokinetics ontology and corpus for text mining

    PubMed Central

    2013-01-01

    Background Drug pharmacokinetics parameters, drug interaction parameters, and pharmacogenetics data have been unevenly collected in different databases and published extensively in the literature. Without appropriate pharmacokinetics ontology and a well annotated pharmacokinetics corpus, it will be difficult to develop text mining tools for pharmacokinetics data collection from the literature and pharmacokinetics data integration from multiple databases. Description A comprehensive pharmacokinetics ontology was constructed. It can annotate all aspects of in vitro pharmacokinetics experiments and in vivo pharmacokinetics studies. It covers all drug metabolism and transportation enzymes. Using our pharmacokinetics ontology, a PK-corpus was constructed to present four classes of pharmacokinetics abstracts: in vivo pharmacokinetics studies, in vivo pharmacogenetic studies, in vivo drug interaction studies, and in vitro drug interaction studies. A novel hierarchical three level annotation scheme was proposed and implemented to tag key terms, drug interaction sentences, and drug interaction pairs. The utility of the pharmacokinetics ontology was demonstrated by annotating three pharmacokinetics studies; and the utility of the PK-corpus was demonstrated by a drug interaction extraction text mining analysis. Conclusions The pharmacokinetics ontology annotates both in vitro pharmacokinetics experiments and in vivo pharmacokinetics studies. The PK-corpus is a highly valuable resource for the text mining of pharmacokinetics parameters and drug interactions. PMID:23374886

  6. Neuroanatomical domain of the foundational model of anatomy ontology

    PubMed Central

    2014-01-01

    Background The diverse set of human brain structure and function analysis methods represents a difficult challenge for reconciling multiple views of neuroanatomical organization. While different views of organization are expected and valid, no widely adopted approach exists to harmonize different brain labeling protocols and terminologies. Our approach uses the natural organizing framework provided by anatomical structure to correlate terminologies commonly used in neuroimaging. Description The Foundational Model of Anatomy (FMA) Ontology provides a semantic framework for representing the anatomical entities and relationships that constitute the phenotypic organization of the human body. In this paper we describe recent enhancements to the neuroanatomical content of the FMA that models cytoarchitectural and morphological regions of the cerebral cortex, as well as white matter structure and connectivity. This modeling effort is driven by the need to correlate and reconcile the terms used in neuroanatomical labeling protocols. By providing an ontological framework that harmonizes multiple views of neuroanatomical organization, the FMA provides developers with reusable and computable knowledge for a range of biomedical applications. Conclusions A requirement for facilitating the integration of basic and clinical neuroscience data from diverse sources is a well-structured ontology that can incorporate, organize, and associate neuroanatomical data. We applied the ontological framework of the FMA to align the vocabularies used by several human brain atlases, and to encode emerging knowledge about structural connectivity in the brain. We highlighted several use cases of these extensions, including ontology reuse, neuroimaging data annotation, and organizing 3D brain models. PMID:24398054

  7. The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience.

    PubMed

    Bug, William J; Ascoli, Giorgio A; Grethe, Jeffrey S; Gupta, Amarnath; Fennema-Notestine, Christine; Laird, Angela R; Larson, Stephen D; Rubin, Daniel; Shepherd, Gordon M; Turner, Jessica A; Martone, Maryann E

    2008-09-01

    A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF.

  8. [Mortality due to bronchopulmonary cancers in workers of 2 foundries].

    PubMed

    Moulin, J J; Lafontaine, M; Mantout, B; Belanger, A; Michel, M; Wild, P; Clavel, T; Fournier, M; Fontana, J M

    1995-01-01

    A mortality study was carried out in two factories producing stainless steel in order to assess lung cancer risk among workers employed in coke oven, blast and open hearth furnaces, foundry, electric furnace, hot and cold rolling mills and pickling areas. Occupational exposures of interest were chromium compounds, nickel compounds, polycyclic aromatic hydrocarbons (PAH), silica and asbestos. All male workers having at least one year of employment between 01.01.1960 and 31.12.1990 were followed up for mortality. The vital status was assessed from birth place registries. Complete job histories since date of first employment were abstracted from the company files. The smoking habits of 50% of the cohort members were known from medical records. The observed number of deaths (obs) were compared with the expected ones based on regional rates with adjustment for age, sex and calendar time (Standardized Mortality Ratio, SMR). The cohorts included 6324 (factory 1) and 5270 (factory 2) workers. The overall mortality did not differ markedly from that expected in both factories: SMR = 0.95 (obs = 1540, p = 0.05) in factory 1 and SMR = 1.06 (obs = 916, non-significant) in factory 2. SMRs for lung cancer did not differ from unity, respectively 0.99 (obs = 105) and 1.00 (obs = 54), in whole cohorts. Non-significant lung cancer excesses were observed among workers of some workshops where exposures of interest might have occurred: coke oven (SMR = 2.04), blast furnace (SMR = 1.36), open hearth furnace (SMR = 1.75), hot rolling mills (SMR = 1.29). These processes, however, are no longer involved in the study factories. Furthermore, no lung cancer excess was observed among workers employed in current workshops: electric furnaces and cold rolling mills.

  9. Direct recycling of municipal ferrous wastes for local foundry application. Final technical report

    SciTech Connect

    Not Available

    1981-01-09

    This project investigated the concept of direct recycling as an appropriate technology (AT) approach to improving resource recovery from wastes in Region III. Direct recycling is the process of bringing waste materials directly to reprocessing facilities with few or no intermediate processing steps. Municipal Ferrous Waste (MFW) was the waste material involved. The Region III states were surveyed for (a) municipal recycling systems incorporating MFW separation and (b) grey iron foundries where MFW could be utilized. Contacts and visits were made with foundry and recycling group personnel. A handbook titled Tin Cans and Trash Recovery was prepared for distribution to interested persons in Region III. This handbook delineates the direct recycling method for MFW, describes recycling potential for areas of different populations in the Region, and lists foundries, recycling groups, and resource persons for the Region. It was distributed widely in Region III and elsewhere.

  10. Ontology Language to Support Description of Experiment Control System Semantics, Collaborative Knowledge-Base Design and Ontology Reuse

    SciTech Connect

    Vardan Gyurjyan, D Abbott, G Heyes, E Jastrzembski, B Moffit, C Timmer, E Wolin

    2009-10-01

    In this paper we discuss the control domain specific ontology that is built on top of the domain-neutral Resource Definition Framework (RDF). Specifically, we will discuss the relevant set of ontology concepts along with the relationships among them in order to describe experiment control components and generic event-based state machines. Control Oriented Ontology Language (COOL) is a meta-data modeling language that provides generic means for representation of physics experiment control processes and components, and their relationships, rules and axioms. It provides a semantic reference frame that is useful for automating the communication of information for configuration, deployment and operation. COOL has been successfully used to develop a complete and dynamic knowledge-base for experiment control systems, developed using the AFECS framework.

  11. 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

  12. 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

  13. 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

  14. Ontology-Based Federated Data Access to Human Studies Information

    PubMed Central

    Sim, Ida; Carini, Simona; Tu, Samson W.; Detwiler, Landon T.; Brinkley, James; Mollah, Shamim A.; Burke, Karl; Lehmann, Harold P.; Chakraborty, Swati; Wittkowski, Knut M.; Pollock, Brad H.; Johnson, Thomas M.; Huser, Vojtech

    2012-01-01

    Human studies are one of the most valuable sources of knowledge in biomedical research, but data about their design and results are currently widely dispersed in siloed systems. Federation of these data is needed to facilitate large-scale data analysis to realize the goals of evidence-based medicine. The Human Studies Database project has developed an informatics infrastructure for federated query of human studies databases, using a generalizable approach to ontology-based data access. Our approach has three main components. First, the Ontology of Clinical Research (OCRe) provides the reference semantics. Second, a data model, automatically derived from OCRe into XSD, maintains semantic synchrony of the underlying representations while facilitating data acquisition using common XML technologies. Finally, the Query Integrator issues queries distributed over the data, OCRe, and other ontologies such as SNOMED in BioPortal. We report on a demonstration of this infrastructure on data acquired from institutional systems and from ClinicalTrials.gov. PMID:23304360

  15. Ensuring HL7-based information model requirements within an ontology framework.

    PubMed

    Ouagne, David; Nadah, Nadia; Schober, Daniel; Choquet, Rémy; Teodoro, Douglas; Colaert, Dirk; Schulz, Stefan; Jaulent, Marie-Christine; Daniel, Christel

    2010-01-01

    This paper describes the building of an HL7-based Information Model Ontology (IMO) that can be exploited by a domain ontology in order to distribute querying over different clinical data repositories. We employed the Open Medical Development Framework (OMDF) based on a model driven development methodology. OMDF provides model transformation features to build an HL7-based information model that covers the conceptual scope of a target project. The resulting IMO is used to mediate between ontologically queries and information retrieval from semantically less defined Hospital Information Systems (HIS). In the context of the DebugIT project - which scope corresponds to the control of infectious diseases and antimicrobial resistances - Information Model Ontology is integrated to the DebugIT domain ontology in order to express queries.

  16. Towards the Creation of a Visual Ontology of Biomedical Imaging Entities

    PubMed Central

    Simpson, Matthew S.; You, Daekeun; Rahman, Md Mahmudur; Antani, Sameer K.; Thoma, George R.; Demner-Fushman, Dina

    2012-01-01

    Image content is frequently the target of biomedical information extraction systems. However, the meaning of this content cannot be easily understood without some associated text. In order to improve the integration of textual and visual information, we are developing a visual ontology for biomedical image retrieval. Our visual ontology maps the appearance of image regions to concepts in an existing textual ontology, thereby inheriting relationships among the visual entities. Such a resource creates a bridge between the visual characteristics of important image regions and their semantic interpretation. We automatically populate our visual ontology by pairing image regions with their associated descriptions. To demonstrate the usefulness of this resource, we have developed a classification method that automatically labels image regions with appropriate concepts based solely on their appearance. Our results for thoracic imaging terms show that our methods are promising first steps towards the creation of a biomedical visual ontology. PMID:23304361

  17. Ontology Re-engineering Use Case: Extending SWEET to map Climate and Forecasting Vocabulary Terms

    NASA Astrophysics Data System (ADS)

    Ramachandran, R.; Graves, S.; Raskin, R.

    2006-05-01

    A common problem faced while developing metadata for scientific data archives is that of keywords. Although keywords are an effective way for searching the resource catalogs, data archive designers may select from one of many different controlled vocabularies to describe their holdings. For example, in Earth Science, Climate and Forecasting (CF Convention) is a controlled vocabulary commonly used within the Modeling community. Similarly, the Global Change Master Directory (GCMD) keywords list is the convention used within the NASA Earth Science Program. The use of controlled vocabularies allows searches on the resource catalogs to be accurate and complete, but the burden of framing the precise query falls on the shoulders of the users. The user has to know the keyword before hand in order to perform a "free text" search. This might be perfectly acceptable in smaller projects where the users are specialized and have the required knowledge, but is impractical in larger projects where the users may have varied levels of domain knowledge. One solution to this problem is the use of an ontology, where the ontology contains higher level abstract concepts and the corresponding mapping to the different controlled vocabulary terms. This use of ontologies eliminates the barrier of entry based on domain knowledge and provides easy-to-use search capabilities to the users. In this presentation, we will describe an ontology designed and created to address this problem. However, this ontology required re-engineering of higher level ontologies, namely the Semantic Web for Earth and Environmental Terminology (SWEET) ontologies, instead of the initial creation of an ontology. Since the traditional methodologies for creating an ontology do not account for reengineering and reuse of higher level ontologies, we propose a new modified methodology. This presentation will describe this methodology and also explore some of the issues and challenges involved in the construction of an

  18. Combining ontologies and workflows to design formal protocols for biological laboratories

    PubMed Central

    2010-01-01

    Background Laboratory protocols in life sciences tend to be written in natural language, with negative consequences on repeatability, distribution and automation of scientific experiments. Formalization of knowledge is becoming popular in science. In the case of laboratory protocols two levels of formalization are needed: one for the entities and individuals operations involved in protocols and another one for the procedures, which can be manually or automatically executed. This study aims to combine ontologies and workflows for protocol formalization. Results A laboratory domain specific ontology and the COW (Combining Ontologies with Workflows) software tool were developed to formalize workflows built on ontologies. A method was specifically set up to support the design of structured protocols for biological laboratory experiments. The workflows were enhanced with ontological concepts taken from the developed domain specific ontology. The experimental protocols represented as workflows are saved in two linked files using two standard interchange languages (i.e. XPDL for workflows and OWL for ontologies). A distribution package of COW including installation procedure, ontology and workflow examples, is freely available from http://www.bmr-genomics.it/farm/cow. Conclusions Using COW, a laboratory protocol may be directly defined by wet-lab scientists without writing code, which will keep the resulting protocol's specifications clear and easy to read and maintain. PMID:20416048

  19. ODISEES: Ontology-Driven Interactive Search Environment for Earth Sciences

    NASA Technical Reports Server (NTRS)

    Rutherford, Matthew T.; Huffer, Elisabeth B.; Kusterer, John M.; Quam, Brandi M.

    2015-01-01

    This paper discusses the Ontology-driven Interactive Search Environment for Earth Sciences (ODISEES) project currently being developed to aid researchers attempting to find usable data among an overabundance of closely related data. ODISEES' ontological structure relies on a modular, adaptable concept modeling approach, which allows the domain to be modeled more or less as it is without worrying about terminology or external requirements. In the model, variables are individually assigned semantic content based on the characteristics of the measurements they represent, allowing intuitive discovery and comparison of data without requiring the user to sift through large numbers of data sets and variables to find the desired information.

  20. Onto-clust--a methodology for combining clustering analysis and ontological methods for identifying groups of comorbidities for developmental disorders.

    PubMed

    Peleg, Mor; Asbeh, Nuaman; Kuflik, Tsvi; Schertz, Mitchell

    2009-02-01

    Children with developmental disorders usually exhibit multiple developmental problems (comorbidities). Hence, such diagnosis needs to revolve on developmental disorder groups. Our objective is to systematically identify developmental disorder groups and represent them in an ontology. We developed a methodology that combines two methods (1) a literature-based ontology that we created, which represents developmental disorders and potential developmental disorder groups, and (2) clustering for detecting comorbid developmental disorders in patient data. The ontology is used to interpret and improve clustering results and the clustering results are used to validate the ontology and suggest directions for its development. We evaluated our methodology by applying it to data of 1175 patients from a child development clinic. We demonstrated that the ontology improves clustering results, bringing them closer to an expert generated gold-standard. We have shown that our methodology successfully combines an ontology with a clustering method to support systematic identification and representation of developmental disorder groups.

  1. Controlled Vocabularies, Mini Ontologies and Interoperability (Invited)

    NASA Astrophysics Data System (ADS)

    King, T. A.; Walker, R. J.; Roberts, D.; Thieman, J.; Ritschel, B.; Cecconi, B.; Genot, V. N.

