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Sample records for foundry ontology development

  1. How orthogonal are the OBO Foundry ontologies?

    PubMed Central

    2011-01-01

    Background Ontologies in biomedicine facilitate information integration, data exchange, search and query of biomedical data, and other critical knowledge-intensive tasks. The OBO Foundry is a collaborative effort to establish a set of principles for ontology development with the eventual goal of creating a set of interoperable reference ontologies in the domain of biomedicine. One of the key requirements to achieve this goal is to ensure that ontology developers reuse term definitions that others have already created rather than create their own definitions, thereby making the ontologies orthogonal. Methods We used a simple lexical algorithm to analyze the extent to which the set of OBO Foundry candidate ontologies identified from September 2009 to September 2010 conforms to this vision. Specifically, we analyzed (1) the level of explicit term reuse in this set of ontologies, (2) the level of overlap, where two ontologies define similar terms independently, and (3) how the levels of reuse and overlap changed during the course of this year. Results We found that 30% of the ontologies reuse terms from other Foundry candidates and 96% of the candidate ontologies contain terms that overlap with terms from the other ontologies. We found that while term reuse increased among the ontologies between September 2009 and September 2010, the level of overlap among the ontologies remained relatively constant. Additionally, we analyzed the six ontologies announced as OBO Foundry members on March 5, 2010, and identified that the level of overlap was extremely low, but, notably, so was the level of term reuse. Conclusions We have created a prototype web application that allows OBO Foundry ontology developers to see which classes from their ontologies overlap with classes from other ontologies in the OBO Foundry (http://obomap.bioontology.org). From our analysis, we conclude that while the OBO Foundry has made significant progress toward orthogonality during the period of this

  2. 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…

  3. 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.

  4. Ontology development for Sufism domain

    NASA Astrophysics Data System (ADS)

    Iqbal, Rizwan

    2012-01-01

    Domain ontology is a descriptive representation of any particular domain which in detail describes the concepts in a domain, the relationships among those concepts and organizes them in a hierarchal manner. It is also defined as a structure of knowledge, used as a means of knowledge sharing to the community. An Important aspect of using ontologies is to make information retrieval more accurate and efficient. Thousands of domain ontologies from all around the world are available online on ontology repositories. Ontology repositories like SWOOGLE currently have over 1000 ontologies covering a wide range of domains. It was found that up to date there was no ontology available covering the domain of "Sufism". This unavailability of "Sufism" domain ontology became a motivation factor for this research. This research came up with a working "Sufism" domain ontology as well a framework, design of the proposed framework focuses on the resolution to problems which were experienced while creating the "Sufism" ontology. The development and working of the "Sufism" domain ontology are covered in detail in this research. The word "Sufism" is a term which refers to Islamic mysticism. One of the reasons to choose "Sufism" for ontology creation is its global curiosity. This research has also managed to create some individuals which inherit the concepts from the "Sufism" ontology. The creation of individuals helps to demonstrate the efficient and precise retrieval of data from the "Sufism" domain ontology. The experiment of creating the "Sufism" domain ontology was carried out on a tool called Protégé. Protégé is a tool which is used for ontology creation, editing and it is open source.

  5. Ontology development for Sufism domain

    NASA Astrophysics Data System (ADS)

    Iqbal, Rizwan

    2011-12-01

    Domain ontology is a descriptive representation of any particular domain which in detail describes the concepts in a domain, the relationships among those concepts and organizes them in a hierarchal manner. It is also defined as a structure of knowledge, used as a means of knowledge sharing to the community. An Important aspect of using ontologies is to make information retrieval more accurate and efficient. Thousands of domain ontologies from all around the world are available online on ontology repositories. Ontology repositories like SWOOGLE currently have over 1000 ontologies covering a wide range of domains. It was found that up to date there was no ontology available covering the domain of "Sufism". This unavailability of "Sufism" domain ontology became a motivation factor for this research. This research came up with a working "Sufism" domain ontology as well a framework, design of the proposed framework focuses on the resolution to problems which were experienced while creating the "Sufism" ontology. The development and working of the "Sufism" domain ontology are covered in detail in this research. The word "Sufism" is a term which refers to Islamic mysticism. One of the reasons to choose "Sufism" for ontology creation is its global curiosity. This research has also managed to create some individuals which inherit the concepts from the "Sufism" ontology. The creation of individuals helps to demonstrate the efficient and precise retrieval of data from the "Sufism" domain ontology. The experiment of creating the "Sufism" domain ontology was carried out on a tool called Protégé. Protégé is a tool which is used for ontology creation, editing and it is open source.

  6. Solar-Terrestrial Ontology Development

    NASA Astrophysics Data System (ADS)

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

    2005-12-01

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

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

    ERIC Educational Resources Information Center

    Ding, Ying; Foo, Schubert

    2002-01-01

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

  8. 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

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

    PubMed Central

    2014-01-01

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

  10. 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…

  11. 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

  12. Software Engineering Approaches to Ontology Development

    NASA Astrophysics Data System (ADS)

    Gaševic, Dragan; Djuric, Dragan; Devedžic, Vladan

    Ontologies, as formal representations of domain knowledge, enable knowledge sharing between different knowledge-based applications. Diverse techniques originating from the field of artificial intelligence are aimed at facilitating ontology development. However, these techniques, although well known to AI experts, are typically unknown to a large population of software engineers. In order to overcome the gap between the knowledge of software engineering practitioners and AI techniques, a few proposals have been made suggesting the use of well-known software engineering techniques, such as UML, for ontology development (Cranefield 2001a).

  13. Ontodog: a web-based ontology community view generation tool.

    PubMed

    Zheng, Jie; Xiang, Zuoshuang; Stoeckert, Christian J; He, Yongqun

    2014-05-01

    Biomedical ontologies are often very large and complex. Only a subset of the ontology may be needed for a specified application or community. For ontology end users, it is desirable to have community-based labels rather than the labels generated by ontology developers. Ontodog is a web-based system that can generate an ontology subset based on Excel input, and support generation of an ontology community view, which is defined as the whole or a subset of the source ontology with user-specified annotations including user-preferred labels. Ontodog allows users to easily generate community views with minimal ontology knowledge and no programming skills or installation required. Currently >100 ontologies including all OBO Foundry ontologies are available to generate the views based on user needs. We demonstrate the application of Ontodog for the generation of community views using the Ontology for Biomedical Investigations as the source ontology. PMID:24413522

  14. 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,…

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

    ERIC Educational Resources Information Center

    Rasmussen, Bonnie

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

  16. Technology development towards a generic InP-based photonic-integration foundry

    NASA Astrophysics Data System (ADS)

    Soares, F. M.; Janiak, K.; Broeke, R. G.; Grote, N.

    2011-05-01

    The main goal of this work is to create a generic foundry service that allows outside users (i.e., universities and small- and-medium enterprises) that do not have fabrication facilities to obtain their own custom-made InP-based photonic-integrated chips (or ASPIC, application-specific photonic-integrated circuits, similar to ASIC in electronics). In this approach, the foundry supplies the user with the cross-section of the interconnect waveguide structure, and the mask layout dimensions and performance of several pre-defined- and wellcharacterized building blocks (BB) such as photodiodes, phase modulators, and spot-size converters (for lowloss fiber-chip coupling). Using this information, the user can generate a mask layout for the foundry by placing the building blocks onto his layout canvas and interconnecting them with the interconnect waveguides. Furthermore, since the material cross-section of the interconnect waveguide is known, the user can design, simulate, and include a mask layout for a desired passive devices such as MMIs, and AWGs, which can subsequently be fabricated at the foundry. We describe the technology development towards obtaining a versatile generic-foundry platform which gives users the freedom to design a large variety of photonic-integrated- devices and circuits. Our generic-foundry technology is based on the fabrication process of our commercially-available high-speed- photodiodes and balanced photodiodes (high-frequency response up to and beyond 100 GHz). We have expanded this fabrication process to include a total of three different types of interconnecting waveguides: a low-contrast-, a medium-contrast, and a high-contrast waveguide, as well as transition BBs to couple light from one waveguide type into the other.

  17. 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

  18. Keyword Ontology Development for Discovering Hydrologic Data

    NASA Astrophysics Data System (ADS)

    Piasecki, Michael; Hooper, Rick; Choi, Yoori

    2010-05-01

    Supply of adequate keywords in data searches is a key element to building search clients. This is particularly true for science or engineering areas that straddle many subjects such as the hydrology field. The main difficulties that arise when trying to search across many disparate data holdings is that there are no norms that describe data sets uniformly (this is a lack of common metadata profiles) in particular when it comes to identifying them with recognizable labels. This leads to problems associated with hyponymy (a word or phrase whose semantic range is included within that of another) and synonymy (several terms are used to describe the same thing or parameter). Particularly the latter is endemic in the hydrologic data world and poses a substantial obstacle when trying to build information systems that can search for data across multiple data sources. This paper discusses the effort that has been undertaken within the Consortium of Universities for the Advancement of Hydrologic Sciences Inc. (CUAHSI: http://www.cuahsi.org) Hydrologic Information Systems (HIS) development group to overcome these semantic heterogeneities by developing a keyword ontology that can be navigated to identify search keywords of ascending or descending generality to identify parameter sets or fairly specific parameters that the search engine should be searching for. The general is to tag or connect any variable name to a presented leaf concept in the ontology that best describes what a specific data set represents. While the search environment is not part of this paper, we will describe the underlying ontology, its extent, the way it is organized and why, and what sources and considerations were taken into account in developing the current version. An initial ontology of 4033 leaf concepts describing physical, chemical and biological properties has been developed. These leaf concepts cover the vast majority of the records contained in major data sources such as the US Geological

  19. 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…

  20. Representing default knowledge in biomedical ontologies: application to the integration of anatomy and phenotype ontologies

    PubMed Central

    Hoehndorf, Robert; Loebe, Frank; Kelso, Janet; Herre, Heinrich

    2007-01-01

    Background Current efforts within the biomedical ontology community focus on achieving interoperability between various biomedical ontologies that cover a range of diverse domains. Achieving this interoperability will contribute to the creation of a rich knowledge base that can be used for querying, as well as generating and testing novel hypotheses. The OBO Foundry principles, as applied to a number of biomedical ontologies, are designed to facilitate this interoperability. However, semantic extensions are required to meet the OBO Foundry interoperability goals. Inconsistencies may arise when ontologies of properties – mostly phenotype ontologies – are combined with ontologies taking a canonical view of a domain – such as many anatomical ontologies. Currently, there is no support for a correct and consistent integration of such ontologies. Results We have developed a methodology for accurately representing canonical domain ontologies within the OBO Foundry. This is achieved by adding an extension to the semantics for relationships in the biomedical ontologies that allows for treating canonical information as default. Conclusions drawn from default knowledge may be revoked when additional information becomes available. We show how this extension can be used to achieve interoperability between ontologies, and further allows for the inclusion of more knowledge within them. We apply the formalism to ontologies of mouse anatomy and mammalian phenotypes in order to demonstrate the approach. Conclusion Biomedical ontologies require a new class of relations that can be used in conjunction with default knowledge, thereby extending those currently in use. The inclusion of default knowledge is necessary in order to ensure interoperability between ontologies. PMID:17925014

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

    PubMed

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

    2015-01-01

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

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

    PubMed Central

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

    2015-01-01

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

  3. 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. PMID:26262398

  4. Representing Kidney Development Using the Gene Ontology

    PubMed Central

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

    2014-01-01

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

  5. 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

  6. 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

  7. Developing a Diagnosis Aiding Ontology Based on Hysteroscopy Image Processing

    NASA Astrophysics Data System (ADS)

    Poulos, Marios; Korfiatis, Nikolaos

    In this paper we describe an ontology design process which will introduce the steps and mechanisms required in order to create and develop an ontology which will be able to represent and describe the contents and attributes of hysteroscopy images, as well as their relationships, thus providing a useful ground for the development of tools related with medical diagnosis from physicians.

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

    PubMed

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

    2016-01-01

    This study aims to develop and evaluate an ontology for adolescents' depression to be used for collecting and analyzing social data. The ontology was developed according to the 'ontology development 101' methodology. Concepts were extracted from clinical practice guidelines and related literatures. The ontology is composed of five sub-ontologies which represent risk factors, sign and symptoms, measurement, diagnostic result and management care. The ontology was evaluated in four different ways: First, we examined the frequency of ontology concept appeared in social data; Second, the content coverage of ontology was evaluated by comparing ontology concepts with concepts extracted from the youth depression counseling records; Third, the structural and representational layer of the ontology were evaluated by 5 ontology and psychiatric nursing experts; Fourth, the scope of the ontology was examined by answering 59 competency questions. The ontology was improved by adding new concepts and synonyms and revising the level of structure. PMID:27332239

  9. 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…

  10. FYPO: the fission yeast phenotype ontology

    PubMed Central

    Harris, Midori A.; Lock, Antonia; Bähler, Jürg; Oliver, Stephen G.; Wood, Valerie

    2013-01-01

    Motivation: To provide consistent computable descriptions of phenotype data, PomBase is developing a formal ontology of phenotypes observed in fission yeast. Results: The fission yeast phenotype ontology (FYPO) is a modular ontology that uses several existing ontologies from the open biological and biomedical ontologies (OBO) collection as building blocks, including the phenotypic quality ontology PATO, the Gene Ontology and Chemical Entities of Biological Interest. Modular ontology development facilitates partially automated effective organization of detailed phenotype descriptions with complex relationships to each other and to underlying biological phenomena. As a result, FYPO supports sophisticated querying, computational analysis and comparison between different experiments and even between species. Availability: FYPO releases are available from the Subversion repository at the PomBase SourceForge project page (https://sourceforge.net/p/pombase/code/HEAD/tree/phenotype_ontology/). The current version of FYPO is also available on the OBO Foundry Web site (http://obofoundry.org/). Contact: mah79@cam.ac.uk or vw253@cam.ac.uk PMID:23658422

  11. Ontology Driven Development and Science Information System Interoperability

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  12. 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.