    2013-12-01

    Interoperability has been an elusive goal, but in recent years advances have been made using controlled vocabularies, mini-ontologies and a lot of collaboration. This has led to increased interoperability between disciplines in the U.S. and between international projects. We discuss the successful pattern followed by SPASE, IVOA and IPDA to achieve this new level of international interoperability. A key aspect of the pattern is open standards and open participation with interoperability achieved with shared services, public APIs, standard formats and open access to data. Many of these standards are expressed as controlled vocabularies and mini ontologies. To illustrate the pattern we look at SPASE related efforts and participation of North America's Heliophysics Data Environment and CDPP; Europe's Cluster Active Archive, IMPEx, EuroPlanet, ESPAS and HELIO; and Japan's magnetospheric missions. Each participating project has its own life cycle and successful standards development must always take this into account. A major challenge for sustained collaboration and interoperability is the limited lifespan of many of the participating projects. Innovative approaches and new tools and frameworks are often developed as competitively selected, limited term projects, but for sustainable interoperability successful approaches need to become part of a long term infrastructure. This is being encouraged and achieved in many domains and we are entering a golden age of interoperability.

  2. Use of Solid Waste (Foundry Slag) Mortar and Bamboo Reinforcement in Seismic Analysis for Single Storey Masonry Building

    NASA Astrophysics Data System (ADS)

    Ahmad, S.; Husain, A.; Ghani, F.; Alam, M. N.

    2013-11-01

    The conversion of large amount of solid waste (foundry slag) into alternate source of building material will contribute not only as a solution to growing waste problem, but also it will conserve the natural resources of other building material and thereby reduce the cost of construction. The present work makes an effort to safe and economic use of recycle mortar (1:6) as a supplementary material. Conventional and recycled twelve prisms were casted with varying percentage of solid waste (foundry slag) added (0, 10, 20, 30 %) replacing cement by weight and tested under compression testing machine. As the replacement is increasing, the strength is decreasing. 10 % replacement curve is very closed to 0 % whereas 20 % is farther and 30 % is farthest. 20 % replacement was chosen for dynamic testing as its strength is within permissible limit as per IS code. A 1:4 scale single storey brick model with half size brick was fabricated on shake table in the lab for dynamic testing using pure friction isolation system (coarse sand as friction material µ = 0.34). Pure friction isolation technique can be adopted economically in developing countries where low-rise building prevails due to their low cost. The superstructure was separated from the foundation at plinth level, so as to permit sliding of superstructure during severe earthquake. The observed values of acceleration and displacement responses compare fairly with the analytical values of the analytical model. It also concluded that 20 % replacement of cement by solid waste (foundry slag) could be safely adopted without endangering the safety of the masonry structures under seismic load.To have an idea that how much energy is dissipated through this isolation, the same model with fixed base was tested and results were compared with the isolated free sliding model and it has been observed that more than 60 % energy is dissipated through this pure friction isolation technique. In case of base isolation, no visible cracks

  3. Evaluation of research in biomedical ontologies.

    PubMed

    Hoehndorf, Robert; Dumontier, Michel; Gkoutos, Georgios V

    2013-11-01

    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.

  4. Revealing ontological commitments by magic.

    PubMed

    Griffiths, Thomas L

    2015-03-01

    Considering the appeal of different magical transformations exposes some systematic asymmetries. For example, it is more interesting to transform a vase into a rose than a rose into a vase. An experiment in which people judged how interesting they found different magic tricks showed that these asymmetries reflect the direction a transformation moves in an ontological hierarchy: transformations in the direction of animacy and intelligence are favored over the opposite. A second and third experiment demonstrated that judgments of the plausibility of machines that perform the same transformations do not show the same asymmetries, but judgments of the interestingness of such machines do. A formal argument relates this sense of interestingness to evidence for an alternative to our current physical theory, with magic tricks being a particularly pure source of such evidence. These results suggest that people's intuitions about magic tricks can reveal the ontological commitments that underlie human cognition.

  5. Representing COA with Probabilistic Ontologies

    DTIC Science & Technology

    2011-06-01

    in utility measures, may be combined with probabilities (RUSSEL; NORVIG , 2002). Ontologies have been proposed as a tool to better express a domain...all non mentioned literals are unknown (RUSSEL; NORVIG , 2002) and must be described in the context nodes. Thus, all available information should be...Information Systems: Meeting the Challenge of the Knowledge Era. : Greenwood Publishing Group, 1996. 183 p. RUSSEL, S.; NORVIG , P. Artificial

  6. 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.

  7. Assessing the threat of firearms: new threat formula, resources, and ontological linking algorithms

    NASA Astrophysics Data System (ADS)

    Hempelmann, Christian F.; Arslan, Abdullah N.; Attardo, Salvatore; Blount, Grady P.; Sirakov, Nikolay Metodiev

    2014-06-01

    The present work is part of an ongoing larger project.2, 3, 11, 12 The goal of this project is to develop a system capable of automatic threat assessment for instances of firearms use in public places. The main components of the system are: an ontology of firearms;1, 14 algorithms to create the visual footprint of the firearms,1, 14 to compare visual information,2, 3, 11, 12 to facilitate search in the ontology, and to generate the links between the conceptual and visual ontologies; as well as a formula to calculate the threat of individual firearms, firearms classes, and ammunition types in different environments. One part of the dual-level ontology for the properties of the firearms captures key visual features used to identify their type or class in images, while the other part captures their threat-relevant conceptual properties. The visual ontology is the result of image segmentation and matching methods, while the conceptual ontology is designed using knowledge-engineering principles and populated semi-automatically from Web resources. The focus of the present paper is two-fold. On the one hand, we will report on an update of the initial threat formula, based on the substantially increased population of the firearm ontology, including ammunition types and comparisons to actual incidents, and allowing for an overall more accurate assessment. On the other hand, the linking algorithms between the visual and conceptual ontologies are elaborated for faster transfer of information leading to an improvement in accuracy of the threat assessment.

  8. 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

  9. A multilayer ontology of instruments for neurological, behavioral and cognitive assessments.

    PubMed

    Batrancourt, Bénédicte; Dojat, Michel; Gibaud, Bernard; Kassel, Gilles

    2015-01-01

    Advances in neuroscience are underpinned by large, multicenter studies and a mass of heterogeneous datasets. When investigating the relationships between brain anatomy and brain functions under normal and pathological conditions, measurements obtained from a broad range of brain imaging techniques are correlated with the information on each subject's neurologic states, cognitive assessments and behavioral scores derived from questionnaires and tests. The development of ontologies in neuroscience appears to be a valuable way of gathering and handling properly these heterogeneous data - particularly through the use of federated architectures. We recently proposed a multilayer ontology for sharing brain images and regions of interest in neuroimaging. Here, we report on an extension of this ontology to the representation of instruments used to assess brain and cognitive functions and behavior in humans. This extension consists of a 'core' ontology that accounts for the properties shared by all instruments supplemented by 'domain' ontologies that conceptualize standard instruments. We also specify how this core ontology has been refined to build domain ontologies dedicated to widely used instruments and how various scores used in the neurosciences are represented. Lastly, we discuss our design choices, the ontology's limitations and planned extensions aimed at querying and reasoning across distributed data sources.

  10. Ontology for E-Learning: A Case Study

    ERIC Educational Resources Information Center

    Colace, Francesco; De Santo, Massimo; Gaeta, Matteo

    2009-01-01

    Purpose: The development of adaptable and intelligent educational systems is widely considered one of the great challenges in scientific research. Among key elements for building advanced training systems, an important role is played by methodologies chosen for knowledge representation. In this scenario, the introduction of ontology formalism can…

  11. Construction of a Clinical Decision Support System for Undergoing Surgery Based on Domain Ontology and Rules Reasoning

    PubMed Central

    Bau, Cho-Tsan; Huang, Chung-Yi

    2014-01-01

    Abstract Objective: To construct a clinical decision support system (CDSS) for undergoing surgery based on domain ontology and rules reasoning in the setting of hospitalized diabetic patients. Materials and Methods: The ontology was created with a modified ontology development method, including specification and conceptualization, formalization, implementation, and evaluation and maintenance. The Protégé–Web Ontology Language editor was used to implement the ontology. Embedded clinical knowledge was elicited to complement the domain ontology with formal concept analysis. The decision rules were translated into JENA format, which JENA can use to infer recommendations based on patient clinical situations. Results: The ontology includes 31 classes and 13 properties, plus 38 JENA rules that were built to generate recommendations. The evaluation studies confirmed the correctness of the ontology, acceptance of recommendations, satisfaction with the system, and usefulness of the ontology for glycemic management of diabetic patients undergoing surgery, especially for domain experts. Conclusions: The contribution of this research is to set up an evidence-based hybrid ontology and an evaluation method for CDSS. The system can help clinicians to achieve inpatient glycemic control in diabetic patients undergoing surgery while avoiding hypoglycemia. PMID:24730353

  12. Spatial cyberinfrastructures, ontologies, and the humanities

    PubMed Central

    Sieber, Renee E.; Wellen, Christopher C.; Jin, Yuan

    2011-01-01

    We report on research into building a cyberinfrastructure for Chinese biographical and geographic data. Our cyberinfrastructure contains (i) the McGill-Harvard-Yenching Library Ming Qing Women's Writings database (MQWW), the only online database on historical Chinese women's writings, (ii) the China Biographical Database, the authority for Chinese historical people, and (iii) the China Historical Geographical Information System, one of the first historical geographic information systems. Key to this integration is that linked databases retain separate identities as bases of knowledge, while they possess sufficient semantic interoperability to allow for multidatabase concepts and to support cross-database queries on an ad hoc basis. Computational ontologies create underlying semantics for database access. This paper focuses on the spatial component in a humanities cyberinfrastructure, which includes issues of conflicting data, heterogeneous data models, disambiguation, and geographic scale. First, we describe the methodology for integrating the databases. Then we detail the system architecture, which includes a tier of ontologies and schema. We describe the user interface and applications that allow for cross-database queries. For instance, users should be able to analyze the data, examine hypotheses on spatial and temporal relationships, and generate historical maps with datasets from MQWW for research, teaching, and publication on Chinese women writers, their familial relations, publishing venues, and the literary and social communities. Last, we discuss the social side of cyberinfrastructure development, as people are considered to be as critical as the technical components for its success. PMID:21444819

  13. Ontology patterns for complex topographic feature yypes

    USGS Publications Warehouse

    Varanka, Dalia E.

    2011-01-01

    Complex feature types are defined as integrated relations between basic features for a shared meaning or concept. The shared semantic concept is difficult to define in commonly used geographic information systems (GIS) and remote sensing technologies. The role of spatial relations between complex feature parts was recognized in early GIS literature, but had limited representation in the feature or coverage data models of GIS. Spatial relations are more explicitly specified in semantic technology. In this paper, semantics for topographic feature ontology design patterns (ODP) are developed as data models for the representation of complex features. In the context of topographic processes, component assemblages are supported by resource systems and are found on local landscapes. The topographic ontology is organized across six thematic modules that can account for basic feature types, resource systems, and landscape types. Types of complex feature attributes include location, generative processes and physical description. Node/edge networks model standard spatial relations and relations specific to topographic science to represent complex features. To demonstrate these concepts, data from The National Map of the U. S. Geological Survey was converted and assembled into ODP.

  14. Technological behaviour and recycling potential of spent foundry sands in clay bricks.

    PubMed

    Alonso-Santurde, R; Andrés, A; Viguri, J R; Raimondo, M; Guarini, G; Zanelli, C; Dondi, M

    2011-03-01

    The feasibility of recycling spent foundry sand in clay bricks was assessed in laboratory, pilot line and industrial trials, using naturally occurring sand as a reference. Raw materials were analyzed by X-ray fluorescence, X-ray diffraction, particle size distribution, and leaching and combined to produce bodies containing up to 35% wt. sand. The extrusion, drying and firing behaviour (plasticity, drying sensitivity, mechanical strength, bulk density, water absorption, and shrinkage) were determined. The microstructure, phase composition, durability and leaching (EN 12457, granular materials, end-life step, European Waste Landfill Directive; NEN 7345, monolithic materials, use-life step, Dutch Building Material Decree) were evaluated for bricks manufactured at optimal firing temperature. These results demonstrate that spent foundry sand can be recycled in clay bricks. There are no relevant technological drawbacks, but the feasibility strongly depends on the properties of the raw materials. Spent foundry sand may be introduced into bricks up to 30% wt. Most of the hazardous elements from the spent foundry sand are inertized during firing and the concentrations of hazardous components in the leachates are below the standard threshold for inert waste category landfill excepting for chromium and lead; however, their environmental risk during their use-life step can be considered negligible.

  15. 78 FR 21123 - Charlotte Pipe and Foundry; Analysis to Aid Public Comment

    Federal Register 2010, 2011, 2012, 2013, 2014

    2013-04-09

    ... Containing Consent Order (``Consent Agreement'') from Charlotte Pipe and Foundry Company (hereinafter ``CP&F... true. I. The Complaint The Complaint makes the following allegations. A. The Respondents CP&F is a... 28207. CP&F is one of the largest producers and sellers of CISP products in the United States....

  16. METRO-APEX Volume 13.1: Industrialist's Manual No. 3, Rusty's Iron Foundry. Revised.

    ERIC Educational Resources Information Center

    University of Southern California, Los Angeles. COMEX Research Project.

    The Industrialist's Manual No. 3 (Rusty's Iron Foundry) is one of a set of twenty-one manuals used in METRO-APEX 1974, a computerized college and professional level, computer-supported, role-play, simulation exercise of a community with "normal" problems. Stress is placed on environmental quality considerations. APEX 1974 is an expansion…

  17. 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

  18. Concentrations of PCDD/PCDFs and PCBs in spent foundry sands

    Technology Transfer Automated Retrieval System (TEKTRAN)

    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...

  19. The characterization and composition of bacterial communities in soils blended with spent foundry sand

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Spent foundry sands (SFSs) are a likely replacement for virgin aggregate used in manufactured soils, such as topsoils, potting soils, and landscaping mixes. While SFSs generally contain low concentrations of trace elements and xenobiotics, concerns about their impact upon environmental receptors ha...

  20. Metals in waste foundry sands and an evaluation of their leaching and transport to groundwater

    Technology Transfer Automated Retrieval System (TEKTRAN)

    While most waste molding foundry sands (WFSs) are not hazardous in nature, regulatory agencies are often reluctant to permit their beneficial use in agricultural and geotechnical applications due to concerns over metal leaching. The objective of this study was to quantify total and Toxicity Characte...

  1. 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

  2. Anatomy Ontology Matching Using Markov Logic Networks

    PubMed Central

    Li, Chunhua; Zhao, Pengpeng; Wu, Jian; Cui, Zhiming

    2016-01-01

    The anatomy of model species is described in ontologies, which are used to standardize the annotations of experimental data, such as gene expression patterns. To compare such data between species, we need to establish relationships between ontologies describing different species. Ontology matching is a kind of solutions to find semantic correspondences between entities of different ontologies. Markov logic networks which unify probabilistic graphical model and first-order logic provide an excellent framework for ontology matching. We combine several different matching strategies through first-order logic formulas according to the structure of anatomy ontologies. Experiments on the adult mouse anatomy and the human anatomy have demonstrated the effectiveness of proposed approach in terms of the quality of result alignment. PMID:27382498

  3. Exploring Mission Concepts with the JPL Innovation Foundry A-Team

    NASA Technical Reports Server (NTRS)

    Ziemer, John K.; Ervin, Joan; Lang, Jared

    2013-01-01

    The JPL Innovation Foundry has established a new approach for exploring, developing, and evaluating early concepts called the A-Team. The A-Team combines innovative collaborative methods with subject matter expertise and analysis tools to help mature mission concepts. Science, implementation, and programmatic elements are all considered during an A-Team study. Methods are grouped by Concept Maturity Level (CML), from 1 through 3, including idea generation and capture (CML 1), initial feasibility assessment (CML 2), and trade space exploration (CML 3). Methods used for each CML are presented, and the key team roles are described from two points of view: innovative methods and technical expertise. A-Team roles for providing innovative methods include the facilitator, study lead, and assistant study lead. A-Team roles for providing technical expertise include the architect, lead systems engineer, and integration engineer. In addition to these key roles, each A-Team study is uniquely staffed to match the study topic and scope including subject matter experts, scientists, technologists, flight and instrument systems engineers, and program managers as needed. Advanced analysis and collaborative engineering tools (e.g. cost, science traceability, mission design, knowledge capture, study and analysis support infrastructure) are also under development for use in A-Team studies and will be discussed briefly. The A-Team facilities provide a constructive environment for innovative ideas from all aspects of mission formulation to eliminate isolated studies and come together early in the development cycle when they can provide the biggest impact. This paper provides an overview of the A-Team, its study processes, roles, methods, tools and facilities.

  4. Instance testing of the family history ontology.

    PubMed

    Peace, Jane; Brennan, Patricia Flatley; Brennan, Patti

    2008-11-06

    The Family History Ontology formalizes nursing conceptualization about family and family history. Traditional methods of instance testing were applied to evaluate the completeness of the ontology and demonstrated favorable domain coverage. Testing also revealed a need for a new category of instance test results, "by inference", for data that can be represented through the use of inference rules associated with the ontology rather than requiring direct manual entry.

  5. C2 Domain Ontology within Our Lifetime

    DTIC Science & Technology

    2009-06-01

    process or an event). [21] Figure 1, adopted from [16], depicts the concept of ontological levels for a post office application based on the Husserl ...University, NJ, 2008. [23] Husserl , E., Id Macmillan. 1931. [24] Basic Formal Ontology (multiple references and artifacts): http://www.ifomis.org/bfo/BFO...Applied Ontology An Introduction, pp 39-56, Transaction Books, Rutgers University, NJ, 2008.  [23] Husserl , E., Ideas: General Introduction to Pure

  6. Aluminium and iron air pollution near an iron casting and aluminium foundry in Turin district (Italy).

    PubMed

    Polizzi, Salvatore; Ferrara, Mauro; Bugiani, Massimiliano; Barbero, Domenico; Baccolo, Tiziana

    2007-09-01

    This work reports the results of an environmental survey carried out in an industrial area in the Province of Turin: its main aim is to assess the levels of iron and aluminium in the outside air during the period from July to September to assess the influence of industrial activity (a cast-iron and aluminium foundry) which is interrupted during the month of August, on the level of metals present in the air. Conducting the analysis during this period of time made it possible to avoid the confounding effect of pollution due to domestic central heating. The measurements were taken from nine areas at different distances from the foundry in the area and according to the direction of the prevailing winds, as deduced from the historical data. The results of this survey show a statistically significant difference in iron and aluminium levels in the outside air in the geographic areas between the two main periods examined: during August (no foundry activity) v/s July-September (foundry activity). The values recorded are: Aluminium 0.4+/-0.45 microg/m(3) v/s 1.12+/-1.29 microg/m(3) (p<0.0001); Iron 0.95+/-0.56 microg/m(3) v/s 1.6+/-1.0 microg/m(3) (p<0.0001). There were no statistically significant differences between the nine sampling points from the point of view of the sampling sites, climate conditions and wind directions. We found no correlation with car traffic, in terms of the number of vehicles, and metals. The values of iron tended to be higher in the areas farther away from the foundry site in the areas located along the path of the prevailing winds.

  7. Arthrogryposis as a Syndrome: Gene Ontology Analysis

    PubMed Central

    Hall, Judith G.; Kiefer, Jeff

    2016-01-01

    Arthrogryposis by definition has multiple congenital contractures. All types of arthrogryposis have decreased in utero fetal movement. Because so many things are involved in normal fetal movement, there are many causes and processes that can go awry. In this era of molecular genetics, we have tried to place the known mutated genes seen in genetic forms of arthrogryposis into biological processes or cellular functions as defined by gene ontology. We hope this leads to better identification of all interacting pathways and processes involved in the development of fetal movement in order to improve diagnosis of the genetic forms of arthrogryposis, to lead to the development of molecular therapies, and to help better define the natural history of various types of arthrogryposis. PMID:27587986

  8. Microglia Ontology and Signaling

    PubMed Central

    ElAli, Ayman; Rivest, Serge

    2016-01-01

    Microglia constitute the powerhouse of the innate immune system in the brain. It is now widely accepted that they are monocytic-derived cells that infiltrate the developing brain at the early embryonic stages, and acquire a resting phenotype characterized by the presence of dense branching processes, called ramifications. Microglia use these dynamic ramifications as sentinels to sense and detect any occurring alteration in brain homeostasis. Once a danger signal is detected, such as molecular factors associated to brain damage or infection, they get activated by acquiring a less ramified phenotype, and mount adequate responses that range from phagocyting cell debris to secreting inflammatory and trophic factors. Here, we review the origin of microglia and we summarize the main molecular signals involved in controlling their function under physiological conditions. In addition, their implication in the pathogenesis of multiple sclerosis and stress is discussed. PMID:27446922

  9. Semantic similarity between ontologies at different scales

    SciTech Connect

    Zhang, Qingpeng; Haglin, David J.

    2016-04-01

    In the past decade, existing and new knowledge and datasets has been encoded in different ontologies for semantic web and biomedical research. The size of ontologies is often very large in terms of number of concepts and relationships, which makes the analysis of ontologies and the represented knowledge graph computational and time consuming. As the ontologies of various semantic web and biomedical applications usually show explicit hierarchical structures, it is interesting to explore the trade-offs between ontological scales and preservation/precision of results when we analyze ontologies. This paper presents the first effort of examining the capability of this idea via studying the relationship between scaling biomedical ontologies at different levels and the semantic similarity values. We evaluate the semantic similarity between three Gene Ontology slims (Plant, Yeast, and Candida, among which the latter two belong to the same kingdom—Fungi) using four popular measures commonly applied to biomedical ontologies (Resnik, Lin, Jiang-Conrath, and SimRel). The results of this study demonstrate that with proper selection of scaling levels and similarity measures, we can significantly reduce the size of ontologies without losing substantial detail. In particular, the performance of Jiang-Conrath and Lin are more reliable and stable than that of the other two in this experiment, as proven by (a) consistently showing that Yeast and Candida are more similar (as compared to Plant) at different scales, and (b) small deviations of the similarity values after excluding a majority of nodes from several lower scales. This study provides a deeper understanding of the application of semantic similarity to biomedical ontologies, and shed light on how to choose appropriate semantic similarity measures for biomedical engineering.

  10. Issues in learning an ontology from text

    PubMed Central

    Brewster, Christopher; Jupp, Simon; Luciano, Joanne; Shotton, David; Stevens, Robert D; Zhang, Ziqi

    2009-01-01

    Ontology construction for any domain is a labour intensive and complex process. Any methodology that can reduce the cost and increase efficiency has the potential to make a major impact in the life sciences. This paper describes an experiment in ontology construction from text for the animal behaviour domain. Our objective was to see how much could be done in a simple and relatively rapid manner using a corpus of journal papers. We used a sequence of pre-existing text processing steps, and here describe the different choices made to clean the input, to derive a set of terms and to structure those terms in a number of hierarchies. We describe some of the challenges, especially that of focusing the ontology appropriately given a starting point of a heterogeneous corpus. Using mainly automated techniques, we were able to construct an 18055 term ontology-like structure with 73% recall of animal behaviour terms, but a precision of only 26%. We were able to clean unwanted terms from the nascent ontology using lexico-syntactic patterns that tested the validity of term inclusion within the ontology. We used the same technique to test for subsumption relationships between the remaining terms to add structure to the initially broad and shallow structure we generated. All outputs are available at . We present a systematic method for the initial steps of ontology or structured vocabulary construction for scientific domains that requires limited human effort and can make a contribution both to ontology learning and maintenance. The method is useful both for the exploration of a scientific domain and as a stepping stone towards formally rigourous ontologies. The filtering of recognised terms from a heterogeneous corpus to focus upon those that are the topic of the ontology is identified to be one of the main challenges for research in ontology learning. PMID:19426458

  11. Probabilistic Ontology Architecture for a Terrorist Identification Decision Support System

    DTIC Science & Technology

    2014-06-01

    Ontology in Protégé. The Support Layer consists of technological artifacts highlighted by the OWL and MEBN languages used to represent the ontology and...additional individuals for an extended knowledge base. 6) Ontology. The Terrorist Identification Ontology is created in OWL using Protégé. The...application areas. 2) Modeling Languages. Ontological engineering was conducted in the Web Ontology Language ( OWL ) due to its incorporation within Protégé

  12. The Pre-Eclampsia Ontology: A Disease Ontology Representing the Domain Knowledge Specific to Pre-Eclampsia

    PubMed Central

    Mizuno, Satoshi; Ogishima, Soichi; Nishigori, Hidekazu; Jamieson, Daniel G.; Verspoor, Karin; Tanaka, Hiroshi; Yaegashi, Nobuo; Nakaya, Jun

    2016-01-01

    Pre-eclampsia (PE) is a clinical syndrome characterized by new-onset hypertension and proteinuria at ≥20 weeks of gestation, and is a leading cause of maternal and perinatal morbidity and mortality. Previous studies have gathered abundant data about PE such as risk factors and pathological findings. However, most of these data are not semantically structured. Clinical data on PE patients are often generated with semantic heterogeneity such as using disparate terminology to describe the same phenomena. In clinical studies, interoperability of heterogenic clinical data is required in various situations. In such a situation, it is necessary to develop an interoperable and standardized semantic framework to research the pathology of PE more comprehensively and to achieve interoperability of heterogenic clinical data of PE patients. In this study, we developed an ontology representing clinical features, treatments, genetic factors, environmental factors, and other aspects of the current knowledge in the domain of PE. We call this pre-eclampsia ontology “PEO”. To achieve interoperability with other ontologies, the core structure of PEO was compliant with the hierarchy of the Basic Formal Ontology (BFO). The PEO incorporates a wide range of key concepts and terms of PE from clinical and biomedical research in structuring the knowledge base that is specific to PE; therefore, PEO is expected to enhance PE-specific information retrieval and knowledge discovery in both clinical and biomedical research fields. PMID:27788142

  13. Security Ontology for Annotating Resources

    DTIC Science & Technology

    2005-08-31

    RSA SHA- 25 H-CCMAC -Blowfish RPM S TdpAeDES (hasNSALevel &assurance;typeS) u-wMD4 "MD5 CAST Skipjack (hasNSALevel = &assurance;type2) CRAYON ...type3) MD5tMD5 CAST Skipjack (hasNSALevel = &assurance;type2) CRAYON (hasNSALevel = &assurance;type1) 28 C.4. NRL Security Assurance Ontology...34&assurance;Type2"/> </SymmetricAlgorithm> <SymmetricAlgorithm rdf:ID=" CRAYON "> <hasNSALevel rdf:resource="&assurance;Typel"/> </SymmetricAlgori thmn

  14. Nosology, ontology and promiscuous realism.

    PubMed

    Binney, Nicholas

    2015-06-01

    Medics may consider worrying about their metaphysics and ontology to be a waste of time. I will argue here that this is not the case. Promiscuous realism is a metaphysical position which holds that multiple, equally valid, classification schemes should be applied to objects (such as patients) to capture different aspects of their complex and heterogeneous nature. As medics at the bedside may need to capture different aspects of their patients' problems, they may need to use multiple classification schemes (multiple nosologies), and thus consider adopting a different metaphysics to the one commonly in use.

  15. Mechanical and toxicological evaluation of concrete artifacts containing waste foundry sand.

    PubMed

    Mastella, Miguel Angelo; Gislon, Edivelton Soratto; Pelisser, Fernando; Ricken, Cláudio; da Silva, Luciano; Angioletto, Elídio; Montedo, Oscar Rubem Klegues

    2014-08-01

    The creation of metal parts via casting uses molds that are generally made from sand and phenolic resin. The waste generated after the casting process is called waste foundry sand (WFS). Depending on the mold composition and the casting process, WFS can contain substances that prevent its direct emission to the environment. In Brazil, this waste is classified according to the Standard ABNT NBR 10004:2004 as a waste Class II (Non-Inert). The recycling of this waste is limited because its characteristics change significantly after use. Although the use (or reuse) of this byproduct in civil construction is a technically feasible alternative, its effects must be evaluated, especially from mechanical and environmental points of view. Thus, the objective of this study is to investigate the effect of the use of WFS in the manufacture of cement artifacts, such as masonry blocks for walls, structural masonry blocks, and paving blocks. Blocks containing different concentrations of WFS (up to 75% by weight) were produced and evaluated using compressive strength tests (35 MPa at 28 days) and toxicity tests on Daphnia magna, Allium cepa (onion root), and Eisenia foetida (earthworm). The results showed that there was not a considerable reduction in the compressive strength, with values of 35 ± 2 MPa at 28 days. The toxicity study with the material obtained from leaching did not significantly interfere with the development of D. magna and E. foetida, but the growth of the A. cepa species was reduced. The study showed that the use of this waste in the production of concrete blocks is feasible from both mechanical and environmental points of view.

  16. Research and application of role theory in ocean carbon cycle ontology construction

    NASA Astrophysics Data System (ADS)

    Jia, Haipeng; Xiong, Jing; Xu, Jianliang; Wang, Jipeng

    2014-12-01

    Many researchers have studied the ocean carbon cycle model trying to regulate the level of CO2 in atmosphere from viewpoint of quantification. Unlike other researches, this paper analyzes the conversion process of carbon element in the ocean from the qualitative viewpoint. There are many complex roles in the ocean carbon cycle, and it is hard to represent the case that an entity plays different role in different environment. An ontology technology Hozo role theory developed by Osaka University Mizoguchi Laboratory is proposed as a solution. The basic concepts and representation mode of Hozo role theory is introduced. The conversion process of ocean carbon cycle is abstracted and an ontology model using Hozo role theory is proposed. Instead of comprehensive common ontology construction method, we propose our own ontology development steps. Then an ontology about ocean carbon cycle is built in order to describe and share the basic knowledge of ocean carbon cycle. A knowledge base of material circulation is proposed based on the ontology. Its construction framework is described and some knowledge base query examples are also illustrated. Conclusions show that the role theory can effectively solve the problem of multirole description in ocean carbon cycle, and knowledge reasoning based on ontology is also effective.