  13. The neurological disease ontology

    PubMed Central

    2013-01-01

    Background We are developing the Neurological Disease Ontology (ND) to provide a framework to enable representation of aspects of neurological diseases that are relevant to their treatment and study. ND is a representational tool that addresses the need for unambiguous annotation, storage, and retrieval of data associated with the treatment and study of neurological diseases. ND is being developed in compliance with the Open Biomedical Ontology Foundry principles and builds upon the paradigm established by the Ontology for General Medical Science (OGMS) for the representation of entities in the domain of disease and medical practice. Initial applications of ND will include the annotation and analysis of large data sets and patient records for Alzheimer’s disease, multiple sclerosis, and stroke. Description ND is implemented in OWL 2 and currently has more than 450 terms that refer to and describe various aspects of neurological diseases. ND directly imports the development version of OGMS, which uses BFO 2. Term development in ND has primarily extended the OGMS terms ‘disease’, ‘diagnosis’, ‘disease course’, and ‘disorder’. We have imported and utilize over 700 classes from related ontology efforts including the Foundational Model of Anatomy, Ontology for Biomedical Investigations, and Protein Ontology. ND terms are annotated with ontology metadata such as a label (term name), term editors, textual definition, definition source, curation status, and alternative terms (synonyms). Many terms have logical definitions in addition to these annotations. Current development has focused on the establishment of the upper-level structure of the ND hierarchy, as well as on the representation of Alzheimer’s disease, multiple sclerosis, and stroke. The ontology is available as a version-controlled file at http://code.google.com/p/neurological-disease-ontology along with a discussion list and an issue tracker. Conclusion ND seeks to provide a formal

  14. 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

  15. 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…

  16. Using an Integrated Ontology and Information Model for Querying and Reasoning about Phenotypes: The Case of Autism

    PubMed Central

    Tu, Samson W.; Tennakoon, Lakshika; O'Connor, Martin; Shankar, Ravi; Das, Amar

    2008-01-01

    The Open Biomedical Ontologies (OBO) Foundry is a coordinated community-wide effort to develop ontologies that support the annotation and integration of scientific data. In work supported by the National Database of Autism Research (NDAR), we are developing an ontology of autism that extends the ontologies available in the OBO Foundry. We undertook a systematic literature review to identify domain terms and relationships relevant to autism phenotypes. To enable user queries and inferences about such phenotypes using data in the NDAR repository, we augmented the domain ontology with an information model. In this paper, we show how our approach, using a combination of description logic and rule-based reasoning, enables high-level phenotypic abstractions to be inferred from subject-specific data. Our integrated domain ontology–information model approach allows scientific data repositories to be augmented with rule-based abstractions that facilitate the ability of researchers to undertake data analysis. PMID:18999231

  17. Using an integrated ontology and information model for querying and reasoning about phenotypes: The case of autism.

    PubMed

    Tu, Samson W; Tu, Samson; Tennakoon, Lakshika; O'Connor, Martin; Connor, Martin; Shankar, Ravi; Das, Amar

    2008-01-01

    The Open Biomedical Ontologies (OBO) Foundry is a coordinated community-wide effort to develop ontologies that support the annotation and integration of scientific data. In work supported by the National Database of Autism Research (NDAR), we are developing an ontology of autism that extends the ontologies available in the OBO Foundry. We undertook a systematic literature review to identify domain terms and relationships relevant to autism phenotypes. To enable user queries and inferences about such phenotypes using data in the NDAR repository, we augmented the domain ontology with an information model. In this paper, we show how our approach, using a combination of description logic and rule-based reasoning, enables high-level phenotypic abstractions to be inferred from subject-specific data. Our integrated domain ontologyinformation model approach allows scientific data repositories to be augmented with rule-based abstractions that facilitate the ability of researchers to undertake data analysis. PMID:18999231

  18. 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.

  19. 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.

  20. 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

  1. Development and Evaluation of an Ontology for Guiding Appropriate Antibiotic Prescribing

    PubMed Central

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

    2011-01-01

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

  2. Semiconductor foundry, lithography, and partners

    NASA Astrophysics Data System (ADS)

    Lin, Burn J.

    2002-07-01

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

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

    NASA Astrophysics Data System (ADS)

    Graybeal, J.

    2008-12-01

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

  4. 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

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

    PubMed

    Ong, Edison; He, Yongqun

    2016-01-01

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

  6. 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

  7. Regulatory affairs issues and legal ontologies in drug development.

    PubMed

    Munteanu, Cristian Robert; Dorado, Julian; Matei-Ilfoveanu, Ion; Nita, Silvia Ana

    2013-01-01

    It usually can take more than ten years from the time a new drug is discovered, until can be launched on the market. Regulatory requirements are part of the process of drug discovery and drug development. It acts at every developmental stage. Regulatory affairs works to establish an effective and uniform balance between voluntary and regulatory compliance and agency responsiveness to consumer needs. It evaluates and coordinates all proposed legal actions to ascertain compliance with regulatory policy. The ontology presented for regulatory affairs and drug research and development gives us the possibility to correlate information from different levels and to discover new relationships between the legal aspects. In addition, the transparency of the information is affected by the inability of existing integration strategies to organize and apply the available knowledge to the range of real scientific and business issue in critical safety and regulatory applications. Therefore, the semantic technologies based on ontologies make the knowledge reusable by several applications across business, from discovery to corporate affairs. PMID:23277001

  8. 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. PMID:21419760

  9. The Representation of Heart Development in the Gene Ontology

    PubMed Central

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

    2012-01-01

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

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

    PubMed Central

    2011-01-01

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

  11. IDOMAL: the malaria ontology revisited

    PubMed Central

    2013-01-01

    Background With about half a billion cases, of which nearly one million fatal ones, malaria constitutes one of the major infectious diseases worldwide. A recently revived effort to eliminate the disease also focuses on IT resources for its efficient control, which prominently includes the control of the mosquito vectors that transmit the Plasmodium pathogens. As part of this effort, IDOMAL has been developed and it is continually being updated. Findings In addition to the improvement of IDOMAL’s structure and the correction of some inaccuracies, there were some major subdomain additions such as a section on natural products and remedies, and the import, from other, higher order ontologies, of several terms, which were merged with IDOMAL terms. Effort was put on rendering IDOMAL fully compatible as an extension of IDO, the Infectious Disease Ontology. The reason for the difficulties in fully reaching that target were the inherent differences between vector-borne diseases and “classical” infectious diseases, which make it necessary to specifically adjust the ontology’s architecture in order to comprise vectors and their populations. Conclusions In addition to a higher coverage of domain-specific terms and optimizing its usage by databases and decision-support systems, the new version of IDOMAL described here allows for more cross-talk between it and other ontologies, and in particular IDO. The malaria ontology is available for downloading at the OBO Foundry (http://www.obofoundry.org/cgi-bin/detail.cgi?id=malaria_ontology) and the NCBO BioPortal (http://bioportal.bioontology.org/ontologies/1311). PMID:24034841

  12. 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

  13. Open Biomedical Ontology-based Medline exploration

    PubMed Central

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

    2009-01-01

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

  14. 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

  15. 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.

  16. 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

  17. 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

  18. Development of an Ontology to Recommend Exercises from Conceptual Maps.

    PubMed

    Ito, Márcia; Ciriaco Pereira, Débora Lina N

    2015-01-01

    The recommendation of exercise plans requires several variables to be considered (e.g., patient's conditions and preferences) and are normally complex to analyze. To facilitate this analysis we proposed the creation of an ontology to assist professionals to recommend exercises. We interviewed 2 experts and this resulted in IDEF diagram and conceptual map. The conceptual map proved to be the preferred way that experts gained more understanding compared with the IDEF diagram. In addition, we also used the conceptual map to validate the formal structure of experts' ideas. From the conceptual map we created an ontology that is being reviewed. After this, we plan to incorporate the ontology into a decision support system that will assist professionals to recommend exercises for their patients. PMID:26262394

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

    PubMed Central

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

    2007-01-01

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

  20. 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…

  1. 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

  2. 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

  3. 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

  4. 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.

  5. Development of an ontology to model medical errors, information needs, and the clinical communication space.

    PubMed Central

    Stetson, P. D.; McKnight, L. K.; Bakken, S.; Curran, C.; Kubose, T. T.; Cimino, J. J.

    2001-01-01

    Medical errors are common, costly and often preventable. Work in understanding the proximal causes of medical errors demonstrates that systems failures predispose to adverse clinical events. Most of these systems failures are due to lack of appropriate information at the appropriate time during the course of clinical care. Problems with clinical communication are common proximal causes of medical errors. We have begun a project designed to measure the impact of wireless computing on medical errors. We report here on our efforts to develop an ontology representing the intersection of medical errors, information needs and the communication space. We will use this ontology to support the collection, storage and interpretation of project data. The ontology's formal representation of the concepts in this novel domain will help guide the rational deployment of our informatics interventions. A real-life scenario is evaluated using the ontology in order to demonstrate its utility. PMID:11825270

  6. 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.

  7. 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

  8. Design and Development of a Guide System for Building an Ontology based on Task/Domain Role Concepts

    NASA Astrophysics Data System (ADS)

    Ishikawa, Seiichi; Kubo, Shigeki; Kozaki, Kouji; Kitamura, Yoshinobu; Mizoguchi, Riichiro

    Recently, ontology is expected to contribute to sharing and reuse of knowledge, and a lot of research on ontology has been carried out. However, useful methodologies for building ontologies are not yet established in spite of the understanding of its necessity. The crucial point of building ontologies is to articulate concepts in the target field. If a concept is defined in a manner depending on a particular context, it is difficult to reuse it in other contexts. Therefore, it is important to distinguish context-dependent concepts from context-independent ones. The difficulty of the discrimination requires development of a methodology and a guide system for building ontologies. This paper proposes AFM (Activity-First Method), a methodology of building domain ontology depending on task analysis, and an ontology building guide system based on AFM. The guide system supports building ontologies by providing an ontology author with building steps, and managing intermediate results. In the first half of this paper, we take an ontology of oil refinery plant operation task as an example and discuss articulation of the role concepts. Role concepts represent conceptual categories of roles of matters in a particular context. This consideration serves as the foundation of this guide system. In the second half of this paper, we show how the guide system supports an ontology building process.

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

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

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

  10. 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.

  11. 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

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

    PubMed

    Chambers, Stephen; Kitney, Richard; Freemont, Paul

    2016-06-15

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

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

    PubMed Central

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

    2015-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2016-07-01

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

  15. Datamining with Ontologies.

    PubMed

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

    2016-01-01

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

  16. 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)

  17. Foundry energy conservation workbook

    SciTech Connect

    Not Available

    1990-12-31

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

  18. 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…

  19. 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…

  20. 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

  1. 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

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

    PubMed

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

    2013-08-01

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

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

    NASA Astrophysics Data System (ADS)

    Lieberman, J. E.

    2014-12-01

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

  4. 77 FR 32998 - Foundry Coke From China

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-06-04

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

  5. European MEMS foundries

    NASA Astrophysics Data System (ADS)

    Salomon, Patric R.

    2003-01-01

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

  6. 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.

  7. An Ontology of Therapies

    NASA Astrophysics Data System (ADS)

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

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

  8. Simple Ontology Format (SOFT)

    Energy Science and Technology Software Center (ESTSC)

    2011-10-01

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

  9. 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

  10. 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

  11. 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

  12. Development of an Obesity Management Ontology Based on the Nursing Process for the Mobile-Device Domain

    PubMed Central

    Kim, Hyun-Young; Min, Yul Ha; Jeon, Eunjoo

    2013-01-01

    Background Lifestyle modification is the most important factor in the management of obesity. It is therefore essential to enhance client participation in voluntary and continuous weight control. Objective The aim of this study was to develop an obesity management ontology for application in the mobile-device domain. We considered the concepts of client participation in behavioral modification for obesity management and focused on minimizing the amount of information exchange between the application and the database when providing tailored interventions. Methods An obesity management ontology was developed in seven phases: (1) defining the scope of obesity management, (2) selecting a foundational ontology, (3) extracting the concepts, (4) assigning relationships between these concepts, (5) evaluating representative layers of ontology content, (6) representing the ontology formally with Protégé, and (7) developing a prototype application for obesity management. Results Behavioral interventions, dietary advice, and physical activity were proposed as obesity management strategies. The nursing process was selected as a foundation of ontology, representing the obesity management process. We extracted 127 concepts, which included assessment data (eg, sex, body mass index, and waist circumference), inferred data to represent nursing diagnoses and evaluations (eg, degree of and reason for obesity, and success or failure of lifestyle modifications), and implementation (eg, education and advice). The relationship linking concepts were “part of”, “instance of”, “derives of”, “derives into”, “has plan”, “followed by”, and “has intention”. The concepts and relationships were formally represented using Protégé. The evaluation score of the obesity management ontology was 4.5 out of 5. An Android-based obesity management application comprising both agent and client parts was developed. Conclusions We have developed an ontology for representing

  13. 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

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

    PubMed

    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

  15. Cognitive Foundry 2.0

    Energy Science and Technology Software Center (ESTSC)

    2007-12-18

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

  16. Ontology Languages and Engineering

    NASA Astrophysics Data System (ADS)

    Horrocks, Ian

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

  17. 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.

  18. THE PLANT ONTOLOGY CONSORTIUM AND PLANT ONTOLOGIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The goal of the Plant OntologyTM Consortium is to produce structured controlled vocabularies, arranged in ontologies, that can be applied to plant-based database information even as knowledge of the biology of the relevant plant taxa (e.g., development, anatomy, morphology, genomics, proteomics) is ...

  19. Web-based expert system for foundry pollution prevention

    NASA Astrophysics Data System (ADS)

    Moynihan, Gary P.

    2004-02-01

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

  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. Foundry sand reclamation

    SciTech Connect

    Filipovitch, A.J.; Bleuenstein, J.M.

    1984-05-22

    A dry method of conditioning spent foundry sand is disclosed. After having sized the sand and removal of tramp metallic elements, the sand is subjected to a sequence of squeezing under a high-stress low kinetic energy system for a period of 5-30 minutes, and then propelled against a target with high-kinetic energy in the presence of a suction for several minutes. This sequence can be preferably repeated to increase the quality of the resulting product which should have 0.1% or less of fine particles, a pH of 6-9, a clay content and organic combustible content of substantially zero. The reclaimed sand will exhibit a density of at least 100 grams/biscuit when compacted for core making or molding.

  2. 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.

  3. Performing ontology.

    PubMed

    Aspers, Patrik

    2015-06-01

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

  4. 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.

  5. 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.

  6. 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…

  7. 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.

  8. 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.

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

    PubMed Central

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

    2011-01-01

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

  10. Applying a biomedical top-level ontology to encode biological taxa.

    PubMed

    Boeker, Martin; Stenzhorn, Holger; Schulz, Stefan

    2008-01-01

    Classifying biological entities in terms of species and taxa is an important endeavor in biology. But even though many statements within current biomedical ontologies are indeed taxon-dependent, no standard way exists to properly introduce taxon or species information into current ontological architectures. Therefore we discuss various practices to represent such information by applying a biomedical top-level ontology combined with other standard approaches like description logics or the OBO Foundry. PMID:18999119

  11. Fast, cheap and out of control: a zero curation model for ontology development.

    PubMed

    Good, Benjamin M; Tranfield, Erin M; Tan, Poh C; Shehata, Marlene; Singhera, Gurpreet K; Gosselink, John; Okon, Elena B; Wilkinson, Mark D

    2006-01-01

    During two days at a conference focused on circulatory and respiratory health, 68 volunteers untrained in knowledge engineering participated in an experimental knowledge capture exercise. These volunteers created a shared vocabulary of 661 terms, linking these terms to each other and to a pre-existing upper ontology by adding 245 hyponym relationships and 340 synonym relationships. While ontology-building has proved to be an expensive and labor-intensive process using most existing methodologies, the rudimentary ontology constructed in this study was composed in only two days at a cost of only 3 t-shirts, 4 coffee mugs, and one chocolate moose. The protocol used to create and evaluate this ontology involved a targeted, web-based interface. The design and implementation of this protocol is discussed along with quantitative and qualitative assessments of the constructed ontology. PMID:17094234

  12. Dust exposure in Finnish foundries.

    PubMed

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

    1976-01-01

    Dust measurements were made in 51 iron, 9 steel, and 8 nonferrous foundries, at which 4,316 foundrymen were working. The sampling lasted at least two entire shifts or work days continuously during various operations in each foundry. The dust samples were collected at fixed sites or in the breathing zones of the workers. The mass concentration was determined by weighing and the respirable dust fraction was separated by liquid sedimentation. The free silica content was determined by X-ray diffraction. In the study a total of 3,188 samples were collected in the foundries and 6,505 determinations were made in the laboratory. The results indicated a definite difference in the dust exposure during various operations. The highest dust exposures were found during furnace, cupola, and pouring ladle repair. During cleaning work, sand mixing, and shake-out operations excessive silica dust concentrations were also measured. The lowest dust concentrations were measured during melting and pouring operations. Moderate dust concentrations were measured during coremaking and molding operations. The results obtained during the same operations of iron and steel foundries were similar. The distribution of the workers into various exposure categories, the content of respirable dust and quartz, the correlation between respirable dust and total dust, and the correlation between respirable silica and total dust concentrations are discussed. Observations concerning dust suppression and control methods are briefly considered. PMID:184524

  13. 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.

  14. Field performance measurements of half-facepiece respirators--foundry operations.

    PubMed

    Myers, W R; Zhuang, Z; Nelson, T

    1996-02-01

    A series of field studies was conducted to measure workplace protection factors (WPF) provided by elastomeric and disposable half-facepiece respirators against different particulate contaminants. The research protocol developed for the study has been described in a previous article. This article presents results from dust and fume exposures at three foundries. The major components of the airborne exposures in these foundries were zinc, lead, and silicon. The major components of the in-facepiece samples were zinc, chlorine, and lead. Significant differences were observed in ambient zinc and lead concentration levels among foundries; however, no significant difference was observed in the in-facepiece concentrations of these elements among foundries. Respirator performance varied within each foundry, but there was no difference in performance when pooling all foundry data. The 5th, 10th and 50th percentile estimates for the pooled foundry and respirator WPF data were about 9, 16, and 114 respectively. The infacepiece concentration data clearly indicate that dust-fume-mist (DFM) class half-facepiece respirators, when conscientiously used, worn, and maintained, in conjunction with other existing controls in these foundries, provided effective worker protection. PMID:8615325

  15. 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

  16. Cognitive Foundry v. 3.0 (OSS)

    Energy Science and Technology Software Center (ESTSC)

    2009-11-18

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

  17. Ontology-Oriented Programming for Biomedical Informatics.

    PubMed

    Lamy, Jean-Baptiste

    2016-01-01

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

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

    NASA Astrophysics Data System (ADS)

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

    2007-12-01

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

  19. 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

  20. 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…

  1. Microtox{trademark} characterization of foundry sand residuals

    SciTech Connect

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

    1998-12-31

    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. Microtox{trademark} 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{trademark} 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{trademark} 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.

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

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed

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

    2015-01-01

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

  4. Space Technology for the Iron Foundry

    NASA Technical Reports Server (NTRS)

    1990-01-01

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

  5. LOOKING NORTHEAST AT FOUNDRY BUILDING. CLOSED DOORS ON LEFT ARE ...

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

    LOOKING NORTHEAST AT FOUNDRY BUILDING. CLOSED DOORS ON LEFT ARE TO MACHINE SHOP, LARGE OPEN DOOR TO THE FOUNDRY, AND THE SMALL OPEN DOOR ON RIGHT TO CORE ROOM. - Knight Foundry, 13 Eureka Street, Sutter Creek, Amador County, CA

  6. 22. LOOKING NORTHEAST AT FOUNDRY BUILDING. CLOSED DOORS ON LEFT ...

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

    22. LOOKING NORTHEAST AT FOUNDRY BUILDING. CLOSED DOORS ON LEFT ARE TO MACHINE SHOP, LARGE OPEN DOOR TO THE FOUNDRY, AND THE SMALL OPEN DOOR ON RIGHT TO CORE ROOM. - Knight Foundry, 13 Eureka Street, Sutter Creek, Amador County, CA

  7. 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.

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

    PubMed Central

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

    2011-01-01

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

  9. 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...

  10. A Foundational Approach to Designing Geoscience Ontologies

    NASA Astrophysics Data System (ADS)

    Brodaric, B.

    2009-05-01

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

  11. 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. PMID:18487840

  12. 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…

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

    PubMed

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

    2014-12-01

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

  14. Plasma on a foundry cupola

    NASA Astrophysics Data System (ADS)

    Pineau, Didier

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

  15. 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.

  16. Foundry Technologies Focused on Environmental and Ecological Applications

    NASA Astrophysics Data System (ADS)

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

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

  17. A Unified Framework for Biomedical Terminologies and Ontologies

    PubMed Central

    Ceusters, Werner; Smith, Barry

    2011-01-01

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

  18. 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.

  19. 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.

  20. 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

  1. 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

  2. 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

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

    PubMed Central

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

    2011-01-01

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

  4. 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…

  5. The Drosophila anatomy ontology

    PubMed Central

    2013-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Coronel, Andrei D.; Saldana, Rafael P.

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

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

    PubMed

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

    2016-06-01

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

  8. 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. PMID:24303270

  9. 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. PMID:25428369

  10. 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

  11. 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

  12. 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

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

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

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

  14. 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

  15. 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

  16. 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

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

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

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

  18. 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

  19. 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

  20. 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

  1. The further development of legal cadastral domain model of China based on ontology

    NASA Astrophysics Data System (ADS)

    Zhang, Weiwei; Du, Qingyun; Zhao, Zhongjun; Guo, Yan; Cheng, Gang

    2008-10-01

    The cadastral plays a very important role in managing spatial and non-spatial legal real property information. And the legal aspect is the important component of the cadastral. And the success of a cadastral system is not dependent on its legal or technical sophistication, but whether it protects land rights adequately and permits those rights to be traded (where appropriate) efficiently, simply, quickly, securely and at low cost. However, the ambiguity of legal cadastral domain has been the major barrier to data integration and interoperability. This paper intends to optimize the concept model of legal cadastral domain based on the model established in my previous paper which can be a first step towards facilitate the effective interchange of cadastral information and the administration of land use. And the way expressing these conceptions and relationships between them was an object-oriented approach in ontology principles. The outcome of this paper is also a basic but better expression legal cadastral domain model of china.

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

    PubMed Central

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

    2013-01-01

    Traditionally, evaluation methods in the field of semantic technologies have focused on the end result of ontology engineering efforts, mainly, on evaluating ontologies and their corresponding qualities and characteristics. This focus has led to the development of a whole arsenal of ontology-evaluation techniques that investigate the quality of ontologies as a product. In this paper, we aim to shed light on the process of ontology engineering construction by introducing and applying a set of measures to analyze hidden social dynamics. We argue that especially for ontologies which are constructed collaboratively, understanding the social processes that have led to its construction is critical not only in understanding but consequently also in evaluating the ontology. With the work presented in this paper, we aim to expose the texture of collaborative ontology engineering processes that is otherwise left invisible. Using historical change-log data, we unveil qualitative differences and commonalities between different collaborative ontology engineering projects. Explaining and understanding these differences will help us to better comprehend the role and importance of social factors in collaborative ontology engineering projects. We hope that our analysis will spur a new line of evaluation techniques that view ontologies not as the static result of deliberations among domain experts, but as a dynamic, collaborative and iterative process that needs to be understood, evaluated and managed in itself. We believe that advances in this direction would help our community to expand the existing arsenal of ontology evaluation techniques towards more holistic approaches. PMID:24311994

  3. 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. PMID:24311994

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

    PubMed

    Tao, Cui; He, Yongqun; Arabandi, Sivaram

    2014-01-01

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

  5. 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.

  6. Legal Ontologies and Loopholes in the Law

    NASA Astrophysics Data System (ADS)

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

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

  7. 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.

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

    PubMed

    Tao, Cui; He, Yongqun; Arabandi, Sivaram

    2016-01-01

    The "Vaccine and Drug Ontology Studies" (VDOS) international workshop series focuses on vaccine- and drug-related ontology modeling and applications. Drugs and vaccines have been critical to prevent and treat human and animal diseases. Work in both (drugs and vaccines) areas is closely related - from preclinical research and development to manufacturing, clinical trials, government approval and regulation, and post-licensure usage surveillance and monitoring. Over the last decade, tremendous efforts have been made in the biomedical ontology community to ontologically represent various areas associated with vaccines and drugs - extending existing clinical terminology systems such as SNOMED, RxNorm, NDF-RT, and MedDRA, developing new models such as the Vaccine Ontology (VO) and Ontology of Adverse Events (OAE), vernacular medical terminologies such as the Consumer Health Vocabulary (CHV). The VDOS workshop series provides a platform for discussing innovative solutions as well as the challenges in the development and applications of biomedical ontologies for representing and analyzing drugs and vaccines, their administration, host immune responses, adverse events, and other related topics. The five full-length papers included in this 2014 thematic issue focus on two main themes: (i) General vaccine/drug-related ontology development and exploration, and (ii) Interaction and network-related ontology studies. PMID:26918107

  9. AIR TOXIC EMISSIONS FROM IRON FOUNDRIES

    EPA Science Inventory

    The paper presents uncontrolled air toxic emission factors for different process operations in a gray iron foundry. he emission factors are based on the results of on-site test measurements available in the literature. he emission factors are presented for organic and inorganic c...

  10. Inflammation ontology design pattern: an exercise in building a core biomedical ontology with descriptions and situations.

    PubMed

    Gangemi, Aldo; Catenacci, Carola; Battaglia, Massimo

    2004-01-01

    Formal ontology has proved to be an extremely useful tool for negotiating intended meaning, for building explicit, formal data sheets, and for the discovery of novel views on existing data structures. This paper describes an example of application of formal ontological methods to the creation of biomedical ontologies. Addressed here is the ambiguous notion of inflammation, which spans across multiple linguistic meanings, multiple layers of reality, and multiple details of granularity. We use UML class diagrams, description logics, and the DOLCE foundational ontology, augmented with the Description and Situation theory, in order to provide the representational and ontological primitives that are necessary for the development of detailed, flexible, and functional biomedical ontologies. An ontology design pattern is proposed as a modelling template for inflammations. PMID:15853264

  11. 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

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

    PubMed

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

    2012-01-01

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

  13. 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

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

    PubMed Central

    Lovering, Ruth C

    2014-01-01

    For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer’s vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer’s vesicle determine asymmetry in the developing heart, the direction of ‘heart jogging’ and the direction of ‘heart looping’.  ‘Heart jogging’ is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward ‘jog’. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish ‘heart jogging orthologs’ are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach. PMID:24627794

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

    PubMed

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

    2013-01-01

    For the majority of organs in developing vertebrate embryos, left-right asymmetry is controlled by a ciliated region; the left-right organizer node in the mouse and human, and the Kuppfer's vesicle in the zebrafish. In the zebrafish, laterality cues from the Kuppfer's vesicle determine asymmetry in the developing heart, the direction of 'heart jogging' and the direction of 'heart looping'.  'Heart jogging' is the term given to the process by which the symmetrical zebrafish heart tube is displaced relative to the dorsal midline, with a leftward 'jog'. Heart jogging is not considered to occur in mammals, although a leftward shift of the developing mouse caudal heart does occur prior to looping, which may be analogous to zebrafish heart jogging. Previous studies have characterized 30 genes involved in zebrafish heart jogging, the majority of which have well defined orthologs in mouse and human and many of these orthologs have been associated with early mammalian heart development.    We undertook manual curation of a specific set of genes associated with heart development and we describe the use of Gene Ontology term enrichment analyses to examine the cellular processes associated with heart jogging.  We found that the human, mouse and zebrafish 'heart jogging orthologs' are involved in similar organ developmental processes across the three species, such as heart, kidney and nervous system development, as well as more specific cellular processes such as cilium development and function. The results of these analyses are consistent with a role for cilia in the determination of left-right asymmetry of many internal organs, in addition to their known role in zebrafish heart jogging.    This study highlights the importance of model organisms in the study of human heart development, and emphasises both the conservation and divergence of developmental processes across vertebrates, as well as the limitations of this approach. PMID:24627794

  16. 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.

  17. Predicting the Extension of Biomedical Ontologies

    PubMed Central

    Pesquita, Catia; Couto, Francisco M.

    2012-01-01

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

  18. Assessment Applications of Ontologies.

    ERIC Educational Resources Information Center

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

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

  19. 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…

  20. 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

  1. 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

  2. Environmental factors and work performance of foundry workers.

    PubMed

    Horino, S

    1977-12-01

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

  3. 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.

  4. 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.

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

    PubMed

    Dönitz, Jürgen; Wingender, Edgar

    2012-01-01

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

  6. 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…

  7. Automatic generation of warehouse mediators using an ontology engine

    SciTech Connect

    Critchlow, T., LLNL

    1998-04-01

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

  8. 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.

  9. 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.

  10. 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.

  11. Towards an Ontology for Reef Islands

    NASA Astrophysics Data System (ADS)

    Duce, Stephanie

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

  12. 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.

  13. 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.

  14. Crowdsourcing the Verification of Relationships in Biomedical Ontologies

    PubMed Central

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

    2013-01-01

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

  15. The SWAN biomedical discourse ontology.

    PubMed

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

    2008-10-01

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

  16. Emotion Education without Ontological Commitment?

    ERIC Educational Resources Information Center

    Kristjansson, Kristjan

    2010-01-01

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

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

    NASA Astrophysics Data System (ADS)

    Raskin, R.

    2005-12-01

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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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

  4. 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

  5. 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…

  6. 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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Plant Availability of Metals in Waste Foundry Sands

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  12. The MMI Device Ontology: Enabling Sensor Integration

    NASA Astrophysics Data System (ADS)

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

    2010-12-01

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

  13. 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…

  14. 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

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

    PubMed Central

    Cimino, James J.; Huser, Vojtech

    2015-01-01

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

  16. 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)

  17. Mapping between the OBO and OWL ontology languages

    PubMed Central

    2011-01-01

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

  18. Gene Ontology annotations and resources.

    PubMed

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

    2013-01-01

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

  19. Ontology driven image search engine

    NASA Astrophysics Data System (ADS)

    Bei, Yun; Dmitrieva, Julia; Belmamoune, Mounia; Verbeek, Fons J.

    2007-01-01

    Image collections are most often domain specific. We have developed a system for image retrieval of multimodal microscopy images. That is, the same object of study visualized with a range of microscope techniques and with a range of different resolutions. In microscopy, image content is depending on the preparation method of the object under study as well as the microscope technique. Both are taken into account in the submission phase as metadata whilst at the same time (domain specific) ontologies are employed as controlled vocabularies to annotate the image. From that point onward, image data are interrelated through the relationships derived from annotated concepts in the ontology. By using concepts and relationships of an ontology, complex queries can be built with true semantic content. Image metadata can be used as powerful criteria to query image data which are directly or indirectly related to original data. The results of image retrieval can be represented using a structural graph by exploiting relationships from ontology rather than a listed table. Applying this to retrieve images from the same subject at different levels of resolution opens a new field for the analysis of image content.