  17. Hybrid ontology for semantic information retrieval model using keyword matching indexing system.

    PubMed

    Uthayan, K R; Mala, G S Anandha

    2015-01-01

    Ontology is the process of growth and elucidation of concepts of an information domain being common for a group of users. Establishing ontology into information retrieval is a normal method to develop searching effects of relevant information users require. Keywords matching process with historical or information domain is significant in recent calculations for assisting the best match for specific input queries. This research presents a better querying mechanism for information retrieval which integrates the ontology queries with keyword search. The ontology-based query is changed into a primary order to predicate logic uncertainty which is used for routing the query to the appropriate servers. Matching algorithms characterize warm area of researches in computer science and artificial intelligence. In text matching, it is more dependable to study semantics model and query for conditions of semantic matching. This research develops the semantic matching results between input queries and information in ontology field. The contributed algorithm is a hybrid method that is based on matching extracted instances from the queries and information field. The queries and information domain is focused on semantic matching, to discover the best match and to progress the executive process. In conclusion, the hybrid ontology in semantic web is sufficient to retrieve the documents when compared to standard ontology.

  18. 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.

  19. Defining Resilience and Vulnerability Based on Ontology Engineering Approach

    NASA Astrophysics Data System (ADS)

    Kumazawa, T.; Matsui, T.; Endo, A.

    2014-12-01

    It is necessary to reflect the concepts of resilience and vulnerability into the assessment framework of "Human-Environmental Security", but it is also in difficulty to identify the linkage between both concepts because of the difference of the academic community which has discussed each concept. The authors have been developing the ontology which deals with the sustainability of the social-ecological systems (SESs). Resilience and vulnerability are also the concepts in the target world which this ontology covers. Based on this point, this paper aims at explicating the semantic relationship between the concepts of resilience and vulnerability based on ontology engineering approach. For this purpose, we first examine the definitions of resilience and vulnerability which the existing literatures proposed. Second, we incorporate the definitions in the ontology dealing with sustainability of SESs. Finally, we focus on the "Water-Energy-Food Nexus Index" to assess Human-Environmental Security, and clarify how the concepts of resilience and vulnerability are linked semantically through the concepts included in these index items.

  20. Information-theoretic evaluation of predicted ontological annotations

    PubMed Central

    Clark, Wyatt T.; Radivojac, Predrag

    2013-01-01

    Motivation: The development of effective methods for the prediction of ontological annotations is an important goal in computational biology, with protein function prediction and disease gene prioritization gaining wide recognition. Although various algorithms have been proposed for these tasks, evaluating their performance is difficult owing to problems caused both by the structure of biomedical ontologies and biased or incomplete experimental annotations of genes and gene products. Results: We propose an information-theoretic framework to evaluate the performance of computational protein function prediction. We use a Bayesian network, structured according to the underlying ontology, to model the prior probability of a protein’s function. We then define two concepts, misinformation and remaining uncertainty, that can be seen as information-theoretic analogs of precision and recall. Finally, we propose a single statistic, referred to as semantic distance, that can be used to rank classification models. We evaluate our approach by analyzing the performance of three protein function predictors of Gene Ontology terms and provide evidence that it addresses several weaknesses of currently used metrics. We believe this framework provides useful insights into the performance of protein function prediction tools. Contact: predrag@indiana.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:23813009

  1. OPIC: Ontology-driven Patient Information Capturing system for epilepsy.

    PubMed

    Sahoo, Satya S; Zhao, Meng; Luo, Lingyun; Bozorgi, Alireza; Gupta, Deepak; Lhatoo, Samden D; Zhang, Guo-Qiang

    2012-01-01

    The widespread use of paper or document-based forms for capturing patient information in various clinical settings, for example in epilepsy centers, is a critical barrier for large-scale, multi-center research studies that require interoperable, consistent, and error-free data collection. This challenge can be addressed by a web-accessible and flexible patient data capture system that is supported by a common terminological system to facilitate data re-usability, sharing, and integration. We present OPIC, an Ontology-driven Patient Information Capture (OPIC) system that uses a domain-specific epilepsy and seizure ontology (EpSO) to (1) support structured entry of multi-modal epilepsy data, (2) proactively ensure quality of data through use of ontology terms in drop-down menus, and (3) identify and index clinically relevant ontology terms in free-text fields to improve accuracy of subsequent analytical queries (e.g. cohort identification). EpSO, modeled using the Web Ontology Language (OWL), conforms to the recommendations of the International League Against Epilepsy (ILAE) classification and terminological commission. OPIC has been developed using agile software engineering methodology for rapid development cycles in close collaboration with domain expert and end users. We report the result from the initial deployment of OPIC at the University Hospitals Case Medical Center (UH CMC) epilepsy monitoring unit (EMU) as part of the NIH-funded project on Sudden Unexpected Death in Epilepsy (SUDEP). Preliminary user evaluation shows that OPIC has achieved its design objectives to be an intuitive patient information capturing system that also reduces the potential for data entry errors and variability in use of epilepsy terms.

  2. Statistical mechanics of ontology based annotations

    NASA Astrophysics Data System (ADS)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.

  3. FROG - Fingerprinting Genomic Variation Ontology

    PubMed Central

    Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: “FingeRprinting Ontology of Genomic variations” is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog. PMID:26244889

  4. FROG - Fingerprinting Genomic Variation Ontology.

    PubMed

    Abinaya, E; Narang, Pankaj; Bhardwaj, Anshu

    2015-01-01

    Genetic variations play a crucial role in differential phenotypic outcomes. Given the complexity in establishing this correlation and the enormous data available today, it is imperative to design machine-readable, efficient methods to store, label, search and analyze this data. A semantic approach, FROG: "FingeRprinting Ontology of Genomic variations" is implemented to label variation data, based on its location, function and interactions. FROG has six levels to describe the variation annotation, namely, chromosome, DNA, RNA, protein, variations and interactions. Each level is a conceptual aggregation of logically connected attributes each of which comprises of various properties for the variant. For example, in chromosome level, one of the attributes is location of variation and which has two properties, allosomes or autosomes. Another attribute is variation kind which has four properties, namely, indel, deletion, insertion, substitution. Likewise, there are 48 attributes and 278 properties to capture the variation annotation across six levels. Each property is then assigned a bit score which in turn leads to generation of a binary fingerprint based on the combination of these properties (mostly taken from existing variation ontologies). FROG is a novel and unique method designed for the purpose of labeling the entire variation data generated till date for efficient storage, search and analysis. A web-based platform is designed as a test case for users to navigate sample datasets and generate fingerprints. The platform is available at http://ab-openlab.csir.res.in/frog.

  5. Applying ontological realism to medically unexplained syndromes.

    PubMed

    Doing-Harris, Kristina; Meystre, Stephane M; Samore, Matthew; Ceusters, Werner

    2013-01-01

    The past decade has witnessed an increased interest in what are called "medically unexplained syndromes" (MUS). We address the question of whether structuring the domain knowledge for MUS can be achieved by applying the principles of Ontological Realism in light of criticisms about their usefulness in areas where science has not yet led to insights univocally endorsed by the relevant communities. We analyzed whether the different perspectives held by MUS researchers can be represented without taking any particular stance and whether existing ontologies based on Ontological Realism can be further built upon. We did not find refutation of the applicability of the principles. We found the Ontology of General Medical Science and Information Artifact Ontology to provide useful frameworks for analyzing certain MUS controversies, although leaving other questions open.

  6. What's in a code? Towards a formal account of the relation of ontologies and coding systems.

    PubMed

    Rector, Alan L

    2007-01-01

    Terminologies are increasingly based on "ontologies" developed in description logics and related languages such as the new Web Ontology Language, OWL. The use of description logic has been expected to reduce ambiguity and make it easier determine logical equivalence, deal with negation, and specify EHRs. However, this promise has not been fully realised: in part because early description logics were relatively inexpressive, in part, because the relation between coding systems, EHRs, and ontologies expressed in description logics has not been fully understood. This paper presents a unifying approach using the expressive formalisms available in the latest version of OWL, OWL 1.1.

  7. Design and evaluation of an ontology based information extraction system for radiological reports.

    PubMed

    Soysal, Ergin; Cicekli, Ilyas; Baykal, Nazife

    2010-01-01

    This paper describes an information extraction system that extracts and converts the available information in free text Turkish radiology reports into a structured information model using manually created extraction rules and domain ontology. The ontology provides flexibility in the design of extraction rules, and determines the information model for the extracted semantic information. Although our information extraction system mainly concentrates on abdominal radiology reports, the system can be used in another field of medicine by adapting its ontology and extraction rule set. We achieved very high precision and recall results during the evaluation of the developed system with unseen radiology reports.

  8. Standardized terminology for clinical trial protocols based on top-level ontological categories.

    PubMed

    Heller, B; Herre, H; Lippoldt, K; Loeffler, M

    2004-01-01

    This paper describes a new method for the ontologically based standardization of concepts with regard to the quality assurance of clinical trial protocols. We developed a data dictionary for medical and trial-specific terms in which concepts and relations are defined context-dependently. The data dictionary is provided to different medical research networks by means of the software tool Onto-Builder via the internet. The data dictionary is based on domain-specific ontologies and the top-level ontology of GOL. The concepts and relations described in the data dictionary are represented in natural language, semi-formally or formally according to their use.

  9. A topographic feature taxonomy for a U.S. national topographic mapping ontology

    USGS Publications Warehouse

    Varanka, Dalia E.

    2013-01-01

    Using legacy feature lists from the U.S. National Topographic Mapping Program of the twentieth century, a taxonomy of features is presented for purposes of developing a national topographic feature ontology for geographic mapping and analysis. After reviewing published taxonomic classifications, six basic classes are suggested; terrain, surface water, ecological regimes, built-up areas, divisions, and events. Aspects of ontology development are suggested as the taxonomy is described.

  10. Text Mining to inform construction of Earth and Environmental Science Ontologies

    NASA Astrophysics Data System (ADS)

    Schildhauer, M.; Adams, B.; Rebich Hespanha, S.

    2013-12-01

    There is a clear need for better semantic representation of Earth and environmental concepts, to facilitate more effective discovery and re-use of information resources relevant to scientists doing integrative research. In order to develop general-purpose Earth and environmental science ontologies, however, it is necessary to represent concepts and relationships that span usage across multiple disciplines and scientific specialties. Traditional knowledge modeling through ontologies utilizes expert knowledge but inevitably favors the particular perspectives of the ontology engineers, as well as the domain experts who interacted with them. This often leads to ontologies that lack robust coverage of synonymy, while also missing important relationships among concepts that can be extremely useful for working scientists to be aware of. In this presentation we will discuss methods we have developed that utilize statistical topic modeling on a large corpus of Earth and environmental science articles, to expand coverage and disclose relationships among concepts in the Earth sciences. For our work we collected a corpus of over 121,000 abstracts from many of the top Earth and environmental science journals. We performed latent Dirichlet allocation topic modeling on this corpus to discover a set of latent topics, which consist of terms that commonly co-occur in abstracts. We match terms in the topics to concept labels in existing ontologies to reveal gaps, and we examine which terms are commonly associated in natural language discourse, to identify relationships that are important to formally model in ontologies. Our text mining methodology uncovers significant gaps in the content of some popular existing ontologies, and we show how, through a workflow involving human interpretation of topic models, we can bootstrap ontologies to have much better coverage and richer semantics. Because we base our methods directly on what working scientists are communicating about their

  11. Flowable fill using waste foundry sand: A substitute for compacted or stabilized soil

    SciTech Connect

    Bhat, S.T.; Lovell, C.W.

    1997-12-31

    Flowable fill is generally a mixture of sand, fly ash, a small amount of cement, and water. Sand is the major component of most flowable fill mixes; consequently, using a waste material as a substitute for natural sand results in the beneficial use of the waste material. Waste foundry sand (WFS) was used as a fine aggregate in this study. Three green sands from ferrous foundries and two class F fly ashes were used. The flow behavior, hardening characteristics, ultimate strength behavior, and permeability characteristics of flowable fill were investigated. The penetration resistance necessary to sustain walkability as the fresh flowable fill hardens was determined. The pH of pore solution of hardened flowable fill indicated that the potential for corrosivity is low. The toxicity tests indicated that some WFSs are environmentally safe.

  12. Magnetic and GPR surveys of a former munitions foundry site at the Denver Federal Center

    USGS Publications Warehouse

    Campbell, David L.; Beanland, Shay; Lucius, Jeffrey E.; Powers, Michael H.

    2000-01-01

    We made magnetometer and ground penetrating radar (GPR) surveys over part of the foundation of a World War II-era foundry located on the Denver Federal Center. The site contains a number of highly magnetic source bodies, concrete foundation walls, and underground openings, buried under a clay cap. The cap is several feet thick and has a conductivity of about 35 mS/m, making the features underneath it a poor target for conventional GPR. Indeed, the raw data look unlike typical GPR data, but rather show reverberation (?) bands under sidewalks and other shallow buried sources. Using a newly-written computer package, we made plan maps of the GPR response at different time slices. The sliced GPR data did not outline buried foundry foundations, as we had hoped it might. The resulting plan maps of the sliced data show sidewalks and other blobby features, some of which correspond to magnetometer highs.

  13. 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.

  14. 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.

  15. 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

  16. 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

  17. Analysis of occupational injuries in four foundries in Alexandria and Beheira from 1998 to 2000.

    PubMed

    Zakaria, Adel; El Maghraby, Gamal

    2003-01-01

    Occupational injuries of foundry workers might occur due to a variety of inherent hazardous conditions in foundries. The aim of the present work is to analyse occupational injuries in four foundries, two in Alexandria, El Nasr and Ramsis and two in Behiera, Misr Spining and Weaving and Misr Rayon Companies in a three years period from 1998 to 2000. The raw injuries data have been gathered from the four foundries and tabulated as related to age group, injured part, cause and mean of injury. Frequency rates and severity rates have been computed for the three years of study. The results of the present study revealed that there was a significant increase of injuries incidence rate in Ramsis Company than in the other three companies especially in age groups 30-40 and 41-50 years (P < 0.01). lower extremities and higher extremities have recorded the highest incidence rate in the four companies in the three years of study, respectively (P < 0.05-P < 0.001). Ramsis company has recorded a significant increase in all injured parts except for head injuries in 1998 (P < 0.05-P < 0.001). Transportation and lifting was the main cause of injuries in the four companies in the three years of study (P < 0.01), however work environment was a main cause of injuries in Ramsis company (P < 0.01). Contact hot object in Ramsis was the main mean of injuries in the three years (P < 0.01) followed by faulty action and striking against and falling objects (P < 0.01). Ramsis Company has recorded the highest frequency rates (P < 0.01-P < 0.001) and severity rates (P < 0.01-P < 0.001).

  18. Improved Foundry Castings Utilizing CAD/CAM (Computer Aided Design/ Computer Aided Manufacture). Volume 1. Overview

    DTIC Science & Technology

    1988-06-30

    several organizations. Members of the project staffs at the University of Pittsburgh, Battelle Columbus Laboratories, Blaw - Knox Foundry and Mill...with the University of Pittsburgh, James Echlin, Blaw - Knox , and A. Roulet, General Dynamics. Computing facilities on the DEC 10 system were made...Akgerman, A. Badawy, C. Wilson, and T. Altan. The project staff at Blaw - Knox included Mssrs. R. Nariman, KI Fahey, and S. Miller. Mr. W. Northey

  19. Historical cohort study of a New Zealand foundry and heavy engineering plant

    PubMed Central

    Firth, H. M.; Elwood, J. M.; Cox, B.; Herbison, G. P.