  20. 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

  1. 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

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

    NASA Astrophysics Data System (ADS)

    Gao, Wei; Zhu, Linli; Wang, Kaiyun

    2015-12-01

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

  3. 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.

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

    PubMed

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

    2013-01-01

    ChEBI (http://www.ebi.ac.uk/chebi) is a database and ontology of chemical entities of biological interest. Over the past few years, ChEBI has continued to grow steadily in content, and has added several new features. In addition to incorporating all user-requested compounds, our annotation efforts have emphasized immunology, natural products and metabolites in many species. All database entries are now 'is_a' classified within the ontology, meaning that all of the chemicals are available to semantic reasoning tools that harness the classification hierarchy. We have completely aligned the ontology with the Open Biomedical Ontologies (OBO) Foundry-recommended upper level Basic Formal Ontology. Furthermore, we have aligned our chemical classification with the classification of chemical-involving processes in the Gene Ontology (GO), and as a result of this effort, the majority of chemical-involving processes in GO are now defined in terms of the ChEBI entities that participate in them. This effort necessitated incorporating many additional biologically relevant compounds. We have incorporated additional data types including reference citations, and the species and component for metabolites. Finally, our website and web services have had several enhancements, most notably the provision of a dynamic new interactive graph-based ontology visualization. PMID:23180789

  5. 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…

  6. 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…

  7. 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.

  8. Types of Concepts in Geoscience Ontologies

    NASA Astrophysics Data System (ADS)

    Brodaric, B.

    2006-05-01

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

  9. TGF-beta signaling proteins and the Protein Ontology

    PubMed Central

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

    2009-01-01

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

  10. 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

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

    PubMed

    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

  12. Measurements of silicon dry-etching rates and profiles in MEMS foundries and their application to MEMS design software

    NASA Astrophysics Data System (ADS)

    Takano, T.; Ikehara, T.; Maeda, R.

    2007-12-01

    Deep reactive ion etching (DRIE) is an important tool in MEMS fabrication to achieve three-dimensional structures. However, the etching profiles are not yet perfect. We had etching test samples fabricated in three MEMS foundries and measured the etching rates, sidewall angles, mask selectivity, and sidewall roughness against the line and space of 2 to 5000 μm. We also performed similar DRIE processes using our system and compared our samples and the samples from the foundries. The measurement results revealed the typical fabrication results in the MEMS foundries and their differences. The data were included in the database of MemsONE, a newly developed MEMS design software, and can be used for the process emulations.

  13. The Gene Ontology: enhancements for 2011.

    PubMed

    2012-01-01

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

  14. 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

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

    PubMed

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

    2015-01-01

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

  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. The pathway ontology – updates and applications

    PubMed Central

    2014-01-01

    Background The Pathway Ontology (PW) developed at the Rat Genome Database (RGD), covers all types of biological pathways, including altered and disease pathways and captures the relationships between them within the hierarchical structure of a directed acyclic graph. The ontology allows for the standardized annotation of rat, and of human and mouse genes to pathway terms. It also constitutes a vehicle for easy navigation between gene and ontology report pages, between reports and interactive pathway diagrams, between pathways directly connected within a diagram and between those that are globally related in pathway suites and suite networks. Surveys of the literature and the development of the Pathway and Disease Portals are important sources for the ongoing development of the ontology. User requests and mapping of pathways in other databases to terms in the ontology further contribute to increasing its content. Recently built automated pipelines use the mapped terms to make available the annotations generated by other groups. Results The two released pipelines – the Pathway Interaction Database (PID) Annotation Import Pipeline and the Kyoto Encyclopedia of Genes and Genomes (KEGG) Annotation Import Pipeline, make available over 7,400 and 31,000 pathway gene annotations, respectively. Building the PID pipeline lead to the addition of new terms within the signaling node, also augmented by the release of the RGD “Immune and Inflammatory Disease Portal” at that time. Building the KEGG pipeline lead to a substantial increase in the number of disease pathway terms, such as those within the ‘infectious disease pathway’ parent term category. The ‘drug pathway’ node has also seen increases in the number of terms as well as a restructuring of the node. Literature surveys, disease portal deployments and user requests have contributed and continue to contribute additional new terms across the ontology. Since first presented, the content of PW has increased by

  19. 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.

  20. Metadata and Ontologies in Learning Resources Design

    NASA Astrophysics Data System (ADS)

    Vidal C., Christian; Segura Navarrete, Alejandra; Menéndez D., Víctor; Zapata Gonzalez, Alfredo; Prieto M., Manuel

    Resource design and development requires knowledge about educational goals, instructional context and information about learner's characteristics among other. An important information source about this knowledge are metadata. However, metadata by themselves do not foresee all necessary information related to resource design. Here we argue the need to use different data and knowledge models to improve understanding the complex processes related to e-learning resources and their management. This paper presents the use of semantic web technologies, as ontologies, supporting the search and selection of resources used in design. Classification is done, based on instructional criteria derived from a knowledge acquisition process, using information provided by IEEE-LOM metadata standard. The knowledge obtained is represented in an ontology using OWL and SWRL. In this work we give evidence of the implementation of a Learning Object Classifier based on ontology. We demonstrate that the use of ontologies can support the design activities in e-learning.

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

    NASA Astrophysics Data System (ADS)

    Cui, Wei; Li, Deren

    2005-10-01

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

  2. "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…

  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. 42. DETAIL VIEW OF TRIPLED, HEAVY TIMBER TRUSSES IN FOUNDRY. ...

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

    42. DETAIL VIEW OF TRIPLED, HEAVY TIMBER TRUSSES IN FOUNDRY. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  5. 41. DETAIL VIEW OF TRIPLED, HEAVY TIMBER TRUSSES IN FOUNDRY. ...

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

    41. DETAIL VIEW OF TRIPLED, HEAVY TIMBER TRUSSES IN FOUNDRY. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  6. 43. DETAIL VIEW OF TRIPLED, HEAVY TIMBER TRUSSES IN FOUNDRY. ...

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

    43. DETAIL VIEW OF TRIPLED, HEAVY TIMBER TRUSSES IN FOUNDRY. - Baltimore & Ohio Railroad, Mount Clare Shops, South side of Pratt Street between Carey & Poppleton Streets, Baltimore, Independent City, MD

  7. A cluster of Acinetobacter Pneumonia in foundry workers

    SciTech Connect

    Cordes, L.G.; Brink, E.W.; Checko, P.J.; Lentnek, A.; Lyons, R.W.; Hayes, P.S.; Wu, T.C.; Tharr, D.G.; Fraser, D.W.

    1981-12-01

    In a 3-month period, three men who had worked for 5 to 19 years as welders or grinders of steel castings in a foundry acquired pneumonia caused by Acinetobacter calcoaceticus variety anitratus serotype 7J. Two of the men died, and postmortem examination showed mixed-dust pneumoconiosis with iron particles in the lungs. A calcoaceticus variety anitratus serotype 7J was isolated from the air in the foundry but the source was not found. The prevalence of antibody titers of 64 or greater to the 7J strain was significantly higher among foundry workers (15%) than among community controls (2%) (p less than 0.01). Sampling showed that the concentrations of total and metallic particles (especially iron) and of free silica in air inhaled by welders and grinders at the foundry frequently exceeded acceptable levels. These findings suggest that chronic exposure to such particles may increase susceptibility to infection by this organism, which rarely affects healthy people.

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

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

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

  9. EMISSION FACTORS FOR IRON FOUNDRIES--CRITERIA AND TOXIC POLLUTANTS

    EPA Science Inventory

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

  10. EMISSION FACTORS FOR IRON FOUNDRIES - CRITERIA AND TOXIC POLLUTANTS

    EPA Science Inventory

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

  11. 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

  12. FOUNDRY SHOP, FORGE SHOP, NORTH ARMORY, EAST ARMORY. Colt ...

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

    FOUNDRY SHOP, FORGE SHOP, NORTH ARMORY, EAST ARMORY. - Colt Fire Arms Company, East Armory Building, 36-150 Huyshope Avenue, 17-170 Van Dyke Avenue, 49 Vredendale Avenue, Hartford, Hartford County, CT

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. An Approach to Support Collaborative Ontology Construction.

    PubMed

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

    2016-01-01

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

  20. 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

  1. Lung cancer in ferrous foundry workers: a review.

    PubMed

    Palmer, W G; Scott, W D

    1981-05-01

    Epidemiologic studies indicate that an increased incidence of lung cancer may be associated with specific work areas in ferrous foundries. With the exception of crane operators, who were found to have an elevated lung cancer rate in one foundry, the excess lung cancer incidence is generally confined to molders, casters, and cleaning room operators whose lung cancer risk is two- to threefold higher than that of standard populations. These studies reflect conditions that existed in the foundries several decades ago. The lung cancer risk today may differ as a result of the introduction of new foundry practices and the use of new molding materials. Benzo(a)pyrene and certain other polycyclic aromatic hydrocarbons have been found in many locations in the foundries. It is not known if tumor promoters, co-carcinogens, or other classes of chemical carcinogens are present. The contribution of tobacco smoke to the lung cancer risk of ferrous foundry workers is also unknown. Current studies are examining the composition and long-term health effects of emissions from molds composed of modern synthetic chemical molding materials as well as those from the more traditional green sand molds. PMID:7013460

  2. 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.

  3. GFVO: the Genomic Feature and Variation Ontology.

    PubMed

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

    2015-01-01

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

  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. 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

  6. Ontological Modeling for Integrated Spacecraft Analysis

    NASA Technical Reports Server (NTRS)

    Wicks, Erica

    2011-01-01

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

  7. 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.

  8. FMA-RadLex: An application ontology of radiological anatomy derived from the foundational model of anatomy reference ontology.

    PubMed

    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

  9. The teleost anatomy ontology: anatomical representation for the genomics age.

    PubMed

    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

    2010-07-01

    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

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

    PubMed

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

    2012-01-01

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

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

    PubMed Central

    2014-01-01

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

  12. Thin film metal surface micromachining: a new enabling foundry technology

    NASA Astrophysics Data System (ADS)

    van Heeren, Henne; Andringa, Toon; Attenborough, K.; Eisenberg, Martin; Meeuws, P.

    2003-01-01

    A new generation of products has been developed at research institutes needing a combination of thin film metal processing and surface micromachining. Especially RF MEMS switches and related products are now entering the market. These products are not only complex in architecture, they also feature relative thick metal layers. The thicknesses of the metal layers give rise to problems in the field of step coverage, dimension control and limited resistance to etching agents. Reliability and yield in production is therefore a major concern. To make robust, compact and reliable structures, combinations of electroplating and Chemical Mechanical Polishing are used. The combinations are not only new in this area; they are rather different from the standards in the semiconductor industry, where the technology was developed. The process modules are used in RF MEMS to create the thick signal lines, as well as the delicate switch and varactor structures. The basic processes, tried and tested in the production of magnetic heads, had to be modified to meet the special demands of RF MEMS. Also new processes had to be introduced to create free hanging membranes. Due to the fragility of the structures, a special technology is being developed in the backend processing: wafer scale packaging. This article gives an overview of the processes, the challenges met and the results of the work on RF MEMS at the OnStream MST foundry.

  13. 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

  14. Mechanisms in biomedical ontology

    PubMed Central

    2012-01-01

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

  15. Ontologies for molecular biology.

    PubMed

    Schulze-Kremer, S

    1998-01-01

    Molecular biology has a communication problem. There are many databases using their own labels and categories for storing data objects and some using identical labels and categories but with a different meaning. A prominent example is the concept "gene" which is used with different semantics by major international genomic databases. Ontologies are one means to provide a semantic repository to systematically order relevant concepts in molecular biology and to bridge the different notions in various databases by explicitly specifying the meaning of and relation between the fundamental concepts in an application domain. Here, the upper level and a database branch of a prospective ontology for molecular biology (OMB) is presented and compared to other ontologies with respect to suitability for molecular biology (http:/(/)igd.rz-berlin.mpg.de/approximately www/oe/mbo.html). PMID:9697223

  16. 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…

  17. 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.

  18. IMGT-ONTOLOGY 2012

    PubMed Central

    Giudicelli, Véronique; Lefranc, Marie-Paule

    2012-01-01

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

  19. Process attributes in bio-ontologies

    PubMed Central

    2012-01-01

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

  20. 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

  1. A RESTful way to Manage Ontologies

    NASA Astrophysics Data System (ADS)

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

    2009-04-01

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

  2. 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.

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

    PubMed Central

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

    2014-01-01

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

  4. The Rise of Ontologies or the Reinvention of Classification.

    ERIC Educational Resources Information Center

    Soergel, Dagobert

    1999-01-01

    Classifications/ontologies, thesauri, and dictionaries serve many functions, which are summarized in this article. As a result of this multiplicity of functions, classifications--often called ontologies--are developed in many communities of research and practice. Unfortunately, there is little communication and mutual learning; thus, efforts are…

  5. An ontology of astronomical object types for the Virtual Observatory

    NASA Astrophysics Data System (ADS)

    Derriere, Sebastian; Richard, André; Preite-Martinez, Andrea

    2007-08-01

    The Semantic Web and ontologies are emerging technologies that enable advanced knowledge management and sharing. Their application to Astronomy can offer new ways of sharing information between astronomers, but also between machines or software components and allow inference engines to perform reasoning on an astronomical knowledge base. The first examples of astronomy-related ontologies are being developed in the european VOTech project.

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

    PubMed Central

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

    2011-01-01

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

  7. POSet Ontology Categorizer

    Energy Science and Technology Software Center (ESTSC)

    2005-03-01

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

  8. POSet Ontology Categorizer

    SciTech Connect

    Miniszewski, Sue M.

    2005-03-01

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

  9. 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…

  10. NOA: a novel Network Ontology Analysis method

    PubMed Central

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

    2011-01-01

    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/. PMID:21543451

  11. 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).

  12. 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

  13. 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

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

    PubMed

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

    2016-01-01

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

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

    PubMed

    Malone, James; Stevens, Robert

    2013-02-01

    In this paper we explore the measurement of activity in ontology projects as an aspect of community ontology building. When choosing whether to use an ontology or whether to participate in its development, having some knowledge of how actively that ontology is developed is an important issue. Our knowledge of biology grows and changes and an ontology must adapt to keep pace with those changes and also adapt with respect to other ontologies and organisational principles. In essence, we need to know if there is an 'active' community involved with a project or whether a given ontology is inactive or moribund. We explore the use of additions, deletions and changes to ontology files, the regularity and frequency of releases, and the number of ontology repository updates to an ontology as the basis for measuring activity in an ontology. We present our results of this study, which show a dramatic range of activity across some of the more prominent community ontologies, illustrating very active and mature efforts through to those which appear to have become dormant for a number of possible reasons. We show that global activity within the community has remained at a similar level over the last 2 years. Measuring additions, deletions and changes, together with release frequency, appear to be useful metrics of activity and useful pointers towards future behaviour. Measuring who is making edits to ontologies is harder to capture; this raises issues of record keeping in ontology projects and in micro-credit, although we have identified one ontologist that appears influential across many community efforts; a Super-Ontologist. We also discuss confounding factors in our activity metric and discuss how it can be improved and adopted as an assessment criterion for community ontology development. Overall, we show that it is possible to objectively measure the activity in an ontology and to make some prediction about future activity. PMID:22554701

  16. 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.

  17. An ontological view of advanced practice nursing.

    PubMed

    Arslanian-Engoren, Cynthia; Hicks, Frank D; Whall, Ann L; Algase, Donna L

    2005-01-01

    Identifying, developing, and incorporating nursing's unique ontological and epistemological perspective into advanced practice nursing practice places priority on delivering care based on research-derived knowledge. Without a clear distinction of our metatheoretical space, we risk blindly adopting the practice values of other disciplines, which may not necessarily reflect those of nursing. A lack of focus may lead current advanced practice nursing curricula and emerging doctorate of nursing practice programs to mirror the logical positivist paradigm and perspective of medicine. This article presents an ontological perspective for advanced practice nursing education, practice, and research. PMID:16350595

  18. 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.

  19. 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.

  20. 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

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

    Technology Transfer Automated Retrieval System (TEKTRAN)

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

  2. 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

  3. 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

  4. SAMPLING AND ANALYSIS OF WASTES GENERATED BY GRAY IRON FOUNDRIES

    EPA Science Inventory

    Thirty (30) wastes generated by 21 gray iron foundries in Pennsylvania and Michigan were sampled and analyzed. The samples were collected by Northrop Services, Inc., in accordance with strict chain-of-custody procedures, and sent to the Environmental Monitoring Systems Laboratory...

  5. 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

  6. 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

  7. 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

  8. 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.

  9. 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

  10. 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…

  11. evelopment and Use of an Environment for Building/Using Ontologies “Hozo”

    NASA Astrophysics Data System (ADS)

    Kozaki, Kouji; Kitamura, Yoshinobu; Sano, Toshinobu; Motomatsu, Shin'ichiro; Ishikawa, Seiichi; Mizoguchi, Riichiro

    Ontological engineering is a successor of knowledge engineering which has been considered as a technology for building knowledge-intensive systems. Although knowledge engineering has contributed to eliciting expertise, organizing it into a computational structure, and building knowledge bases, AI researchers have noticed the necessity of a more robust and theoretically sound engineering which enables knowledge sharing/reuse and formulation of the problem solving process itself. Knowledge engineering has thus developed into “ontological engineering” where “ontology” is the key concept to investigate. Although the necessity of an ontology and ontological engineering is well-understood, there has been few success stories about ontology construction and its deployment to date. The reason for this is that the principles of ontology design is not clear enough. Therefore, a methodology of ontology design and a computer system supporting ontology design are needed. Our research goals include a methodology of ontology design, and development of an environment for building and using ontologies. This article outlines an environment for building and using ontologies “Hozo” which is under development. Hozo is designed based on a fundamental consideration of an ontological theory. And it has been extensively used in many projects to develop various ontologies. As an example, this paper presents an activity of ontology construction and its deployment in an interface system for an oil-refinery plant operation which has been done under the umbrella of Human-Media Project for five years. And we demonstrate the ability of Hozo through the ontology building/using process.

  12. Ontology Mappings to Improve Learning Resource Search

    ERIC Educational Resources Information Center

    Gasevic, Dragan; Hatala, Marek

    2006-01-01

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

  13. 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…

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

    PubMed

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

    2007-01-01

    The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge about techniques and best practice on ontology development. In the bio-ontology domain, these two camps have often come into conflict, especially where pragmatism comes into conflict with perceived best practice. One of these areas is the insistence of computer scientists on a well-defined semantic basis for the Knowledge Representation language being used. In this article, we will first describe why this community is so insistent. Second, we will illustrate this by examining the semantics of the Web Ontology Language and the semantics placed on the Directed Acyclic Graph as used by the Gene Ontology. Finally we will reconcile the two representations, including the broader Open Biomedical Ontologies format. The ability to exchange between the two representations means that we can capitalise on the features of both languages. Such utility can only arise by the understanding of the semantics of the languages being used. By this illustration of the usefulness of a clear, well-defined language semantics, we wish to promote a wider understanding of the computer science perspective amongst potential users within the biological community. PMID:17311682

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

    PubMed Central

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

    2007-01-01

    The bio-ontology community falls into two camps: first we have biology domain experts, who actually hold the knowledge we wish to capture in ontologies; second, we have ontology specialists, who hold knowledge about techniques and best practice on ontology development. In the bio-ontology domain, these two camps have often come into conflict, especially where pragmatism comes into conflict with perceived best practice. One of these areas is the insistence of computer scientists on a well-defined semantic basis for the Knowledge Representation language being used. In this article, we will first describe why this community is so insistent. Second, we will illustrate this by examining the semantics of the Web Ontology Language and the semantics placed on the Directed Acyclic Graph as used by the Gene Ontology. Finally we will reconcile the two representations, including the broader Open Biomedical Ontologies format. The ability to exchange between the two representations means that we can capitalise on the features of both languages. Such utility can only arise by the understanding of the semantics of the languages being used. By this illustration of the usefulness of a clear, well-defined language semantics, we wish to promote a wider understanding of the computer science perspective amongst potential users within the biological community. PMID:17311682

  16. 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

  17. 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.

  18. 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. PMID:23251424

  19. A Unified Anatomy Ontology of the Vertebrate Skeletal System

    PubMed Central

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

    2012-01-01

    The skeleton is of fundamental importance in research in comparative vertebrate morphology, paleontology, biomechanics, developmental biology, and systematics. Motivated by research questions that require computational access to and comparative reasoning across the diverse skeletal phenotypes of vertebrates, we developed a module of anatomical concepts for the skeletal system, the Vertebrate Skeletal Anatomy Ontology (VSAO), to accommodate and unify the existing skeletal terminologies for the species-specific (mouse, the frog Xenopus, zebrafish) and multispecies (teleost, amphibian) vertebrate anatomy ontologies. Previous differences between these terminologies prevented even simple queries across databases pertaining to vertebrate morphology. This module of upper-level and specific skeletal terms currently includes 223 defined terms and 179 synonyms that integrate skeletal cells, tissues, biological processes, organs (skeletal elements such as bones and cartilages), and subdivisions of the skeletal system. The VSAO is designed to integrate with other ontologies, including the Common Anatomy Reference Ontology (CARO), Gene Ontology (GO), Uberon, and Cell Ontology (CL), and it is freely available to the community to be updated with additional terms required for research. Its structure accommodates anatomical variation among vertebrate species in development, structure, and composition. Annotation of diverse vertebrate phenotypes with this ontology will enable novel inquiries across the full spectrum of phenotypic diversity. PMID:23251424

  20. 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

  1. 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

  2. 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

  3. ICEPO: the ion channel electrophysiology ontology

    PubMed Central

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

    2016-01-01

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

  4. Ontology-Based Administration of Web Directories

    NASA Astrophysics Data System (ADS)

    Horvat, Marko; Gledec, Gordan; Bogunović, Nikola

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

  5. ICEPO: the ion channel electrophysiology ontology.

    PubMed

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

    2016-01-01

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

  6. 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

  7. Ontology Performance Profiling and Model Examination: First Steps

    NASA Astrophysics Data System (ADS)

    Wang, Taowei David; Parsia, Bijan

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

  8. Planarization techniques for vertically integrated metallic MEMS on silicon foundry circuits

    NASA Astrophysics Data System (ADS)

    Lee, J.-B.; English, J.; Ahn, C.-H.; Allen, M. G.

    1997-06-01

    Various micromachining techniques exist to realize integrated microelectromechanical systems (MEMS), which include sensors, signal processing and/or driving circuits, and/or actuators in one small die. Post-processing techniques performed on foundry-fabricated circuits (e.g., MOSIS) are attractive since such an approach eliminates the need for an in-house integrated circuit fabrication line to produce integrated MEMS. A method based on the combination of metallic (e.g., electroplating) micromachining techniques with multichip module deposited (MCM-D) processes is a possible candidate to realize vertically-stacked integrated MEMS using the post-processing of integrated circuits (post-IC) approach. In order to realize such devices, planarization of the surface of foundry-fabricated circuit chips or wafers is often required. In such planarization layers, mechanical and chemical stability, as well as adhesion between the circuit-containing substrate and the micromachined devices, should be addressed. A PI/BCB/PI sandwich interlayer system, which utilizes both advantages of DuPont polyimide PI 2611 and Dow benzocyclobutene (BCB) Cyclotene 3022 series, was developed as a planarization interlayer for vertically integrated MEMS. The PI/BCB/PI interlayer system shows an over 95% degree of planarization (DOP) as well as passes the Method 107G Thermal Shock from the military standard MIL-STD-202F. A 0960-1317/7/2/002/img7 interlayer system was also developed as an alternative to the PI/BCB/PI system.

  9. 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. PMID:26477200

  10. 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.…

  11. 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

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

    PubMed Central

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

    2011-01-01

    The National Center for Biomedical Ontology (NCBO) is one of the National Centers for Biomedical Computing funded under the NIH Roadmap Initiative. Contributing to the national computing infrastructure, NCBO has developed BioPortal, a web portal that provides access to a library of biomedical ontologies and terminologies (http://bioportal.bioontology.org) via the NCBO Web services. BioPortal enables community participation in the evaluation and evolution of ontology content by providing features to add mappings between terms, to add comments linked to specific ontology terms and to provide ontology reviews. The NCBO Web services (http://www.bioontology.org/wiki/index.php/NCBO_REST_services) enable this functionality and provide a uniform mechanism to access ontologies from a variety of knowledge representation formats, such as Web Ontology Language (OWL) and Open Biological and Biomedical Ontologies (OBO) format. The Web services provide multi-layered access to the ontology content, from getting all terms in an ontology to retrieving metadata about a term. Users can easily incorporate the NCBO Web services into software applications to generate semantically aware applications and to facilitate structured data collection. PMID:21672956

  13. 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.

  14. 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. PMID:26208658

  15. Prevalence of Occupational Asthma and Respiratory Symptoms in Foundry Workers

    PubMed Central

    Kayhan, Servet; Tutar, Umit; Cinarka, Halit; Gumus, Aziz; Koksal, Nurhan

    2013-01-01

    This cross-sectional study was conducted in a foundry factory to assess the prevalence of respiratory symptoms and occupational asthma in foundry workers. Physical examination, spirometric evaluation, chest radiograph, and a questionnaire related to respiratory symptoms were performed. Monitoring of peak expiratory flow rates, spirometric reversibility test, and high-resolution computed tomographies were performed for the participants having respiratory symptoms and/or impaired respiratory function test. A total of 347 participants including 286 workers from production department and 61 subjects who worked in nonproduction departments were enrolled in this study. It is found that phlegm (n: 71, 20.46%) and cough (n: 52, 14.98%) were the most frequent symptoms. The other symptoms were breathlessness (n: 28, 8.06%), chest tightness (n: 14, 4.03%), and wheezing (n: 7, 2.01%) . The prevalence of occupational asthma was found to be more frequent among the subjects who worked in the production department (n: 48, 16.78% ) than the other persons who worked in the nonproduction department (n: 3, 4.91%) by chi-square test (P: 0.001). To prevent hazardous respiratory effects of the foundry production, an early diagnosis of occupational asthma is very important. Cessation of cigarette smoking and using of protective masks during the working time should be encouraged. PMID:24175093

  16. Respiratory abnormalities among workers in an iron and steel foundry.

    PubMed Central

    Johnson, A; Moira, C Y; MacLean, L; Atkins, E; Dybuncio, A; Cheng, F; Enarson, D

    1985-01-01

    A study of the health of 78 workers in an iron and steel foundry in Vancouver, British Columbia, was carried out and the results compared with those found in 372 railway repair yard workers who were not significantly exposed to air contaminants at work. The foundry workers were exposed to PepSet, which consists of diphenyl methane diisocyanate (MDI) and phenol formaldehyde and their decomposition products as well as to silica containing particulates. A questionnaire was administered by trained interviewers, and chest radiography, allergy skin tests, pulmonary function tests, and methacholine inhalation tests were carried out as well as measurement levels of dust and MDI. Compared with the controls, the foundry workers had more respiratory symptoms and a significantly lower mean FEV1 and FEF25-75% after adjustments had been made for differences in age, height, and smoking habit. Three workers (4.8%) had radiographic evidence of pneumoconiosis and 12 (18.2%) had asthma defined as presence of bronchial hyperreactivity, cough, and additional respiratory symptoms such as wheeze, chest tightness, or breathlessness. Sensitisation to MDI is probably the cause of asthma in these workers. PMID:2982392

  17. 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.

  18. 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.

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

    SciTech Connect

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

    1983-08-01

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

  20. An ontology of scientific experiments.

    PubMed

    Soldatova, Larisa N; King, Ross D

    2006-12-22

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

  1. Ontological System for Context Artifacts and Resources

    NASA Astrophysics Data System (ADS)

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

    2012-12-01

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

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

    PubMed Central

    2012-01-01

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

  3. Towards an ontological theory of substance intolerance and hypersensitivity.

    PubMed

    Hogan, William R

    2011-02-01

    A proper ontological treatment of intolerance--including hypersensitivity--to various substances is critical to patient care and research. However, existing methods and standards for documenting these conditions have flaws that inhibit these goals, especially translational research that bridges the two activities. In response, I outline a realist approach to the ontology of substance intolerance, including hypersensitivity conditions. I defend a view of these conditions as a subtype of disease. Specifically, a substance intolerance is a disease whose pathological process(es) are realized upon exposure to a quantity of substance of a particular type, and this quantity would normally not cause the realization of the pathological process(es). To develop this theory, it was necessary to build pieces of a theory of pathological processes. Overall, however, the framework of the Ontology for General Medical Science (which uses Basic Formal Ontology as its uppermost level) was a more-than-adequate foundation on which to build the theory. PMID:20152933

  4. 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.

  5. Towards an Ontological Theory of Substance Intolerance and Hypersensitivity

    PubMed Central

    Hogan, William R.

    2010-01-01

    A proper ontological treatment of intolerance—including hypersensitivity—to various substances is critical to patient care and research. However, existing methods and standards for documenting these conditions have flaws that inhibit these goals, especially translational research that bridges the two activities. In response, I outline a realist approach to the ontology of substance intolerance, including hypersensitivity conditions. I defend a view of these conditions as a subtype of disease. Specifically, a substance intolerance is a disease whose pathological process(es) are realized upon exposure to a quantity of substance of a particular type, and this quantity would normally not cause the realization of the pathological process(es). To develop this theory, it was necessary to build pieces of a theory of pathological processes. Overall, however, the framework of the Ontology for General Medical Science (which uses Basic Formal Ontology as its uppermost level) was a more-than-adequate foundation on which to build the theory. PMID:20152933

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

    PubMed

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

    2016-01-01

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

  7. Geo-Ontology: Empowering new Discoveries in Earth Sciences

    NASA Astrophysics Data System (ADS)

    Sinha, A.; Lin, K.; Raskin, R.; Barnes, C.; McGuinness, D.; Najdi, J.