    1999-01-01

    OBJECTIVES: To investigate the mortality of workers who had been exposed to asbestos, machining fluids and foundry work in a foundry and heavy engineering plant in the railway rolling stock manufacturing industry in New Zealand. METHODS: Historical cohort study design. RESULTS: For the total workforce of 3522 men employed between 1945 and 1991, follow up was 90% of person-years to 31 December 1991. Significantly increased standardised mortality ratios (SMRs) were found for all causes of death combined (SMR 1.07; 95% confidence interval (95% CI) 1.01 to 1.14), all malignancies (SMR 1.15; 95% CI 1.01 to 1.31), circulatory (SMR 1.16; 95% CI 1.07 to 1.27) and musculoskeletal diseases (SMR 3.06; 95% CI 1.39 to 5.84), all digestive cancers (SMR 1.29; 95% CI 1.04 to 1.59), all respiratory cancers (SMR 1.34; 95% CI 1.08 to 1.65), cancer of the oesophagus (SMR 1.97; 95% CI 1.01 to 3.45), and mesothelioma of the pleura (SMR 6.58; 95% CI 1.24 to 19.49). Three deaths from pleural mesothelioma were recorded, with latency times of 51, 53, and 57 years. There were no dose-response relations between exposure to asbestos, machining fluids or foundry work, or by duration of employment in the plant, and any cause of death. CONCLUSIONS: This study found small increases in risk for several causes of death among foundry and heavy engineering workers; however, these increases were small and the possible effects of smoking and other lifestyle factors could not be excluded. There was evidence of asbestos related disease in those involved in engineering work in the past.   PMID:10448319

  20. CNTRO: A Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives.

    PubMed

    Tao, Cui; Wei, Wei-Qi; Solbrig, Harold R; Savova, Guergana; Chute, Christopher G

    2010-11-13

    Using Semantic-Web specifications to represent temporal information in clinical narratives is an important step for temporal reasoning and answering time-oriented queries. Existing temporal models are either not compatible with the powerful reasoning tools developed for the Semantic Web, or designed only for structured clinical data and therefore are not ready to be applied on natural-language-based clinical narrative reports directly. We have developed a Semantic-Web ontology which is called Clinical Narrative Temporal Relation ontology. Using this ontology, temporal information in clinical narratives can be represented as RDF (Resource Description Framework) triples. More temporal information and relations can then be inferred by Semantic-Web based reasoning tools. Experimental results show that this ontology can represent temporal information in real clinical narratives successfully.

  1. Mapping of Core Components Based e-Business Standards into Ontology

    NASA Astrophysics Data System (ADS)

    Magdalenić, Ivan; Vrdoljak, Boris; Schatten, Markus

    A mapping of Core Components specification based e-business standards to an ontology is presented. The Web Ontology Language (OWL) is used for ontology development. In order to preserve the existing hierarchy of the standards, an emphasis is put on the mapping of Core Components elements to specific constructs in OWL. The main purpose of developing an e-business standards' ontology is to create a foundation for an automated mapping system that would be able to convert concepts from various standards in an independent fashion. The practical applicability and verification of the presented mappings is tested on the mapping of Universal Business Language version 2.0 and Cross Industry Invoice version 2.0 to OWL.

  2. CiTO, the Citation Typing Ontology

    PubMed Central

    2010-01-01

    CiTO, the Citation Typing Ontology, is an ontology for describing the nature of reference citations in scientific research articles and other scholarly works, both to other such publications and also to Web information resources, and for publishing these descriptions on the Semantic Web. Citation are described in terms of the factual and rhetorical relationships between citing publication and cited publication, the in-text and global citation frequencies of each cited work, and the nature of the cited work itself, including its publication and peer review status. This paper describes CiTO and illustrates its usefulness both for the annotation of bibliographic reference lists and for the visualization of citation networks. The latest version of CiTO, which this paper describes, is CiTO Version 1.6, published on 19 March 2010. CiTO is written in the Web Ontology Language OWL, uses the namespace http://purl.org/net/cito/, and is available from http://purl.org/net/cito/. This site uses content negotiation to deliver to the user an OWLDoc Web version of the ontology if accessed via a Web browser, or the OWL ontology itself if accessed from an ontology management tool such as Protégé 4 (http://protege.stanford.edu/). Collaborative work is currently under way to harmonize CiTO with other ontologies describing bibliographies and the rhetorical structure of scientific discourse. PMID:20626926

  3. Ontology-Based Multiple Choice Question Generation

    PubMed Central

    Al-Yahya, Maha

    2014-01-01

    With recent advancements in Semantic Web technologies, a new trend in MCQ item generation has emerged through the use of ontologies. Ontologies are knowledge representation structures that formally describe entities in a domain and their relationships, thus enabling automated inference and reasoning. Ontology-based MCQ item generation is still in its infancy, but substantial research efforts are being made in the field. However, the applicability of these models for use in an educational setting has not been thoroughly evaluated. In this paper, we present an experimental evaluation of an ontology-based MCQ item generation system known as OntoQue. The evaluation was conducted using two different domain ontologies. The findings of this study show that ontology-based MCQ generation systems produce satisfactory MCQ items to a certain extent. However, the evaluation also revealed a number of shortcomings with current ontology-based MCQ item generation systems with regard to the educational significance of an automatically constructed MCQ item, the knowledge level it addresses, and its language structure. Furthermore, for the task to be successful in producing high-quality MCQ items for learning assessments, this study suggests a novel, holistic view that incorporates learning content, learning objectives, lexical knowledge, and scenarios into a single cohesive framework. PMID:24982937

  4. A case-control study of lung cancer at a foundry and two engine plants.

    PubMed

    Austin, H; Delzell, E; Lally, C; Rotimi, C; Oestenstad, K

    1997-04-01

    A nested case-control study of lung cancer was conducted among workers at an iron foundry and two engine manufacturing plants whose lung cancer mortality rates were slightly higher than expected. The study included 231 lung cancer cases and 408 controls for whom complete work histories were obtained. There was no association between usual plant of employment and lung cancer mortality. The odds ratio for persons employed for 20 or more years in the foundry compared with persons employed in the engine plants was 0.90 (95% confidence interval: 0.55, 1.5). Long-term employment as an engine plant worker was associated with odds ratios slightly, but not statistically significantly, below unity. In the foundry, only usual employment in the material handling departmental group and any employment in the quality control departmental group were statistically significantly directly related to lung cancer risk. However, the number of subjects so employed was small and there was no dose-response relation between length of employment in these departmental groups and lung cancer risk. Cases were less frequently employed than were controls in engine plant machining and assembly jobs and departments. It is concluded that employment in this facility was either unrelated, or only weakly related, to lung cancer risk.

  5. Occupational exposure to volatile nitrosamines in foundries using the Ashland core-making process

    SciTech Connect

    Ducos, P.; Gaudin, R.; Maire, C.; Mavelle, T.; Bouchikhi, B.; Derby, G.

    1988-10-01

    Eight foundries using the Ashland process for the production of cores were surveyed to assess the occupational exposure to carcinogenic volatile nitrosamines. Personal and area samples were collected by means of artifact-free cartridges during the core-making and the molding/casting/shake-out operations. Analyses were carried out with gas chromatography/Hall detector and gas chromatography/TEA (thermal energy analyzer) for validation. The core-making workshops had the highest concentration for at least two nitrosamines, N-nitrosodimethylamine (NDMA) and N-nitrosoethylmethylamine (NEMA), but the levels of NDMA never exceeded 0.35 microgram/m3 with an arithmetic mean between 0.23 and 0.02 microgram/m3. In a number of samplings, two other peaks, both on TEA and Hall detector, could not be identified. The foundries per se (molding/casting/shake-out) had lower nitrosamine levels (CNDMAmax = 0.15 microgram/m3, CNDMA less than 0.03 microgram/m3). For the first time NEMA was identified as an industrial contaminant in foundries but its concentration was always lower than that of NDMA. The nitrosamines found were presumably produced from dimethylethylamine (DMEA). Industries producing or using tertiary or secondary amines should be controlled for their possible nitrosamine contamination.

  6. The plant ontology as a tool for comparative plant anatomy and genomic analyses.

    PubMed

    Cooper, Laurel; Walls, Ramona L; Elser, Justin; Gandolfo, Maria A; Stevenson, Dennis W; Smith, Barry; Preece, Justin; Athreya, Balaji; Mungall, Christopher J; Rensing, Stefan; Hiss, Manuel; Lang, Daniel; Reski, Ralf; Berardini, Tanya Z; Li, Donghui; Huala, Eva; Schaeffer, Mary; Menda, Naama; Arnaud, Elizabeth; Shrestha, Rosemary; Yamazaki, Yukiko; Jaiswal, Pankaj

    2013-02-01

    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary ('ontology') of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs.

  7. Evolutionary Characters, Phenotypes and Ontologies: Curating Data from the Systematic Biology Literature

    PubMed Central

    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.

    2010-01-01

    Background 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. Methodology/Principal Findings 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. Conclusions/Significance 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

  8. Hierarchical Analysis of the Omega Ontology

    SciTech Connect

    Joslyn, Cliff A.; Paulson, Patrick R.

    2009-12-01

    Initial delivery for mathematical analysis of the Omega Ontology. We provide an analysis of the hierarchical structure of a version of the Omega Ontology currently in use within the US Government. After providing an initial statistical analysis of the distribution of all link types in the ontology, we then provide a detailed order theoretical analysis of each of the four main hierarchical links present. This order theoretical analysis includes the distribution of components and their properties, their parent/child and multiple inheritance structure, and the distribution of their vertical ranks.

  9. Ontological Stratification in an Ecology of Infohabitants

    NASA Astrophysics Data System (ADS)

    Abramov, V. A.; Goossenaerts, J. B. M.; de Wilde, P.; Correia, L.

    This paper reports progress from the EEII research project where ontological stratification is applied in the study of openness. We explain a stratification approach to reduce the overall complexity of conceptual models, and to enhance their modularity. A distinction is made between ontological and epistemological stratification. The application of the stratification approach to agent system design is explained and illustrated. A preliminary characterization of the relevant strata is given. The wider relevance of this result for information infrastructure design is addressed: ontological stratification will be key to the model management and semantic interoperability in a ubiquitous and model driven information infrastructure.

  10. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment

    PubMed Central

    Bertone, Matthew A.; Mikó, István; Yoder, Matthew J.; Seltmann, Katja C.; Balhoff, James P.; Deans, Andrew R.

    2013-01-01

    Matching is an important step for increasing interoperability between heterogeneous ontologies. Here, we present alignments we produced as domain experts, using a manual mapping process, between the Hymenoptera Anatomy Ontology and other existing arthropod anatomy ontologies (representing spiders, ticks, mosquitoes and Drosophila melanogaster). The resulting alignments contain from 43 to 368 mappings (correspondences), all derived from domain-expert input. Despite the many pairwise correspondences, only 11 correspondences were found in common between all ontologies, suggesting either major intrinsic differences between each ontology or gaps in representing each group’s anatomy. Furthermore, we compare our findings with putative correspondences from Bioportal (derived from LOOM software) and summarize the results in a total evidence alignment. We briefly discuss characteristics of the ontologies and issues with the matching process. Database URL: http://purl.obolibrary.org/obo/hao/2012-07-18/arthropod-mappings.obo PMID:23303300

  11. Matching arthropod anatomy ontologies to the Hymenoptera Anatomy Ontology: results from a manual alignment.

    PubMed

    Bertone, Matthew A; Mikó, István; Yoder, Matthew J; Seltmann, Katja C; Balhoff, James P; Deans, Andrew R

    2013-01-01

    Matching is an important step for increasing interoperability between heterogeneous ontologies. Here, we present alignments we produced as domain experts, using a manual mapping process, between the Hymenoptera Anatomy Ontology and other existing arthropod anatomy ontologies (representing spiders, ticks, mosquitoes and Drosophila melanogaster). The resulting alignments contain from 43 to 368 mappings (correspondences), all derived from domain-expert input. Despite the many pairwise correspondences, only 11 correspondences were found in common between all ontologies, suggesting either major intrinsic differences between each ontology or gaps in representing each group's anatomy. Furthermore, we compare our findings with putative correspondences from Bioportal (derived from LOOM software) and summarize the results in a total evidence alignment. We briefly discuss characteristics of the ontologies and issues with the matching process.

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

    PubMed Central

    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. Objectives: 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. Methods: 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. Results: 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. Conclusion: The use of an ontology can overcome issues of semantic and syntactic heterogeneity to facilitate record linkage. PMID:26392849

  13. eNanoMapper: harnessing ontologies to enable data integration for nanomaterial risk assessment.

    PubMed

    Hastings, Janna; Jeliazkova, Nina; Owen, Gareth; Tsiliki, Georgia; Munteanu, Cristian R; Steinbeck, Christoph; Willighagen, Egon

    2015-01-01

    Engineered nanomaterials (ENMs) are being developed to meet specific application needs in diverse domains across the engineering and biomedical sciences (e.g. drug delivery). However, accompanying the exciting proliferation of novel nanomaterials is a challenging race to understand and predict their possibly detrimental effects on human health and the environment. The eNanoMapper project (www.enanomapper.net) is creating a pan-European computational infrastructure for toxicological data management for ENMs, based on semantic web standards and ontologies. Here, we describe the development of the eNanoMapper ontology based on adopting and extending existing ontologies of relevance for the nanosafety domain. The resulting eNanoMapper ontology is available at http://purl.enanomapper.net/onto/enanomapper.owl. We aim to make the re-use of external ontology content seamless and thus we have developed a library to automate the extraction of subsets of ontology content and the assembly of the subsets into an integrated whole. The library is available (open source) at http://github.com/enanomapper/slimmer/. Finally, we give a comprehensive survey of the domain content and identify gap areas. ENM safety is at the boundary between engineering and the life sciences, and at the boundary between molecular granularity and bulk granularity. This creates challenges for the definition of key entities in the domain, which we also discuss.

  14. Building a Cell and Anatomy Ontology of Caenorhabditis Elegans

    PubMed Central

    Sternberg, Paul W.

    2003-01-01

    We are endowed with a rich knowledge about Caenorhabditis elegans. Its stereotyped anatomy and development has stimulated research and resulted in the accumulation of cell-based information concerning gene expression, and the role of specific cells in developmental signalling and behavioural circuits. To make the information more accessible to sophisticated queries and automated retrieval systems, WormBase has begun to construct a C. elegans cell and anatomy ontology. Here we present our strategies and progress. PMID:18629098

  15. The chemical information ontology: provenance and disambiguation for chemical data on the biological semantic web.

    PubMed

    Hastings, Janna; Chepelev, Leonid; Willighagen, Egon; Adams, Nico; Steinbeck, Christoph; Dumontier, Michel

    2011-01-01

    Cheminformatics is the application of informatics techniques to solve chemical problems in silico. There are many areas in biology where cheminformatics plays an important role in computational research, including metabolism, proteomics, and systems biology. One critical aspect in the application of cheminformatics in these fields is the accurate exchange of data, which is increasingly accomplished through the use of ontologies. Ontologies are formal representations of objects and their properties using a logic-based ontology language. Many such ontologies are currently being developed to represent objects across all the domains of science. Ontologies enable the definition, classification, and support for querying objects in a particular domain, enabling intelligent computer applications to be built which support the work of scientists both within the domain of interest and across interrelated neighbouring domains. Modern chemical research relies on computational techniques to filter and organise data to maximise research productivity. The objects which are manipulated in these algorithms and procedures, as well as the algorithms and procedures themselves, enjoy a kind of virtual life within computers. We will call these information entities. Here, we describe our work in developing an ontology of chemical information entities, with a primary focus on data-driven research and the integration of calculated properties (descriptors) of chemical entities within a semantic web context. Our ontology distinguishes algorithmic, or procedural information from declarative, or factual information, and renders of particular importance the annotation of provenance to calculated data. The Chemical Information Ontology is being developed as an open collaborative project. More details, together with a downloadable OWL file, are available at http://code.google.com/p/semanticchemistry/ (license: CC-BY-SA).