    2005-12-01

    The rapid growth of data-rich resources associated with Earth and other planetary studies, including maps created by in-situ and remote sensing techniques, as well as spatial and aspatial relational databases, is driving new requirements for an information infrastructure that will facilitate scientific discovery. Ongoing research suggests that an ontology-based framework will facilitate registration, management, integration and analysis of databases and other data objects in a web-based environment. For earth scientists, ontologies can be viewed as a representation paradigm that can be used to capture formal declarative specifications of geologic objects, phenomena, and their interrelationships (e.g. subclass, part of, above, etc.). Ontologies may be used to capture classification schemes such as those for minerals, rocks, geologic time scale, or geologic structures, and thereby provide an organizational structure for automatically classifying earth science data. This is only possible because ontologies contain explicit definitions of terms used by scientists to associate meaning to the data or relationships between datasets. Ongoing development and growth of an ontology-based framework for the solid earth requires utilization of existing community-accepted high level ontologies such as SWEET (Semantic Web for Earth and Environmental Terminology) and NADM (North American Geological Data Model). The high level SWEET ontology contains formal definitions for terms used in earth and space sciences, and it encodes structure that recognizes the spatial distribution of earth environments (earth realm) and the interfaces between different realms. These earth realms have associated properties with appropriate units and provide an extensible upper level terminology. Extension of these concepts to high-resolution ontologies where data reside is well underway. For example, we have developed new ontology-based packages containing Planetary Materials (elements, isotopes, rocks

  8. The SWAN Scientific Discourse Ontology

    PubMed Central

    Ciccarese, Paolo; Wu, Elizabeth; Kinoshita, June; Wong, Gwendolyn T.; Ocana, Marco; Ruttenberg, Alan

    2015-01-01

    SWAN (Semantic Web Application in Neuromedicine) is a project to construct a semantically-organized, community-curated, distributed knowledge base of Theory, Evidence, and Discussion in biomedicine. Unlike Wikipedia and similar approaches, SWAN’s ontology is designed to represent and foreground both harmonizing and contradictory assertions within the total community discourse. Releases of the software, content and ontology will be initially by and for the Alzheimer Disease (AD) research community, with the obvious potential for extension into other disease research areas. The Alzheimer Research Forum, a 4,000-member web community for AD researchers, will host SWAN’s initial public release, currently scheduled for late 2007. This paper presents the current version of SWAN’s ontology of scientific discourse and presents our current thinking about its evolution including extensions and alignment with related communities, projects and ontologies. PMID:18583197

  9. 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.

  10. 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)...

  11. 77 FR 15123 - Foundry Coke From China; Scheduling of an Expedited Five-Year Review

    Federal Register 2010, 2011, 2012, 2013, 2014

    2012-03-14

    ... its notice of institution (76 FR 74810, December 1, 2011) of the subject five-year review was adequate... COMMISSION Foundry Coke From China; Scheduling of an Expedited Five-Year Review AGENCY: United States...)) (the Act) to determine whether revocation of the antidumping duty order on foundry coke from...

  12. 40 CFR 63.10900 - What parts of the General Provisions apply to my large foundry?

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... requirements of the General Provisions (40 CFR part 63, subpart A) according to Table 3 of this subpart. (b) If... apply to my large foundry? 63.10900 Section 63.10900 Protection of Environment ENVIRONMENTAL PROTECTION... Foundries Area Sources Requirements for New and Existing Affected Sources Classified As Large Iron and...

  13. Amelioration of physical strength in waste foundry green sands for reuse as a soil amendment

    Technology Transfer Automated Retrieval System (TEKTRAN)

    As available landfill space and profit margins steadily decrease, it becomes more important for U.S. foundries to find ways of diverting 8-12 million tons of waste foundry sand (WFS) away from landfills each year. A major drawback to the reuse of some WFSs as a soil amendment is their high soil str...

  14. COMPOSTING WASTE FOUNDRY SAND WITH LEAVES TO AMEND ADVERSE PHYSICAL PROPERTIES

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Indiana ranks second in the nation in waste foundry sand production with one million tons annually disposed in landfills. As available landfill space and profit margins steadily decrease, it becomes more important to find ways of diverting waste foundry sand away from landfills and identify benefici...

  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. 76 FR 74810 - Foundry Coke From China; Institution of a Five-Year Review

    Federal Register 2010, 2011, 2012, 2013, 2014

    2011-12-01

    ..., and F (19 CFR part 207), as most recently amended at 76 FR 61937 (October 6, 2011). \\1\\ No response to... duty order on imports of foundry coke from China (66 FR 48025). Following five-year reviews by Commerce... order on imports of foundry coke from China (72 FR 1214). The Commission is now conducting a...

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

    Code of Federal Regulations, 2010 CFR

    2010-07-01

    ... CATEGORIES (CONTINUED) National Emission Standards for Hazardous Air Pollutants for Iron and Steel Foundries... source is each new or existing iron and steel foundry. (b) This subpart covers emissions from metal... lines, automated shakeout lines, and mold and core making lines. This subpart also covers...

  18. SWEET 2.1 Ontologies

    NASA Astrophysics Data System (ADS)

    Raskin, R. G.

    2010-12-01

    The Semantic Web for Earth and Environmental Terminology (SWEET) ontologies represent a mid- to upper-level concept space for all of Earth and Planetary Science and associated data and applications The latest version (2.1) has been reorganized to improve long-term maintainability. Accompanying the ontologies is a mapping to the CF Standard Name Table and the GCMD Science Keywords. As a higher level concept space, terms can be readily mapped across these vocabularies through the intermediate use of SWEET.

  19. COnto-Diff: generation of complex evolution mappings for life science ontologies.

    PubMed

    Hartung, Michael; Groß, Anika; Rahm, Erhard

    2013-02-01

    Life science ontologies evolve frequently to meet new requirements or to better reflect the current domain knowledge. The development and adaptation of large and complex ontologies is typically performed collaboratively by several curators. To effectively manage the evolution of ontologies it is essential to identify the difference (Diff) between ontology versions. Such a Diff supports the synchronization of changes in collaborative curation, the adaptation of dependent data such as annotations, and ontology version management. We propose a novel approach COnto-Diff to determine an expressive and invertible diff evolution mapping between given versions of an ontology. Our approach first matches the ontology versions and determines an initial evolution mapping consisting of basic change operations (insert/update/delete). To semantically enrich the evolution mapping we adopt a rule-based approach to transform the basic change operations into a smaller set of more complex change operations, such as merge, split, or changes of entire subgraphs. The proposed algorithm is customizable in different ways to meet the requirements of diverse ontologies and application scenarios. We evaluate the proposed approach for large life science ontologies including the Gene Ontology and the NCI Thesaurus and compare it with PromptDiff. We further show how the Diff results can be used for version management and annotation migration in collaborative curation. PMID:22580476

  20. Semantic enrichment for medical ontologies.

    PubMed

    Lee, Yugyung; Geller, James

    2006-04-01

    The Unified Medical Language System (UMLS) contains two separate but interconnected knowledge structures, the Semantic Network (upper level) and the Metathesaurus (lower level). In this paper, we have attempted to work out better how the use of such a two-level structure in the medical field has led to notable advances in terminologies and ontologies. However, most ontologies and terminologies do not have such a two-level structure. Therefore, we present a method, called semantic enrichment, which generates a two-level ontology from a given one-level terminology and an auxiliary two-level ontology. During semantic enrichment, concepts of the one-level terminology are assigned to semantic types, which are the building blocks of the upper level of the auxiliary two-level ontology. The result of this process is the desired new two-level ontology. We discuss semantic enrichment of two example terminologies and how we approach the implementation of semantic enrichment in the medical domain. This implementation performs a major part of the semantic enrichment process with the medical terminologies, with difficult cases left to a human expert. PMID:16185937

  1. Mortality at an automotive engine foundry and machining complex.

    PubMed

    Park, R M

    2001-05-01

    Mortality was analyzed for an automotive engine foundry and machining complex, with process exposures derived from department assignments. Logistic regression models of mortality odds ratios (ORs) were calculated for 2546 deaths, and numbers of work-related deaths were estimated. Lung cancer mortality in the foundry was increased where cleaning and finishing of castings was performed (OR, 1.7; 95% CI, 1.15 to 2.4 [at mean exposure duration of exposed cases]) and in care-making after 1967 (OR, 1.5; 95% CI, 1.11 to 2.0). Black workers had excess lung cancer mortality in machining heat-treat operations (OR, 2.5, 95% CI, 1.4 to 4.3) and excess nonmalignant respiratory disease mortality in molding (OR, 2.5; 95% CI, 1.16 to 5.5) and core-making (OR, 2.7; 95% CI, 1.25 to 5.8). Stomach cancer mortality was elevated among workers with metalworking fluid exposures in precision grinding (OR, 2.4; 95% CI, 1.14 to 5.1). Heart disease mortality was increased among all workers in molding (OR, 1.6; 95% CI, 1.09 to 2.3), as was stroke mortality among workers exposed to metalworking fluids (OR, 1.8; 95% CI, 1.22 to 2.7). Malignant and nonmalignant liver disease mortality was elevated in assembly/testing and precision grinding. In this modern foundry, 11% of deaths were estimated to be work-related despite it's being largely in regulatory compliance over its 40-year existence. Machining plant exposures accounted for 3% or more of deaths there. PMID:11382184

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

    PubMed

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

    2006-01-01

    The central hypothesis underlying this communication is that the methodology and conceptual rigor of a philosophically inspired formal ontology can bring significant benefits in the development and maintenance of application ontologies [A. Flett, M. Dos Santos, W. Ceusters, Some Ontology Engineering Procedures and their Supporting Technologies, EKAW2002, 2003]. This hypothesis has been tested in the collaboration between Language and Computing (L&C), a company specializing in software for supporting natural language processing especially in the medical field, and the Institute for Formal Ontology and Medical Information Science (IFOMIS), an academic research institution concerned with the theoretical foundations of ontology. In the course of this collaboration L&C's ontology, LinKBase, which is designed to integrate and support reasoning across a plurality of external databases, has been subjected to a thorough auditing on the basis of the principles underlying IFOMIS's Basic Formal Ontology (BFO) [B. Smith, Basic Formal Ontology, 2002. http://ontology.buffalo.edu/bfo]. The goal is to transform a large terminology-based ontology into one with the ability to support reasoning applications. Our general procedure has been the implementation of a meta-ontological definition space in which the definitions of all the concepts and relations in LinKBase are standardized in the framework of first-order logic. In this paper we describe how this principles-based standardization has led to a greater degree of internal coherence of the LinKBase structure, and how it has facilitated the construction of mappings between external databases using LinKBase as translation hub. We argue that the collaboration here described represents a new phase in the quest to solve the so-called "Tower of Babel" problem of ontology integration [F. Montayne, J. Flanagan, Formal Ontology: The Foundation for Natural Language Processing, 2003. http://www.landcglobal.com/]. PMID:16153885

  3. 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

  4. A task-based approach for Gene Ontology evaluation

    PubMed Central

    2013-01-01

    Background The Gene Ontology and its associated annotations are critical tools for interpreting lists of genes. Here, we introduce a method for evaluating the Gene Ontology annotations and structure based on the impact they have on gene set enrichment analysis, along with an example implementation. This task-based approach yields quantitative assessments grounded in experimental data and anchored tightly to the primary use of the annotations. Results Applied to specific areas of biological interest, our framework allowed us to understand the progress of annotation and structural ontology changes from 2004 to 2012. Our framework was also able to determine that the quality of annotations and structure in the area under test have been improving in their ability to recall underlying biological traits. Furthermore, we were able to distinguish between the impact of changes to the annotation sets and ontology structure. Conclusion Our framework and implementation lay the groundwork for a powerful tool in evaluating the usefulness of the Gene Ontology. We demonstrate both the flexibility and the power of this approach in evaluating the current and past state of the Gene Ontology as well as its applicability in developing new methods for creating gene annotations. PMID:23734599

  5. Structuring an event ontology for disease outbreak detection

    PubMed Central

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

    2008-01-01

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

  6. 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. PMID:26529777

  7. Ontological Approach to Reduce Complexity in Polypharmacy

    PubMed Central

    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. PMID:24551346

  8. Automated Database Mediation Using Ontological Metadata Mappings

    PubMed Central

    Marenco, Luis; Wang, Rixin; Nadkarni, Prakash

    2009-01-01

    Objective To devise an automated approach for integrating federated database information using database ontologies constructed from their extended metadata. Background One challenge of database federation is that the granularity of representation of equivalent data varies across systems. Dealing effectively with this problem is analogous to dealing with precoordinated vs. postcoordinated concepts in biomedical ontologies. Model Description The authors describe an approach based on ontological metadata mapping rules defined with elements of a global vocabulary, which allows a query specified at one granularity level to fetch data, where possible, from databases within the federation that use different granularities. This is implemented in OntoMediator, a newly developed production component of our previously described Query Integrator System. OntoMediator's operation is illustrated with a query that accesses three geographically separate, interoperating databases. An example based on SNOMED also illustrates the applicability of high-level rules to support the enforcement of constraints that can prevent inappropriate curator or power-user actions. Summary A rule-based framework simplifies the design and maintenance of systems where categories of data must be mapped to each other, for the purpose of either cross-database query or for curation of the contents of compositional controlled vocabularies. PMID:19567801

  9. 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.

  10. CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives

    PubMed Central

    Tao, Cui; Solbrig, Harold R.; Chute, Christopher G.

    2011-01-01

    The Clinical Narrative Temporal Relation Ontology (CNTRO) has been developed for the purpose of allowing temporal information of clinical data to be semantically annotated and queried, and using inference to expose new temporal features and relations based on the semantic assertions and definitions of the temporal aspects in the ontology. While CNTRO provides a formal semantic foundation to leverage the semantic-web techniques, it is still necessary to arrive at a shared set of semantics and operational rules with commonly used ontologies for the time domain. This paper introduces CNTRO 2.0, which tries to harmonize CNTRO 1.0 and a list of existing time ontologies or top-level ontologies into a unified model—an OWL based ontology of temporal relations for clinical research. PMID:22211182

  11. CNTRO 2.0: A Harmonized Semantic Web Ontology for Temporal Relation Inferencing in Clinical Narratives.

    PubMed

    Tao, Cui; Solbrig, Harold R; Chute, Christopher G

    2011-01-01

    The Clinical Narrative Temporal Relation Ontology (CNTRO) has been developed for the purpose of allowing temporal information of clinical data to be semantically annotated and queried, and using inference to expose new temporal features and relations based on the semantic assertions and definitions of the temporal aspects in the ontology. While CNTRO provides a formal semantic foundation to leverage the semantic-web techniques, it is still necessary to arrive at a shared set of semantics and operational rules with commonly used ontologies for the time domain. This paper introduces CNTRO 2.0, which tries to harmonize CNTRO 1.0 and a list of existing time ontologies or top-level ontologies into a unified model-an OWL based ontology of temporal relations for clinical research. PMID:22211182

  12. The @neurIST ontology of intracranial aneurysms: providing terminological services for an integrated IT infrastructure.

    PubMed

    Boeker, Martin; Stenzhorn, Holger; Kumpf, Kai; Bijlenga, Philippe; Schulz, Stefan; Hanser, Susanne

    2007-01-01

    The @neurIST ontology is currently under development within the scope of the European project @neurIST intended to serve as a module in a complex architecture aiming at providing a better understanding and management of intracranial aneurysms and subarachnoid hemorrhages. Due to the integrative structure of the project the ontology needs to represent entities from various disciplines on a large spatial and temporal scale. Initial term acquisition was performed by exploiting a database scaffold, literature analysis and communications with domain experts. The ontology design is based on the DOLCE upper ontology and other existing domain ontologies were linked or partly included whenever appropriate (e.g., the FMA for anatomical entities and the UMLS for definitions and lexical information). About 2300 predominantly medical entities were represented but also a multitude of biomolecular, epidemiological, and hemodynamic entities. The usage of the ontology in the project comprises terminological control, text mining, annotation, and data mediation. PMID:18693797

  13. 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

  14. Proceedings of a Sickle Cell Disease Ontology workshop - Towards the first comprehensive ontology for Sickle Cell Disease.

    PubMed

    Mulder, Nicola; Nembaware, Victoria; Adekile, Adekunle; Anie, Kofi A; Inusa, Baba; Brown, Biobele; Campbell, Andrew; Chinenere, Furahini; Chunda-Liyoka, Catherine; Derebail, Vimal K; Geard, Amy; Ghedira, Kais; Hamilton, Carol M; Hanchard, Neil A; Haendel, Melissa; Huggins, Wayne; Ibrahim, Muntaser; Jupp, Simon; Kamga, Karen Kengne; Knight-Madden, Jennifer; Lopez-Sall, Philomène; Mbiyavanga, Mamana; Munube, Deogratias; Nirenberg, Damian; Nnodu, Obiageli; Ofori-Acquah, Solomon Fiifi; Ohene-Frempong, Kwaku; Opap, Kenneth Babu; Panji, Sumir; Park, Miriam; Pule, Gift; Royal, Charmaine; Sangeda, Raphael; Tayo, Bamidele; Treadwell, Marsha; Tshilolo, Léon; Wonkam, Ambroise

    2016-06-01

    Sickle cell disease (SCD) is a debilitating single gene disorder caused by a single point mutation that results in physical deformation (i.e. sickling) of erythrocytes at reduced oxygen tensions. Up to 75% of SCD in newborns world-wide occurs in sub-Saharan Africa, where neonatal and childhood mortality from sickle cell related complications is high. While SCD research across the globe is tackling the disease on multiple fronts, advances have yet to significantly impact on the health and quality of life of SCD patients, due to lack of coordination of these disparate efforts. Ensuring data across studies is directly comparable through standardization is a necessary step towards realizing this goal. Such a standardization requires the development and implementation of a disease-specific ontology for SCD that is applicable globally. Ontology development is best achieved by bringing together experts in the domain to contribute their knowledge. The SCD community and H3ABioNet members joined forces at a recent SCD Ontology workshop to develop an ontology covering aspects of SCD under the classes: phenotype, diagnostics, therapeutics, quality of life, disease modifiers and disease stage. The aim of the workshop was for participants to contribute their expertise to development of the structure and contents of the SCD ontology. Here we describe the proceedings of the Sickle Cell Disease Ontology Workshop held in Cape Town South Africa in February 2016 and its outcomes. The objective of the workshop was to bring together experts in SCD from around the world to contribute their expertise to the development of various aspects of the SCD ontology. PMID:27354937

  15. 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

  16. Ultrafine and respirable particles in an automotive grey iron foundry.

    PubMed

    Evans, Douglas E; Heitbrink, William A; Slavin, Thomas J; Peters, Thomas M

    2008-01-01

    Ultrafine particle number and respirable particle mass concentrations were measured throughout an automotive grey iron foundry during winter, spring and summer using a particle concentration mapping procedure. Substantial temporal and spatial variability was observed in all seasons and attributed, in part, to the batch nature of operations, process emission variability and frequent work interruptions. The need for fine mapping grids was demonstrated, where elevations in particle concentrations were highly localized. Ultrafine particle concentrations were generally greatest during winter when incoming make-up air was heated with direct fire, natural gas burners. Make-up air drawn from roof level had elevated respirable mass and ultrafine number concentrations above ambient outdoor levels, suggesting inadvertent recirculation of foundry process emissions. Elevated respirable mass concentrations were highly localized on occasions (e.g. abrasive blasting and grinding), depended on the area within the facility where measurements were obtained, but were largely unaffected by season. Particle sources were further characterized by measuring their respective number and mass concentrations by particle size. Sources that contributed to ultrafine particles included process-specific sources (e.g. melting and pouring operations), and non-process sources (e.g. direct fire natural gas heating units, a liquid propane-fuelled sweeper and cigarette smoking) were additionally identified. PMID:18056626

  17. 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.

  18. Reducing exposures during the pouring operations of a brass foundry.

    PubMed

    Edmonds, M A; Gressel, M G; O'Brien, D M; Clark, N J

    1993-05-01

    The focus of this exposure assessment and control technology study was a brass foundry and the lead exposures of workers involved in the transportation and pouring of metal. Controls in place at the foundry included ventilation systems at the furnace and along the continuous and stationary pouring lines. Real-time measurements were made to determine which tasks were the primary exposure sources, and a hand-held aerosol monitor was used to measure real-time aerosol exposures (as a surrogate for lead) in the workers' breathing zones. Data were collected over two 30-min sampling periods while worker activities were monitored using a video camera. Analysis of the data showed that the greatest aerosol exposures occurred during the transportation of an unventilated, full ladle, resulting in an average concentration of at least twice that of the other tasks. The study concluded that the addition of exhaust ventilation such as a moveable hood and duct system during the ladle transport and pouring tasks, and the implementation of a side draft hood at the pigging area, could result in a reduction of worker exposure to aerosols during the continuous pouring operation by up to 40%. The controls and techniques suggested in this study could be applied to pouring operations throughout the industry to reduce worker exposure to metal fumes. PMID:8498361

  19. DataFoundry: information management for scientific data.

    PubMed

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

    2000-03-01

    Data warehouses and data marts have been successfully applied to a multitude of commercial business applications. They have proven to be invaluable tools by integrating information from distributed, heterogeneous sources and summarizing this data for use throughout the enterprise. Although the need for information dissemination is as vital in science as in business, working warehouses in this community are scarce because traditional warehousing techniques do not transfer to scientific environments. There are two primary reasons for this difficulty. First, schema integration is more difficult for scientific databases than for business sources, because of the complexity of the concepts and the associated relationships. While this difference has not yet been fully explored, it is an important consideration when determining how to integrate autonomous sources. Second, scientific data sources have highly dynamic data representations (schemata). When a data source participating in a warehouse changes its schema, both the mediator transferring data to the warehouse and the warehouse itself need to be updated to reflect these modifications. The cost of repeatedly performing these updates in a traditional warehouse, as is required in a dynamic environment, is prohibitive. This paper discusses these issues within the context of the DataFoundry project, an ongoing research effort at Lawrence Livermore National Laboratory. DataFoundry utilizes a unique integration strategy to identify corresponding instances while maintaining differences between data from different sources, and a novel architecture and an extensive meta-data infrastructure, which reduce the cost of maintaining a warehouse. PMID:10761774

  20. 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

  1. 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

  2. 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

  3. 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.

  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. 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.

  7. 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.

  8. 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

  9. 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

  10. 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.

  11. The semantic metadatabase (SEMEDA): ontology based integration of federated molecular biological data sources.

    PubMed

    Köhler, Jacob; Schulze-Kremer, Steffen

    2002-01-01

    A system for "intelligent" semantic integration and querying of federated databases is being implemented by using three main components: A component which enables SQL access to integrated databases by database federation (MARGBench), an ontology based semantic metadatabase (SEMEDA) and an ontology based query interface (SEMEDA-query). In this publication we explain and demonstrate the principles, architecture and the use of SEMEDA. Since SEMEDA is implemented as 3 tiered web application database providers can enter all relevant semantic and technical information about their databases by themselves via a web browser. SEMEDA' s collaborative ontology editing feature is not restricted to database integration, and might also be useful for ongoing ontology developments, such as the "Gene Ontology" [2]. SEMEDA can be found at http://www-bm.cs.uni-magdeburg.de/semeda/. We explain how this ontologically structured information can be used for semantic database integration. In addition, requirements to ontologies for molecular biological database integration are discussed and relevant existing ontologies are evaluated. We further discuss how ontologies and structured knowledge sources can be used in SEMEDA and whether they can be merged supplemented or updated to meet the requirements for semantic database integration. PMID:12542408

  12. 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.

  13. 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

  14. 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

  15. Techni-Cast: Foundry Saves Energy with Compressed Air System Retrofit

    SciTech Connect

    none,

    2004-03-01

    In 2002, Techni-Cast improved its compressed air system at its foundry in Southgate, California. The project allowed the foundry to reduce its compressor capacity by 50%, which greatly reduced the foundry's energy and maintenance costs. The annual energy and maintenance savings from the project implementation are 242,000 kWh and $24,200, and the project's cost was $38,000. Because the plant received a $10,000 incentive payment from the California Public Utilities Commission, the total project cost was reduced to $28,000, yielding a 14-month simple payback.

  16. Techni-Cast: Foundry Saves Energy with Compressed Air System Retrofit

    SciTech Connect

    Not Available

    2001-03-01

    In 2002, Techni-Cast improved its compressed air system at its foundry in Southgate, California. The project allowed the foundry to reduce its compressor capacity by 50%, which greatly reduced the foundry's energy and maintenance costs. The annual energy and maintenance savings from the project implementation are 242,000 kWh and $24,200, and the projects cost was $38,000. Because the plant received a $10,000 incentive payment from the California Public Utilities Commission, the total project cost was reduced to $28,000, yielding a 14-month simple payback.

  17. Evolving BioAssay Ontology (BAO): modularization, integration and applications

    PubMed Central

    2014-01-01

    The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and

  18. Evolving BioAssay Ontology (BAO): modularization, integration and applications.

    PubMed

    Abeyruwan, Saminda; Vempati, Uma D; Küçük-McGinty, Hande; Visser, Ubbo; Koleti, Amar; Mir, Ahsan; Sakurai, Kunie; Chung, Caty; Bittker, Joshua A; Clemons, Paul A; Brudz, Steve; Siripala, Anosha; Morales, Arturo J; Romacker, Martin; Twomey, David; Bureeva, Svetlana; Lemmon, Vance; Schürer, Stephan C

    2014-01-01

    The lack of established standards to describe and annotate biological assays and screening outcomes in the domain of drug and chemical probe discovery is a severe limitation to utilize public and proprietary drug screening data to their maximum potential. We have created the BioAssay Ontology (BAO) project (http://bioassayontology.org) to develop common reference metadata terms and definitions required for describing relevant information of low-and high-throughput drug and probe screening assays and results. The main objectives of BAO are to enable effective integration, aggregation, retrieval, and analyses of drug screening data. Since we first released BAO on the BioPortal in 2010 we have considerably expanded and enhanced BAO and we have applied the ontology in several internal and external collaborative projects, for example the BioAssay Research Database (BARD). We describe the evolution of BAO with a design that enables modeling complex assays including profile and panel assays such as those in the Library of Integrated Network-based Cellular Signatures (LINCS). One of the critical questions in evolving BAO is the following: how can we provide a way to efficiently reuse and share among various research projects specific parts of our ontologies without violating the integrity of the ontology and without creating redundancies. This paper provides a comprehensive answer to this question with a description of a methodology for ontology modularization using a layered architecture. Our modularization approach defines several distinct BAO components and separates internal from external modules and domain-level from structural components. This approach facilitates the generation/extraction of derived ontologies (or perspectives) that can suit particular use cases or software applications. We describe the evolution of BAO related to its formal structures, engineering approaches, and content to enable modeling of complex assays and integration with other ontologies and

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

    PubMed

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

    2013-01-01

    Epidemiological monitoring of the schistosomiasis' spreading brings together many practitioners working at different levels of granularity (biology, host individual, host population), who have different perspectives (biology, clinic and epidemiology) on the same phenomenon. Biological perspective deals with pathogens (e.g. life cycle) or physiopathology while clinical perspective deals with hosts (e.g. healthy or infected host, diagnosis, treatment, etc.). In an epidemiological perspective corresponding to the host population level of granularity, the schistosomiasis disease is characterized according to the way (causes, risk factors, etc.) it spreads in this population over space and time. In this paper we provide an ontological analysis and design for the Schistosomiasis domain knowledge and spreading dynamics. IDOSCHISTO - the schistosomiasis ontology - is designed as an extension of the Infectious Disease Ontology (IDO). This ontology aims at supporting the schistosomiasis monitoring process during a spreading crisis by enabling data integration, semantic interoperability, for collaborative work on one hand and for risk analysis and decision making on the other hand. PMID:23920598

  20. 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. PMID:26519402

  1. 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…

  2. 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...

  3. The construction and practice of GIS ontology service mechanism

    NASA Astrophysics Data System (ADS)

    Yang, Kun; Wang, Jun; Peng, Shuang-yun; Cheng, Hong-ping

    2005-10-01

    With the development of Semantic Web technology, the spatial information service based on ontology is an effective way for sharing and interoperation of heterogeneous information resources in the distributed network environment. Based on the deep analysis for the spatial information service mechanism of geo-ontology, the system construction strategy and service workflow and combined with the present mainstream commercial GIS software packages, three solutions of system construction for spatial information sharing and interoperation have been proposed here in this paper. The different geographic information application systems distributed on the internet may be integrated dynamically and openly by using one of the three solutions for realizing the sharing and interoperation of heterogeneous spatial information resources in the distributing environment. In order to realize the practical applications of spatial information sharing and interoperation in different brunches of police system, a prototype system for crime case information sharing based on geo-ontology has also been developed by using the methods described above.

  4. OntoSoft: An Ontology for Capturing Scientific Software Metadata

    NASA Astrophysics Data System (ADS)

    Gil, Y.

    2015-12-01

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

  5. 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.

  6. Lead poisoning in a foundry--New Jersey, 1990

    SciTech Connect

    Not Available

    1991-11-29

    In May 1990, the New Jersey State Department of Health (NJSDH) received laboratory reports of elevated blood lead levels (( BLLs) greater than or equal to 25 micrograms/dL) for 13 workers employed at a small foundry in New Jersey. Six of the workers had BLLs that exceeded 60 micrograms/dL; the highest was 277 micrograms/dL. According to the Occupational Safety and Health Administration's (OSHA) lead standard,* these six persons should have been removed immediately from further exposure to lead until their BLLs returned to acceptable ranges. NJSDH contacted the persons with elevated BLLs to obtain additional information about their lead exposures and health status. None of these persons had been evaluated medically or removed from the source of lead exposure.