  16. A study on non-metallic inclusions in foundry steel process

    NASA Astrophysics Data System (ADS)

    Harris, Marc Leonard

    The effects of sample area and automated SEM/EDS feature analysis parameters (step size, magnification and threshold) on nonmetallic inclusion characterization results has been investigated and optimized. A post-processing program was developed to automatically determine average inclusion chemistry, total element concentrations within inclusions, and for generating joint ternary diagrams with size visualization for representing nonmetallic inclusion populations. Using these tools the evolution of nonmetallic inclusions was examined for 4320 steel at a participating industrial steel foundry. The steel was sampled throughout electric arc furnace melting through ladle refining to the final casting where an in-mold sampling procedure was developed to procure numerous test samples representative of final heavy section castings in effort to further understand the effect of different metallurgical factors on impact toughness for slow solidification rate high strength cast steel. Nonmetallic inclusion nucleation, growth, and flotation were monitored through liquid steel processing by size-classified area fraction. The use of zirconium as an addition for nitrogen/oxygen removal was found to lead to a large number of ZrO2 inclusions, which resulted in insufficient flotation due to the higher density of zirconia and, less effective calcium treatment. No ZrN formation was observed owing to the high FeO acid slag practice used. Argon stirring was found to mitigate the flotation problems associated with the zirconium addition and significantly contribute to the removal of large size (>5microm) inclusions. In-mold heavy section samples were tested at -40°C and 25°C to examine how different microstructural features such as nonmetallic inclusions, porosity, and hardness influence the impact energy of the steel for brittle and ductile fracture modes. SEM fractography was used to characterize failures modes: brittle, ductile, and quasi-ductile at energies ranging from 14-40 ft

  17. 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.

  18. A Data Quality Ontology for the Secondary Use of EHR Data

    PubMed Central

    Johnson, Steven G.; Speedie, Stuart; Simon, Gyorgy; Kumar, Vipin; Westra, Bonnie L.

    2015-01-01

    The secondary use of EHR data for research is expected to improve health outcomes for patients, but the benefits will only be realized if the data in the EHR is of sufficient quality to support these uses. A data quality (DQ) ontology was developed to rigorously define concepts and enable automated computation of data quality measures. The healthcare data quality literature was mined for the important terms used to describe data quality concepts and harmonized into an ontology. Four high-level data quality dimensions (“correctness”, “consistency”, “completeness” and “currency”) categorize 19 lower level measures. The ontology serves as an unambiguous vocabulary, which defines concepts more precisely than natural language; it provides a mechanism to automatically compute data quality measures; and is reusable across domains and use cases. A detailed example is presented to demonstrate its utility. The DQ ontology can make data validation more common and reproducible. PMID:26958293

  19. A Data Quality Ontology for the Secondary Use of EHR Data.

    PubMed

    Johnson, Steven G; Speedie, Stuart; Simon, Gyorgy; Kumar, Vipin; Westra, Bonnie L

    2015-01-01

    The secondary use of EHR data for research is expected to improve health outcomes for patients, but the benefits will only be realized if the data in the EHR is of sufficient quality to support these uses. A data quality (DQ) ontology was developed to rigorously define concepts and enable automated computation of data quality measures. The healthcare data quality literature was mined for the important terms used to describe data quality concepts and harmonized into an ontology. Four high-level data quality dimensions ("correctness", "consistency", "completeness" and "currency") categorize 19 lower level measures. The ontology serves as an unambiguous vocabulary, which defines concepts more precisely than natural language; it provides a mechanism to automatically compute data quality measures; and is reusable across domains and use cases. A detailed example is presented to demonstrate its utility. The DQ ontology can make data validation more common and reproducible.

  20. Sustainability innovation foundry %3CU%2B2013%3E FY13 : merging research and operations.

    SciTech Connect

    Mizner, Jack Harry,; Passell, Howard David; Keller, Elizabeth James Kistin; Gordon, Margaret Ellen; McNeish, Jerry A.; Sullivan, Kristina

    2013-12-01

    Sustainability is a critical national security issue for the U.S. and other nations. Sandia National Laboratories (SNL) is already a global leader in sustainability science and technology (SS&T) as documented in this report. This report documents the ongoing work conducted this year as part of the Sustainability Innovation Foundry (SIF). The efforts of the SIF support Sandia's national and international security missions related to sustainability and resilience revolving around energy use, water use, and materials, both on site at Sandia and externally. The SIF leverages existing Sandia research and development (R&D) in sustainability science and technology to support new solutions to complex problems. The SIF also builds on existing Sandia initiatives to support transformation of Sandia into a fully sustainable entity in terms of materials, energy, and water use. In the long term, the SIF will demonstrate the efficacy of sustainability technology developed at Sandia through prototyping and test bed approaches and will provide a common platform for support of solutions to the complex problems surrounding sustainability. Highlights from this year include the Sustainability Idea Challenge, improvements in facilities energy use, lectures and presentations from relevant experts in sustainability [Dr. Barry Hughes, University of Denver], and significant development of the Institutional Transformation (IX) modeling tools to support evaluation of proposed modifications to the SNL infrastructure to realize energy savings.

  1. Behavior change interventions: the potential of ontologies for advancing science and practice.

    PubMed

    Larsen, Kai R; Michie, Susan; Hekler, Eric B; Gibson, Bryan; Spruijt-Metz, Donna; Ahern, David; Cole-Lewis, Heather; Ellis, Rebecca J Bartlett; Hesse, Bradford; Moser, Richard P; Yi, Jean

    2017-02-01

    A central goal of behavioral medicine is the creation of evidence-based interventions for promoting behavior change. Scientific knowledge about behavior change could be more effectively accumulated using "ontologies." In information science, an ontology is a systematic method for articulating a "controlled vocabulary" of agreed-upon terms and their inter-relationships. It involves three core elements: (1) a controlled vocabulary specifying and defining existing classes; (2) specification of the inter-relationships between classes; and (3) codification in a computer-readable format to enable knowledge generation, organization, reuse, integration, and analysis. This paper introduces ontologies, provides a review of current efforts to create ontologies related to behavior change interventions and suggests future work. This paper was written by behavioral medicine and information science experts and was developed in partnership between the Society of Behavioral Medicine's Technology Special Interest Group (SIG) and the Theories and Techniques of Behavior Change Interventions SIG. In recent years significant progress has been made in the foundational work needed to develop ontologies of behavior change. Ontologies of behavior change could facilitate a transformation of behavioral science from a field in which data from different experiments are siloed into one in which data across experiments could be compared and/or integrated. This could facilitate new approaches to hypothesis generation and knowledge discovery in behavioral science.

  2. Reuse of terminological resources for efficient ontological engineering in Life Sciences.

    PubMed

    Jimeno-Yepes, Antonio; Jiménez-Ruiz, Ernesto; Berlanga-Llavori, Rafael; Rebholz-Schuhmann, Dietrich

    2009-10-01

    This paper is intended to explore how to use terminological resources for ontology engineering. Nowadays there are several biomedical ontologies describing overlapping domains, but there is not a clear correspondence between the concepts that are supposed to be equivalent or just similar. These resources are quite precious but their integration and further development are expensive. Terminologies may support the ontological development in several stages of the lifecycle of the ontology; e.g. ontology integration. In this paper we investigate the use of terminological resources during the ontology lifecycle. We claim that the proper creation and use of a shared thesaurus is a cornerstone for the successful application of the Semantic Web technology within life sciences. Moreover, we have applied our approach to a real scenario, the Health-e-Child (HeC) project, and we have evaluated the impact of filtering and re-organizing several resources. As a result, we have created a reference thesaurus for this project, named HeCTh.

  3. A framework for using reference ontologies as a foundation for the semantic web.

    PubMed

    Brinkley, James F; Suciu, Dan; Detwiler, Landon T; Gennari, John H; Rosse, Cornelius

    2006-01-01

    The semantic web is envisioned as an evolving set of local ontologies that are gradually linked together into a global knowledge network. Many such local "application" ontologies are being built, but it is difficult to link them together because of incompatibilities and lack of adherence to ontology standards. "Reference" ontologies are an emerging ontology type that attempt to represent deep knowledge of basic science in a principled way that allows them to be re-used in multiple ways, just as the basic sciences are re-used in clinical applications. As such they have the potential to be a foundation for the semantic web if methods can be developed for deriving application ontologies from them. We describe a computational framework for this purpose that is generalized from the database concept of "views", and describe the research issues that must be solved to implement such a framework. We argue that the development of such a framework is becoming increasingly feasible due to a convergence of advances in several fields.

  4. Reuse of terminological resources for efficient ontological engineering in Life Sciences

    PubMed Central

    Jimeno-Yepes, Antonio; Jiménez-Ruiz, Ernesto; Berlanga-Llavori, Rafael; Rebholz-Schuhmann, Dietrich

    2009-01-01

    This paper is intended to explore how to use terminological resources for ontology engineering. Nowadays there are several biomedical ontologies describing overlapping domains, but there is not a clear correspondence between the concepts that are supposed to be equivalent or just similar. These resources are quite precious but their integration and further development are expensive. Terminologies may support the ontological development in several stages of the lifecycle of the ontology; e.g. ontology integration. In this paper we investigate the use of terminological resources during the ontology lifecycle. We claim that the proper creation and use of a shared thesaurus is a cornerstone for the successful application of the Semantic Web technology within life sciences. Moreover, we have applied our approach to a real scenario, the Health-e-Child (HeC) project, and we have evaluated the impact of filtering and re-organizing several resources. As a result, we have created a reference thesaurus for this project, named HeCTh. PMID:19796401

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

    SciTech Connect

    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. Lastly, 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.

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

    DOE PAGES

    Dietze, Heiko; Berardini, Tanya Z.; Foulger, Rebecca E.; ...

    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 newmore » 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. Lastly, 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.« less

  7. An Ontology for Uncertainty in Climate Change Projections

    NASA Astrophysics Data System (ADS)

    King, A. W.

    2011-12-01

    Paraphrasing Albert Einstein's aphorism about scientific quantification: not all uncertainty that counts can be counted, and not all uncertainty that can be counted counts. The meaning of the term "uncertainty" in climate change science and assessment is itself uncertain. Different disciplines and perspectives bring different nuances if not meanings of the term to the conversation. For many scientists, uncertainty is somehow associated with statistical dispersion and standard error. For many users of climate change information, uncertainty is more related to their confidence, or lack thereof, in climate models. These "uncertainties" may be related, but they are not identical, and there is considerable room for confusion and misunderstanding. A knowledge framework, a system of concepts and vocabulary, for communicating uncertainty can add structure to the characterization and quantification of uncertainty and aid communication among scientists and users. I have developed an ontology for uncertainty in climate change projections derived largely from the report of the W3C Uncertainty Reasoning for the World Wide Web Incubator Group (URW3-XG) dealing with the problem of uncertainty representation and reasoning on the World Wide Web. I have adapted this ontology for uncertainty about information to uncertainty about climate change. Elements of the ontology apply with little or no translation to the information of climate change projections, with climate change almost a use case. Other elements can be translated into language used in climate-change discussions; translating aleatory uncertainty in the UncertaintyNature class as irreducible uncertainty is an example. I have added classes for source of uncertainty (UncertaintySource) (different model physics, for example) and metrics of uncertainty (UncertaintyMetric), at least, in the case of the latter, for those instances of uncertainty that can be quantified (i.e., counted). The statistical standard deviation isa member

  8. Federated ontology-based queries over cancer data

    PubMed Central

    2012-01-01

    interface has been developed, supporting ontology-based queries over caGrid data sources. An extensive evaluation of the query reformulation technique is included. Conclusions To support personalised medicine in oncology, it is crucial to retrieve and integrate molecular, pathology, radiology and clinical data in an efficient manner. The semantic heterogeneity of the data makes this a challenging task. Ontologies provide a formal framework to support querying and integration. This paper provides an ontology-based solution for querying distributed databases over service-oriented, model-driven infrastructures. PMID:22373043

  9. XOA: Web-Enabled Cross-Ontological Analytics

    SciTech Connect

    Riensche, Roderick M.; Baddeley, Bob; Sanfilippo, Antonio P.; Posse, Christian; Gopalan, Banu

    2007-07-09

    The paper being submitted (as an "extended abstract" prior to conference acceptance) provides a technical description of our proof-of-concept prototype for the XOA method. Abstract: To address meaningful questions, scientists need to relate information across diverse classification schemes such as ontologies, terminologies and thesauri. These resources typically address a single knowledge domain at a time and are not cross-indexed. Information that is germane to the same object may therefore remain unlinked with consequent loss of knowledge discovery across disciplines and even sub-domains of the same discipline. We propose to address these problems by fostering semantic interoperability through the development of ontology alignment web services capable of enabling cross-scale knowledge discovery, and demonstrate a specific application of such an approach to the biomedical domain.

  10. Expansion of the Gene Ontology knowledgebase and resources

    PubMed Central

    2017-01-01

    The Gene Ontology (GO) is a comprehensive resource of computable knowledge regarding the functions of genes and gene products. As such, it is extensively used by the biomedical research community for the analysis of -omics and related data. Our continued focus is on improving the quality and utility of the GO resources, and we welcome and encourage input from researchers in all areas of biology. In this update, we summarize the current contents of the GO knowledgebase, and present several new features and improvements that have been made to the ontology, the annotations and the tools. Among the highlights are 1) developments that facilitate access to, and application of, the GO knowledgebase, and 2) extensions to the resource as well as increasing support for descriptions of causal models of biological systems and network biology. To learn more, visit http://geneontology.org/. PMID:27899567

  11. China’s National Health Policies: An Ontological Analysis

    PubMed Central

    Dai, Guobin; Deng, Fang; Ramaprasad, Arkalgud; Syn, Thant

    2016-01-01

    The health care system in China is facing a multitude of challenges owing to the changing demographics of the country, the evolving economics of health care, and the emerging epidemiology of health as well as diseases. China’s many national health care policies are documented in Chinese text documents. It is necessary to map the policies synoptically, systemically, and systematically to discover their emphases and biases, assess them, and modify them in the future. Using a logically constructed ontology of health care policies based on the common bodies of knowledge as a lens, we map the current policies to reveal their ‘bright’, ‘light’, and ‘blind/blank’ spots. The ontological map will help (a) develop a roadmap for future health care policies in China, and (b) compare and contrast China’s health care policies with other countries’. PMID:28210417

  12. Property enhancement by grain refinement of zinc-aluminium foundry alloys

    NASA Astrophysics Data System (ADS)

    Krajewski, W. K.; Greer, A. L.; Piwowarski, G.; Krajewski, P. K.

    2016-03-01

    Development of cast alloys with good mechanical properties and involving less energy consumption during their melting is one of the key demands of today's industry. Zinc foundry alloys of high and medium Al content, i.e. Zn-(15-30) wt.% Al and Zn-(8-12) wt.% Al, can satisfy these requirements. The present paper summarizes the work [1-9] on improving properties of sand-cast ZnAl10 (Zn-10 wt.% Al) and ZnAl25 (Zn-25 wt. % Al) alloys by melt inoculation. Special attention was devoted to improving ductility, whilst preserving high damping properties at the same time. The composition and structural modification of medium- and high-aluminium zinc alloys influence their strength, tribological properties and structural stability. In a series of studies, Zn - (10-12) wt. % Al and Zn - (25-26) wt.% Al - (1-2.5) wt.% Cu alloys have been doped with different levels of added Ti. The melted alloys were inoculated with ZnTi-based refiners and it was observed that the dendritic structure is significantly finer already after addition of 50 - 100 ppm Ti to the melted alloys. The alloy's structure and mechanical properties have been studied using: SEM (scanning electron microscopy), LM (light microscopy), dilatometry, pin-on-disc wear, and tensile strength measurements. Grain refinement leads to significant improvement of ductility in the binary high-aluminium Zn-(25-27) Al alloys while in the medium-aluminium alloys the effect is rather weak. In the ternary alloys Zn-26Al-Cu, replacing a part of Cu with Ti allows dimensional changes to be reduced while preserving good tribological properties. Furthermore, the high initial damping properties were nearly entirely preserved after inoculation. The results obtained allow us to characterize grain refinement of the examined high-aluminium zinc alloys as a promising process leading to the improvement of their properties. At the same time, using low melting ZnTi-based master alloys makes it possible to avoid the excessive melt overheating

  13. Using Multiple Ontologies to Integrate Complex Biological Data

    PubMed Central

    Petri, Victoria; Pasko, Dean; Bromberg, Susan; Wu, Wenhua; Chen, Jiali; Nenasheva, Nataliya; Kwitek, Anne; Twigger, Simon; Jacob, Howard

    2005-01-01

    The strength of the rat as a model organism lies in its utility in pharmacology, biochemistry and physiology research. Data resulting from such studies is difficult to represent in databases and the creation of user-friendly data mining tools has proved difficult. The Rat Genome Database has developed a comprehensive ontology-based data structure and annotation system to integrate physiological data along with environmental and experimental factors, as well as genetic and genomic information. RGD uses multiple ontologies to integrate complex biological information from the molecular level to the whole organism, and to develop data mining and presentation tools. This approach allows RGD to indicate not only the phenotypes seen in a strain but also the specific values under each diet and atmospheric condition, as well as gender differences. Harnessing the power of ontologies in this way allows the user to gather and filter data in a customized fashion, so that a researcher can retrieve all phenotype readings for which a high hypoxia is a factor. Utilizing the same data structure for expression data, pathways and biological processes, RGD will provide a comprehensive research platform which allows users to investigate the conditions under which biological processes are altered and to elucidate the mechanisms of disease. PMID:18629202

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

    PubMed Central

    Cui, Licong

    2015-01-01

    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

  15. 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

  16. Reasoning Based Quality Assurance of Medical Ontologies: A Case Study

    PubMed Central

    Horridge, Matthew; Parsia, Bijan; Noy, Natalya F.; Musenm, Mark A.

    2014-01-01

    The World Health Organisation is using OWL as a key technology to develop ICD-11 – the next version of the well-known International Classification of Diseases. Besides providing better opportunities for data integration and linkages to other well-known ontologies such as SNOMED-CT, one of the main promises of using OWL is that it will enable various forms of automated error checking. In this paper we investigate how automated OWL reasoning, along with a Justification Finding Service can be used as a Quality Assurance technique for the development of large and complex ontologies such as ICD-11. Using the International Classification of Traditional Medicine (ICTM) – Chapter 24 of ICD-11 – as a case study, and an expert panel of knowledge engineers, we reveal the kinds of problems that can occur, how they can be detected, and how they can be fixed. Specifically, we found that a logically inconsistent version of the ICTM ontology could be repaired using justifications (minimal entailing subsets of an ontology). Although over 600 justifications for the inconsistency were initially computed, we found that there were three main manageable patterns or categories of justifications involving TBox and ABox axioms. These categories represented meaningful domain errors to an expert panel of ICTM project knowledge engineers, who were able to use them to successfully determine the axioms that needed to be revised in order to fix the problem. All members of the expert panel agreed that the approach was useful for debugging and ensuring the quality of ICTM. PMID:25954373

  17. Speeding up ontology creation of scientific terms

    NASA Astrophysics Data System (ADS)

    Bermudez, L. E.; Graybeal, J.

    2005-12-01

    An ontology is a formal specification of a controlled vocabulary. Ontologies are composed of classes (similar to categories), individuals (members of classes) and properties (attributes of the individuals). Having vocabularies expressed in a formal specification like the Web Ontology Language (OWL) enables interoperability due to the comprehensiveness of OWL by software programs. Two main non-inclusive strategies exist when constructing an ontology: an up-down approach and a bottom-up approach. The former one is directed towards the creation of top classes first (main concepts) and then finding the required subclasses and individuals. The later approach starts from the individuals and then finds similar properties promoting the creation of classes. At the Marine Metadata Interoperability (MMI) Initiative we used a bottom-up approach to create ontologies from simple-vocabularies (those that are not expressed in a conceptual way). We found that the vocabularies were available in different formats (relational data bases, plain files, HTML, XML, PDF) and sometimes were composed of thousands of terms, making the ontology creation process a very time consuming activity. To expedite the conversion process we created a tool VOC2OWL that takes a vocabulary in a table like structure (CSV or TAB format) and a conversion-property file to create automatically an ontology. We identified two basic structures of simple-vocabularies: Flat vocabularies (e.g., phone directory) and hierarchical vocabularies (e.g., taxonomies). The property file defines a list of attributes for the conversion process for each structure type. The attributes included metadata information (title, description, subject, contributor, urlForMoreInformation) and conversion flags (treatAsHierarchy, generateAutoIds) and other conversion information needed to create the ontology (columnForPrimaryClass, columnsToCreateClassesFrom, fileIn, fileOut, namespace, format). We created more than 50 ontologies and

  18. Building a Human Health Risk Assessment Ontology (RsO): A Proposed Framework.

    PubMed

    McKone, Thomas E; Feng, Lydia

    2015-11-01

    Over the last decade the health and environmental research communities have made significant progress in collecting and improving access to genomic, toxicology, exposure, health, and disease data useful to health risk assessment. One of the barriers to applying these growing volumes of information in fields such as risk assessment is the lack of informatics tools to organize, curate, and evaluate thousands of journal publications and hundreds of databases to provide new insights on relationships among exposure, hazard, and disease burden. Many fields are developing ontologies as a way of organizing and analyzing large amounts of complex information from multiple scientific disciplines. Ontologies include a vocabulary of terms and concepts with defined logical relationships to each other. Building from the recently published exposure ontology and other relevant health and environmental ontologies, this article proposes an ontology for health risk assessment (RsO) that provides a structural framework for organizing risk assessment information and methods. The RsO is anchored by eight major concepts that were either identified by exploratory curations of the risk literature or the exposure-ontology working group as key for describing the risk assessment domain. These concepts are: (1) stressor, (2) receptor, (3) outcome, (4) exposure event, (5) dose-response approach, (6) dose-response metric, (7) uncertainty, and (8) measure of risk. We illustrate the utility of these concepts for the RsO with example curations of published risk assessments for ionizing radiation, arsenic in drinking water, and persistent pollutants in salmon.

  19. Ontology Mapping Neural Network: An Approach to Learning and Inferring Correspondences among Ontologies

    ERIC Educational Resources Information Center

    Peng, Yefei

    2010-01-01

    An ontology mapping neural network (OMNN) is proposed in order to learn and infer correspondences among ontologies. It extends the Identical Elements Neural Network (IENN)'s ability to represent and map complex relationships. The learning dynamics of simultaneous (interlaced) training of similar tasks interact at the shared connections of the…

  20. Ontology-based data integration between clinical and research systems.

    PubMed

    Mate, Sebastian; Köpcke, Felix; Toddenroth, Dennis; Martin, Marcus; Prokosch, Hans-Ulrich; Bürkle, Thomas; Ganslandt, Thomas

    2015-01-01

    Data from the electronic medical record comprise numerous structured but uncoded elements, which are not linked to standard terminologies. Reuse of such data for secondary research purposes has gained in importance recently. However, the identification of relevant data elements and the creation of database jobs for extraction, transformation and loading (ETL) are challenging: With current methods such as data warehousing, it is not feasible to efficiently maintain and reuse semantically complex data extraction and trans-formation routines. We present an ontology-supported approach to overcome this challenge by making use of abstraction: Instead of defining ETL procedures at the database level, we use ontologies to organize and describe the medical concepts of both the source system and the target system. Instead of using unique, specifically developed SQL statements or ETL jobs, we define declarative transformation rules within ontologies and illustrate how these constructs can then be used to automatically generate SQL code to perform the desired ETL procedures. This demonstrates how a suitable level of abstraction may not only aid the interpretation of clinical data, but can also foster the reutilization of methods for un-locking it.

  1. Design and evaluation of a bacterial clinical infectious diseases ontology.

    PubMed

    Gordon, Claire L; Pouch, Stephanie; Cowell, Lindsay G; Boland, Mary Regina; Platt, Heather L; Goldfain, Albert; Weng, Chunhua

    2013-01-01

    With antimicrobial resistance increasing worldwide, there is a great need to use automated antimicrobial decision support systems (ADSSs) to lower antimicrobial resistance rates by promoting appropriate antimicrobial use. However, they are infrequently used mostly because of their poor interoperability with different health information technologies. Ontologies can augment portable ADSSs by providing an explicit knowledge representation for biomedical entities and their relationships, helping to standardize and integrate heterogeneous data resources. We developed a bacterial clinical infectious diseases ontology (BCIDO) using Protégé-OWL. BCIDO defines a controlled terminology for clinical infectious diseases along with domain knowledge commonly used in hospital settings for clinical infectious disease treatment decision-making. BCIDO has 599 classes and 2355 object properties. Terms were imported from or mapped to Systematized Nomenclature of Medicine, Unified Medical Language System, RxNorm and National Center for Bitechnology Information Organismal Classification where possible. Domain expert evaluation using the "laddering" technique, ontology visualization, and clinical notes and scenarios, confirmed the correctness and potential usefulness of BCIDO.

  2. The biomedical ethics ontology proposal: excellent aims, questionable methods.

    PubMed

    Dubois, James M

    2009-03-01

    KOEPSELL ET AL. (2009) DESCRIBE AN IDEAL biomedical ethics committee environment with efficiencies such as electronic and universal application forms and consent templates, automated decision-trees, and broad sharing of data. However, it is unclear that a biomedical ethics ontology (BMEO) is necessary or even helpful in establishing such environment. Two features of any applied ontology are particularly problematic in establishing a useful BMEO: (1) an ontology is a description of a domain of reality; and (2) the description is subject to ongoing revision as it is developed through open processes, e.g., the use of a wiki. A BMEO would need to address two main kinds of entities, regulatory definitions and ethical concepts, and is ill-suited to both. Regulatory definitions are fiats and ought to be adopted verbatim to ensure compliance, but in such cases we do not need the assistance of ontologists, and their modes of working (constant revision within open wiki-based communities) might even be counterproductive. Ethical concepts within pluralistic societies are social constructs, not a priori concepts or biological natural kinds, and the prospects of generating intuitive definitions that enjoy broad acceptance across cultures and institutional settings are slim. In making these arguments, I draw from the writings of leading applied ontologists and Koepsell et al.'s own proof of concept.

  3. The ontology of quantum field theory: Structural realism vindicated?

    PubMed

    Glick, David

    2016-10-01

    In this paper I elicit a prediction from structural realism and compare it, not to a historical case, but to a contemporary scientific theory. If structural realism is correct, then we should expect physics to develop theories that fail to provide an ontology of the sort sought by traditional realists. If structure alone is responsible for instrumental success, we should expect surplus ontology to be eliminated. Quantum field theory (QFT) provides the framework for some of the best confirmed theories in science, but debates over its ontology are vexed. Rather than taking a stand on these matters, the structural realist can embrace QFT as an example of just the kind of theory SR should lead us to expect. Yet, it is not clear that QFT meets the structuralist's positive expectation by providing a structure for the world. In particular, the problem of unitarily inequivalent representations threatens to undermine the possibility of QFT providing a unique structure for the world. In response to this problem, I suggest that the structuralist should endorse pluralism about structure.

  4. Ontology-Based Data Integration between Clinical and Research Systems

    PubMed Central

    Mate, Sebastian; Köpcke, Felix; Toddenroth, Dennis; Martin, Marcus; Prokosch, Hans-Ulrich

    2015-01-01

    Data from the electronic medical record comprise numerous structured but uncoded ele-ments, which are not linked to standard terminologies. Reuse of such data for secondary research purposes has gained in importance recently. However, the identification of rele-vant data elements and the creation of database jobs for extraction, transformation and loading (ETL) are challenging: With current methods such as data warehousing, it is not feasible to efficiently maintain and reuse semantically complex data extraction and trans-formation routines. We present an ontology-supported approach to overcome this challenge by making use of abstraction: Instead of defining ETL procedures at the database level, we use ontologies to organize and describe the medical concepts of both the source system and the target system. Instead of using unique, specifically developed SQL statements or ETL jobs, we define declarative transformation rules within ontologies and illustrate how these constructs can then be used to automatically generate SQL code to perform the desired ETL procedures. This demonstrates how a suitable level of abstraction may not only aid the interpretation of clinical data, but can also foster the reutilization of methods for un-locking it. PMID:25588043

  5. Ontology-Based Prediction and Prioritization of Gene Functional Annotations.

    PubMed

    Chicco, Davide; Masseroli, Marco

    2016-01-01

    Genes and their protein products are essential molecular units of a living organism. The knowledge of their functions is key for the understanding of physiological and pathological biological processes, as well as in the development of new drugs and therapies. The association of a gene or protein with its functions, described by controlled terms of biomolecular terminologies or ontologies, is named gene functional annotation. Very many and valuable gene annotations expressed through terminologies and ontologies are available. Nevertheless, they might include some erroneous information, since only a subset of annotations are reviewed by curators. Furthermore, they are incomplete by definition, given the rapidly evolving pace of biomolecular knowledge. In this scenario, computational methods that are able to quicken the annotation curation process and reliably suggest new annotations are very important. Here, we first propose a computational pipeline that uses different semantic and machine learning methods to predict novel ontology-based gene functional annotations; then, we introduce a new semantic prioritization rule to categorize the predicted annotations by their likelihood of being correct. Our tests and validations proved the effectiveness of our pipeline and prioritization of predicted annotations, by selecting as most likely manifold predicted annotations that were later confirmed.

  6. 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

  7. 100% foundry compatible packaging and full wafer release and die separation technique for surface micromachined devices

    SciTech Connect

    OLIVER,ANDREW D.; MATZKE,CAROLYN M.

    2000-04-06

    A completely foundry compatible chip-scale package for surface micromachines has been successfully demonstrated. A pyrex (Corning 7740) glass cover is placed over the released surface micromachined die and anodically bonded to a planarized polysilicon bonding ring. Electrical feedthroughs for the surface micromachine pass underneath the polysilicon sealing ring. The package has been found to be hermetic with a leak rate of less than 5 x 10{sup {minus}8} atm cm{sup {minus}3}/s. This technology has applications in the areas of hermetic encapsulation and wafer level release and die separation.

  8. Utilizing Descriptive Statements from the Biodiversity Heritage Library to Expand the Hymenoptera Anatomy Ontology

    PubMed Central

    Seltmann, Katja C.; Pénzes, Zsolt; Yoder, Matthew J.; Bertone, Matthew A.; Deans, Andrew R.

    2013-01-01

    Hymenoptera, the insect order that includes sawflies, bees, wasps, and ants, exhibits an incredible diversity of phenotypes, with over 145,000 species described in a corpus of textual knowledge since Carolus Linnaeus. In the absence of specialized training, often spanning decades, however, these articles can be challenging to decipher. Much of the vocabulary is domain-specific (e.g., Hymenoptera biology), historically without a comprehensive glossary, and contains much homonymous and synonymous terminology. The Hymenoptera Anatomy Ontology was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy, as well as provide support for domain experts so they may actively benefit from the anatomy ontology development. As part of HAO development, an active learning, dictionary-based, natural language recognition tool was implemented to facilitate Hymenoptera anatomy term discovery in literature. We present this tool, referred to as the ‘Proofer’, as part of an iterative approach to growing phenotype-relevant ontologies, regardless of domain. The process of ontology development results in a critical mass of terms that is applied as a filter to the source collection of articles in order to reveal term occurrence and biases in natural language species descriptions. Our results indicate that taxonomists use domain-specific terminology that follows taxonomic specialization, particularly at superfamily and family level groupings and that the developed Proofer tool is effective for term discovery, facilitating ontology construction. PMID:23441153

  9. Utilizing descriptive statements from the biodiversity heritage library to expand the Hymenoptera Anatomy Ontology.

    PubMed

    Seltmann, Katja C; Pénzes, Zsolt; Yoder, Matthew J; Bertone, Matthew A; Deans, Andrew R

    2013-01-01

    Hymenoptera, the insect order that includes sawflies, bees, wasps, and ants, exhibits an incredible diversity of phenotypes, with over 145,000 species described in a corpus of textual knowledge since Carolus Linnaeus. In the absence of specialized training, often spanning decades, however, these articles can be challenging to decipher. Much of the vocabulary is domain-specific (e.g., Hymenoptera biology), historically without a comprehensive glossary, and contains much homonymous and synonymous terminology. The Hymenoptera Anatomy Ontology was developed to surmount this challenge and to aid future communication related to hymenopteran anatomy, as well as provide support for domain experts so they may actively benefit from the anatomy ontology development. As part of HAO development, an active learning, dictionary-based, natural language recognition tool was implemented to facilitate Hymenoptera anatomy term discovery in literature. We present this tool, referred to as the 'Proofer', as part of an iterative approach to growing phenotype-relevant ontologies, regardless of domain. The process of ontology development results in a critical mass of terms that is applied as a filter to the source collection of articles in order to reveal term occurrence and biases in natural language species descriptions. Our results indicate that taxonomists use domain-specific terminology that follows taxonomic specialization, particularly at superfamily and family level groupings and that the developed Proofer tool is effective for term discovery, facilitating ontology construction.

  10. Emmanuel Levinas and the ontology of eating.

    PubMed

    Goldstein, David

    2010-01-01

    This essay examines the existential philosophy of Emmanuel Levinas in relation to issues of food and eating. I argue that for Levinas, the act of eating is central to founding the ethical self, and that any understanding of Levinas's approach to embodiment must begin with what it means for us to ingest the outside world. Even in Levinas's earliest work, food is already a freighted ontological category. As his ideas mature, eating is transformed from the grounding for an ethical system to the system itself. The act of giving bread to another person takes its place as the ethical gesture par excellence. The story is not that we eat. The story is that we eat and develop a relationship to eating, and that relationship in turn helps determine our sense of ourselves in the world. Eating is the ethical event. The essay ends by asking how Levinas can help us answer the question, what would it mean to imagine every bite I take, or give to another, as a direct engagement with my own and my neighbor's existence?

  11. Ontology of Space Physics for e-Science Applications Based on ISO 19156

    NASA Astrophysics Data System (ADS)

    Galkin, I. A.; Fung, S. F.; Benson, R. F.; Heynderickx, D.; Charisi, A.; Lowe, D.; Ventouras, S.; Ritschel, B.; Hapgood, M. A.; Belehaki, A.; Roberts, D. A.; King, T. A.; Narock, T.

    2014-12-01

    A structural, ontological presentation of the discipline domain concepts and their relationships is a powerful e-science tool: it enables data search and discovery by content of the observations. Even a simple classification of the concepts using the parent-child hierarchies enables analyses by association, thus bringing a greater insight in the data. Ontology specifications have been put to many uses in space physics, primarily to harmonize data analysis across multiple data resources and thus facilitate interoperability. Among the multitude of ontology writeups, the SPASE data model stands out as a prominent, highly detailed collection of keywords for heliophysics. We will present an ontology design that draws its strengths from SPASE and further enhances it with a greater structural organization of the keyword vocabularies, in particular related to wave phenomena, as well as describes a variety of events and activities in the Sun-Earth system beyond the quiet-time behaviour. The new ontology is being developed for the Near Earth Space Data Infrastructure for e-Science (ESPAS) project funded by the 7th European Framework, whose data model is based on a suite of ISO 19156 standards for Observations and Measurements (O&M). The O&M structure and language have driven the ESPAS ontology organization, with the Observed Property vocabulary as its cornerstone. The ontology development has progressed beyond the O&M framework to include domain-specific components required to describe the space physics concepts in a dictionary-controlled, unambiguous manner. Not surprisingly, wave phenomena and events presented the greatest challenge to the ESPAS ontology team as they demanded characterization of processes involved in the wave generation, propagation, modification, and reception, as well as the propagation medium itself. One of the notable outcomes of this effort is the ability of the new ontology schema to accommodate and categorize, for example, the URSI standard

  12. The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses

    PubMed Central

    Cooper, Laurel; Walls, Ramona L.; Elser, Justin; Gandolfo, Maria A.; Stevenson, Dennis W.; Smith, Barry; Preece, Justin; Athreya, Balaji; Mungall, Christopher J.; Rensing, Stefan; Hiss, Manuel; Lang, Daniel; Reski, Ralf; Berardini, Tanya Z.; Li, Donghui; Huala, Eva; Schaeffer, Mary; Menda, Naama; Arnaud, Elizabeth; Shrestha, Rosemary; Yamazaki, Yukiko; Jaiswal, Pankaj

    2013-01-01

    The Plant Ontology (PO; http://www.plantontology.org/) is a publicly available, collaborative effort to develop and maintain a controlled, structured vocabulary (‘ontology’) of terms to describe plant anatomy, morphology and the stages of plant development. The goals of the PO are to link (annotate) gene expression and phenotype data to plant structures and stages of plant development, using the data model adopted by the Gene Ontology. From its original design covering only rice, maize and Arabidopsis, the scope of the PO has been expanded to include all green plants. The PO was the first multispecies anatomy ontology developed for the annotation of genes and phenotypes. Also, to our knowledge, it was one of the first biological ontologies that provides translations (via synonyms) in non-English languages such as Japanese and Spanish. As of Release #18 (July 2012), there are about 2.2 million annotations linking PO terms to >110,000 unique data objects representing genes or gene models, proteins, RNAs, germplasm and quantitative trait loci (QTLs) from 22 plant species. In this paper, we focus on the plant anatomical entity branch of the PO, describing the organizing principles, resources available to users and examples of how the PO is integrated into other plant genomics databases and web portals. We also provide two examples of comparative analyses, demonstrating how the ontology structure and PO-annotated data can be used to discover the patterns of expression of the LEAFY (LFY) and terpene synthase (TPS) gene homologs. PMID:23220694

  13. 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

  14. Modularizing Spatial Ontologies for Assisted Living Systems

    NASA Astrophysics Data System (ADS)

    Hois, Joana

    Assisted living systems are intended to support daily-life activities in user homes by automatizing and monitoring behavior of the environment while interacting with the user in a non-intrusive way. The knowledge base of such systems therefore has to define thematically different aspects of the environment mostly related to space, such as basic spatial floor plan information, pieces of technical equipment in the environment and their functions and spatial ranges, activities users can perform, entities that occur in the environment, etc. In this paper, we present thematically different ontologies, each of which describing environmental aspects from a particular perspective. The resulting modular structure allows the selection of application-specific ontologies as necessary. This hides information and reduces complexity in terms of the represented spatial knowledge and reasoning practicability. We motivate and present the different spatial ontologies applied to an ambient assisted living application.

  15. Ontology-enriched Visualization of Human Anatomy

    SciTech Connect

    Pouchard, LC

    2005-12-20

    The project focuses on the problem of presenting a human anatomical 3D model associated with other types of human systemic information ranging from physiological to anatomical information while navigating the 3D model. We propose a solution that integrates a visual 3D interface and navigation features with the display of structured information contained in an ontology of anatomy where the structures of the human body are formally and semantically linked. The displayed and annotated anatomy serves as a visual entry point into a patient's anatomy, medical indicators and other information. The ontology of medical information provides labeling to the highlighted anatomical parts in the 3D display. Because of the logical organization and links between anatomical objects found in the ontology and associated 3D model, the analysis of a structure by a physician is greatly enhanced. Navigation within the 3D visualization and between this visualization and objects representing anatomical concepts within the model is also featured.

  16. TrOn: an anatomical ontology for the beetle Tribolium castaneum.

    PubMed

    Dönitz, Jürgen; Grossmann, Daniela; Schild, Inga; Schmitt-Engel, Christian; Bradler, Sven; Prpic, Nikola-Michael; Bucher, Gregor

    2013-01-01

    In a morphological ontology the expert's knowledge is represented in terms, which describe morphological structures and how these structures relate to each other. With the assistance of ontologies this expert knowledge is made processable by machines, through a formal and standardized representation of terms and their relations to each other. The red flour beetle Tribolium castaneum, a representative of the most species rich animal taxon on earth (the Coleoptera), is an emerging model organism for development, evolution, physiology, and pest control. In order to foster Tribolium research, we have initiated the Tribolium Ontology (TrOn), which describes the morphology of the red flour beetle. The content of this ontology comprises so far most external morphological structures as well as some internal ones. All modeled structures are consistently annotated for the developmental stages larva, pupa and adult. In TrOn all terms are grouped into three categories: Generic terms represent morphological structures, which are independent of a developmental stage. In contrast, downstream of such terms are concrete terms which stand for a dissectible structure of a beetle at a specific life stage. Finally, there are mixed terms describing structures that are only found at one developmental stage. These terms combine the characteristics of generic and concrete terms with features of both. These annotation principles take into account the changing morphology of the beetle during development and provide generic terms to be used in applications or for cross linking with other ontologies and data resources. We use the ontology for implementing an intuitive search function at the electronic iBeetle-Base, which stores morphological defects found in a genome wide RNA interference (RNAi) screen. The ontology is available for download at http://ibeetle-base.uni-goettingen.de.

  17. An open annotation ontology for science on web 3.0

    PubMed Central

    2011-01-01

    Background There is currently a gap between the rich and expressive collection of published biomedical ontologies, and the natural language expression of biomedical papers consumed on a daily basis by scientific researchers. The purpose of this paper is to provide an open, shareable structure for dynamic integration of biomedical domain ontologies with the scientific document, in the form of an Annotation Ontology (AO), thus closing this gap and enabling application of formal biomedical ontologies directly to the literature as it emerges. Methods Initial requirements for AO were elicited by analysis of integration needs between biomedical web communities, and of needs for representing and integrating results of biomedical text mining. Analysis of strengths and weaknesses of previous efforts in this area was also performed. A series of increasingly refined annotation tools were then developed along with a metadata model in OWL, and deployed for feedback and additional requirements the ontology to users at a major pharmaceutical company and a major academic center. Further requirements and critiques of the model were also elicited through discussions with many colleagues and incorporated into the work. Results This paper presents Annotation Ontology (AO), an open ontology in OWL-DL for annotating scientific documents on the web. AO supports both human and algorithmic content annotation. It enables “stand-off” or independent metadata anchored to specific positions in a web document by any one of several methods. In AO, the document may be annotated but is not required to be under update control of the annotator. AO contains a provenance model to support versioning, and a set model for specifying groups and containers of annotation. AO is freely available under open source license at http://purl.org/ao/, and extensive documentation including screencasts is available on AO’s Google Code page: http://code.google.com/p/annotation-ontology/ . Conclusions The

  18. A Posteriori Ontology Engineering for Data-Driven Science

    SciTech Connect

    Gessler, Damian Dg; Joslyn, Cliff A.; Verspoor, Karin M.

    2013-05-28

    Science—and biology in particular—has a rich tradition in categorical knowledge management. This continues today in the generation and use of formal ontologies. Unfortunately, the link between hard data and ontological content is predominately qualitative, not quantitative. The usual approach is to construct ontologies of qualitative concepts, and then annotate the data to the ontologies. This process has seen great value, yet it is laborious, and the success to which ontologies are managing and organizing the full information content of the data is uncertain. An alternative approach is the converse: use the data itself to quantitatively drive ontology creation. Under this model, one generates ontologies at the time they are needed, allowing them to change as more data influences both their topology and their concept space. We outline a combined approach to achieve this, taking advantage of two technologies, the mathematical approach of Formal Concept Analysis (FCA) and the semantic web technologies of the Web Ontology Language (OWL).

  19. Tools and Strategies for Product Life Cycle Management ñ A Case Study in Foundry

    NASA Astrophysics Data System (ADS)

    Patil, Rajashekar; Kumar, S. Mohan; Abhilash, E.

    2012-08-01

    Advances in information and communication technology (ICT) have opened new possibilities of collaborations among the customers, suppliers, manufactures and partners to effectively tackle various business challenges. Product Life Cycle Management(PLM) has been a proven approach for Original Equipment Manufacturers (OEMs) to increase their productivity, improve their product quality, speed up delivery, and increase their profit and to become more efficient. However, their Tier 2 and Tier 3 suppliers like foundry industries are still in their infancy without adopting PLM. Hence to enhance their understanding, the basic concepts, the tools and strategies for PLM are presented is this paper. By selecting and implementing appropriate PLM strategies in a small foundry, an attempt was also made to understand the immediate benefits of using PLM tools (commercial PLM software and digital manufacturing tools). This study indicated a reduction in lead time and improved utilization of organizational resources in the production of automobile impeller. These observations may be further extrapolated to other multiproduct, multi-discipline and multi-customer companies to realize the advantages of using PLM technology

  20. CODEX: exploration of semantic changes between ontology versions.

    PubMed

    Hartung, Michael; Gross, Anika; Rahm, Erhard

    2012-03-15

    Life science ontologies substantially change over time to meet the requirements of their users and to include the newest domain knowledge. Thus, an important task is to know what has been modified between two versions of an ontology (diff). This diff should contain all performed changes as compact and understandable as possible. We present CODEX (Complex Ontology Diff Explorer), a tool that allows determining semantic changes between two versions of an ontology, which users can interactively analyze in multiple ways.