  7. 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

  8. Describing the Breakbone Fever: IDODEN, an Ontology for Dengue Fever

    PubMed Central

    Mitraka, Elvira; Topalis, Pantelis; Dritsou, Vicky; Dialynas, Emmanuel; Louis, Christos

    2015-01-01

    Background Ontologies represent powerful tools in information technology because they enhance interoperability and facilitate, among other things, the construction of optimized search engines. To address the need to expand the toolbox available for the control and prevention of vector-borne diseases we embarked on the construction of specific ontologies. We present here IDODEN, an ontology that describes dengue fever, one of the globally most important diseases that are transmitted by mosquitoes. Methodology/Principal Findings We constructed IDODEN using open source software, and modeled it on IDOMAL, the malaria ontology developed previously. IDODEN covers all aspects of dengue fever, such as disease biology, epidemiology and clinical features. Moreover, it covers all facets of dengue entomology. IDODEN, which is freely available, can now be used for the annotation of dengue-related data and, in addition to its use for modeling, it can be utilized for the construction of other dedicated IT tools such as decision support systems. Conclusions/Significance The availability of the dengue ontology will enable databases hosting dengue-associated data and decision-support systems for that disease to perform most efficiently and to link their own data to those stored in other independent repositories, in an architecture- and software-independent manner. PMID:25646954

  9. 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

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

    PubMed

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

    2008-09-01

    A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neuroscience-relevant resources. Although the original NIF specification called for a loosely structured controlled vocabulary for describing neuroscience resources, as the NIF system evolved, the requirement for a formally structured ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious. This requirement led to the NIF standardized (NIFSTD) ontology, a comprehensive collection of common neuroscience domain terminologies woven into an ontologically consistent, unified representation of the biomedical domains typically used to describe neuroscience data (e.g., anatomy, cell types, techniques), as well as digital resources (tools, databases) being created throughout the neuroscience community. NIFSTD builds upon a structure established by the BIRNLex, a lexicon of concepts covering clinical neuroimaging research developed by the Biomedical Informatics Research Network (BIRN) project. Each distinct domain module is represented using the Web Ontology Language (OWL). As much as has been practical, NIFSTD reuses existing community ontologies that cover the required biomedical domains, building the more specific concepts required to annotate NIF resources. By following this principle, an extensive vocabulary was assembled in a relatively short period of time for NIF information annotation, organization, and retrieval, in a form that promotes easy extension and modification. We report here on the structure of the NIFSTD, and its predecessor BIRNLex, the principles followed in its construction and provide examples of its use within NIF. PMID:18975148

  11. 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

  12. Domain ontologies in software engineering: use of Protégé with the EON architecture.

    PubMed

    Musen, M A

    1998-11-01

    Domain ontologies are formal descriptions of the classes of concepts and the relationships among those concepts that describe an application area. The Protégé software-engineering methodology provides a clear division between domain ontologies and domain-independent problem-solvers that, when mapped to domain ontologies, can solve application tasks. The Protégé approach allows domain ontologies to inform the total software-engineering process, and for ontologies to be shared among a variety of problem-solving components. We illustrate the approach by describing the development of EON, a set of middleware components that automate various aspects of protocol-directed therapy. Our work illustrates the organizing effect that domain ontologies can have on the software-development process. Ontologies, like all formal representations, have limitations in their ability to capture the semantics of application areas. Nevertheless, the capability of ontologies to encode clinical distinctions not usually captured by controlled medical terminologies provides significant advantages for developers and maintainers of clinical software applications. PMID:9865052

  13. 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.

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

    PubMed Central

    2013-01-01

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

  15. 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

  16. 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.

  17. Semantic Similarity in Biomedical Ontologies

    PubMed Central

    Pesquita, Catia; Faria, Daniel; Falcão, André O.; Lord, Phillip; Couto, Francisco M.

    2009-01-01

    In recent years, ontologies have become a mainstream topic in biomedical research. When biological entities are described using a common schema, such as an ontology, they can be compared by means of their annotations. This type of comparison is called semantic similarity, since it assesses the degree of relatedness between two entities by the similarity in meaning of their annotations. The application of semantic similarity to biomedical ontologies is recent; nevertheless, several studies have been published in the last few years describing and evaluating diverse approaches. Semantic similarity has become a valuable tool for validating the results drawn from biomedical studies such as gene clustering, gene expression data analysis, prediction and validation of molecular interactions, and disease gene prioritization. We review semantic similarity measures applied to biomedical ontologies and propose their classification according to the strategies they employ: node-based versus edge-based and pairwise versus groupwise. We also present comparative assessment studies and discuss the implications of their results. We survey the existing implementations of semantic similarity measures, and we describe examples of applications to biomedical research. This will clarify how biomedical researchers can benefit from semantic similarity measures and help them choose the approach most suitable for their studies. Biomedical ontologies are evolving toward increased coverage, formality, and integration, and their use for annotation is increasingly becoming a focus of both effort by biomedical experts and application of automated annotation procedures to create corpora of higher quality and completeness than are currently available. Given that semantic similarity measures are directly dependent on these evolutions, we can expect to see them gaining more relevance and even becoming as essential as sequence similarity is today in biomedical research. PMID:19649320

  18. Lightweight Community-Driven Ontology Evolution

    NASA Astrophysics Data System (ADS)

    Siorpaes, Katharina

    Only few well-maintained domain ontologies can be found on the Web. The likely reasons for the lack of useful domain ontologies include that (1) informal means to convey intended meaning more efficiently are used for ontology specification only to a very limited extent, (2) many relevant domains of discourse show a substantial degree of conceptual dynamics, (3) ontology representation languages are hard to understand for the majority of (potential) ontology users and domain experts, and (4) the community does not have control over the ontology evolution. In this thesis, we propose to (1) ground a methodology for community-grounded ontology building on the culture and philosophy of wikis by giving users who have no or little expertise in ontology engineering the opportunity to contribute in all stages of the ontology lifecycle and (2) exploit the combination of human and computational intelligence to discover and resolve inconsistencies and align lightweight domain ontologies. The contribution of this thesis is a methodology and prototype for community-grounded building and evolution of lightweight domain ontologies.

  19. Scalable representations of diseases in biomedical ontologies

    PubMed Central

    2011-01-01

    Background The realm of pathological entities can be subdivided into pathological dispositions, pathological processes, and pathological structures. The latter are the bearer of dispositions, which can then be realized by their manifestations — pathologic processes. Despite its ontological soundness, implementing this model via purpose-oriented domain ontologies will likely require considerable effort, both in ontology construction and maintenance, which constitutes a considerable problem for SNOMED CT, presently the largest biomedical ontology. Results We describe an ontology design pattern which allows ontologists to make assertions that blur the distinctions between dispositions, processes, and structures until necessary. Based on the domain upper-level ontology BioTop, it permits ascriptions of location and participation in the definition of pathological phenomena even without an ontological commitment to a distinction between these three categories. An analysis of SNOMED CT revealed that numerous classes in the findings/disease hierarchy are ambiguous with respect to process vs. disposition. Here our proposed approach can easily be applied to create unambiguous classes. No ambiguities could be defined regarding the distinction of structure and non-structure classes, but here we have found problematic duplications. Conclusions We defend a judicious use of disjunctive, and therefore ambiguous, classes in biomedical ontologies during the process of ontology construction and in the practice of ontology application. The use of these classes is permitted to span across several top-level categories, provided it contributes to ontology simplification and supports the intended reasoning scenarios. PMID:21624161

  20. 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

  1. Ontology-based federated data access to human studies information.

    PubMed

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

    2012-01-01

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

  2. 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

  3. From classification to epilepsy ontology and informatics.

    PubMed

    Zhang, Guo-Qiang; Sahoo, Satya S; Lhatoo, Samden D

    2012-07-01

    The 2010 International League Against Epilepsy (ILAE) classification and terminology commission report proposed a much needed departure from previous classifications to incorporate advances in molecular biology, neuroimaging, and genetics. It proposed an interim classification and defined two key requirements that need to be satisfied. The first is the ability to classify epilepsy in dimensions according to a variety of purposes including clinical research, patient care, and drug discovery. The second is the ability of the classification system to evolve with new discoveries. Multidimensionality and flexibility are crucial to the success of any future classification. In addition, a successful classification system must play a central role in the rapidly growing field of epilepsy informatics. An epilepsy ontology, based on classification, will allow information systems to facilitate data-intensive studies and provide a proven route to meeting the two foregoing key requirements. Epilepsy ontology will be a structured terminology system that accommodates proposed and evolving ILAE classifications, the National Institutes of Health/National Institute of Neurological Disorders and Stroke (NIH/NINDS) Common Data Elements, the International Classification of Diseases (ICD) systems and explicitly specifies all known relationships between epilepsy concepts in a proper framework. This will aid evidence-based epilepsy diagnosis, investigation, treatment and research for a diverse community of clinicians and researchers. Benefits range from systematization of electronic patient records to multimodal data repositories for research and training manuals for those involved in epilepsy care. Given the complexity, heterogeneity, and pace of research advances in the epilepsy domain, such an ontology must be collaboratively developed by key stakeholders in the epilepsy community and experts in knowledge engineering and computer science. PMID:22765502

  4. From Classification to Epilepsy Ontology and Informatics

    PubMed Central

    Zhang, Guo-Qiang; Sahoo, Satya S; Lhatoo, Samden D

    2012-01-01

    Summary The 2010 International League Against Epilepsy (ILAE) classification and terminology commission report proposed a much needed departure from previous classifications to incorporate advances in molecular biology, neuroimaging, and genetics. It proposed an interim classification and defined two key requirements that need to be satisfied. The first is the ability to classify epilepsy in dimensions according to a variety of purposes including clinical research, patient care, and drug discovery. The second is the ability of the classification system to evolve with new discoveries. Multi-dimensionality and flexibility are crucial to the success of any future classification. In addition, a successful classification system must play a central role in the rapidly growing field of epilepsy informatics. An epilepsy ontology, based on classification, will allow information systems to facilitate data-intensive studies and provide a proven route to meeting the two foregoing key requirements. Epilepsy ontology will be a structured terminology system that accommodates proposed and evolving ILAE classifications, the NIH/NINDS Common Data Elements, the ICD systems and explicitly specifies all known relationships between epilepsy concepts in a proper framework. This will aid evidence based epilepsy diagnosis, investigation, treatment and research for a diverse community of clinicians and researchers. Benefits range from systematization of electronic patient records to multi-modal data repositories for research and training manuals for those involved in epilepsy care. Given the complexity, heterogeneity and pace of research advances in the epilepsy domain, such an ontology must be collaboratively developed by key stakeholders in the epilepsy community and experts in knowledge engineering and computer science. PMID:22765502

  5. 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.

  6. An Ontology for the Discovery of Time-series Data

    NASA Astrophysics Data System (ADS)

    Hooper, R. P.; Choi, Y.; Piasecki, M.; Zaslavsky, I.; Valentine, D. W.; Whitenack, T.

    2010-12-01

    An ontology was developed to enable a single-dimensional keyword search of time-series data collected at fixed points, such as stream gage records, water quality observations, or repeated biological measurements collected at fixed stations. The hierarchical levels were developed to allow navigation from general concepts to more specific ones, terminating in a leaf concept, which is the specific property measured. For example, the concept “nutrient” has child concepts of “nitrogen”, “phosphorus”, and “carbon”; each of these children concepts are then broken into the actual constituent measured (e.g., “total kjeldahl nitrogen” or “nitrate + nitrite”). In this way, a non-expert user can find all nutrients containing nitrogen without knowing all the species measured, but an expert user can go immediately to the compound of interest. In addition, a property, such as dissolved silica, can appear as a leaf concept under nutrients or weathering products. This flexibility allows users from various disciplines to find properties of interest. The ontology can be viewed at http://water.sdsc.edu/hiscentral/startree.aspx. Properties measured by various data publishers (e.g., universities and government agencies) are tagged with leaf concepts from this ontology. A discovery client, HydroDesktop, creates a search request by defining the spatial and temporal extent of interest and a keyword taken from the discovery ontology. Metadata returned from the catalog describes the time series which meet the specified search criteria. This ontology is considered to be an initial description of physical, chemical and biological properties measured in water and suspended sediment. Future plans call for creating a moderated forum for the scientific community to add to and to modify this ontology. Further information for the Hydrologic Information Systems project, of which this is a part, is available at http://his.cuahsi.org.

  7. An ontological model of the practice transformation process.

    PubMed

    Sen, Arun; Sinha, Atish P

    2016-06-01

    Patient-centered medical home is defined as an approach for providing comprehensive primary care that facilitates partnerships between individual patients and their personal providers. The current state of the practice transformation process is ad hoc and no methodological basis exists for transforming a practice into a patient-centered medical home. Practices and hospitals somehow accomplish the transformation and send the transformation information to a certification agency, such as the National Committee for Quality Assurance, completely ignoring the development and maintenance of the processes that keep the medical home concept alive. Many recent studies point out that such a transformation is hard as it requires an ambitious whole-practice reengineering and redesign. As a result, the practices suffer change fatigue in getting the transformation done. In this paper, we focus on the complexities of the practice transformation process and present a robust ontological model for practice transformation. The objective of the model is to create an understanding of the practice transformation process in terms of key process areas and their activities. We describe how our ontology captures the knowledge of the practice transformation process, elicited from domain experts, and also discuss how, in the future, that knowledge could be diffused across stakeholders in a healthcare organization. Our research is the first effort in practice transformation process modeling. To build an ontological model for practice transformation, we adopt the Methontology approach. Based on the literature, we first identify the key process areas essential for a practice transformation process to achieve certification status. Next, we develop the practice transformation ontology by creating key activities and precedence relationships among the key process areas using process maturity concepts. At each step, we employ a panel of domain experts to verify the intermediate representations of the

  8. 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.

  9. 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

  10. 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.

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

    PubMed

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

    2016-08-01

    Software tools play a critical role in the development and maintenance of biomedical ontologies. One important task that is difficult without software tools is ontology quality assurance. In previous work, we have introduced different kinds of abstraction networks to provide a theoretical foundation for ontology quality assurance tools. Abstraction networks summarize the structure and content of ontologies. One kind of abstraction network that we have used repeatedly to support ontology quality assurance is the partial-area taxonomy. It summarizes structurally and semantically similar concepts within an ontology. However, the use of partial-area taxonomies was ad hoc and not generalizable. In this paper, we describe the Ontology Abstraction Framework (OAF), a unified framework and software system for deriving, visualizing, and exploring partial-area taxonomy abstraction networks. The OAF includes support for various ontology representations (e.g., OWL and SNOMED CT's relational format). A Protégé plugin for deriving "live partial-area taxonomies" is demonstrated. PMID:27345947

  12. Generative Graph Grammar of Neo-Vaiśeṣika Formal Ontology (NVFO)

    NASA Astrophysics Data System (ADS)

    Tavva, Rajesh; Singh, Navjyoti

    NLP applications for Sanskrit so far work within computational paradigm of string grammars. However, to compute 'meanings', as in traditional śā bdabodha prakriyā-s, there is a need to develop suitable graph grammars. Ontological structures are fundamentally graphs. We work within the formal framework of Neo-Vaiśeṣika Formal Ontology (NVFO) to propose a generative graph grammar. The proposed formal grammar only produces well-formed graphs that can be readily interpreted in accordance with Vaiśeṣ ika Ontology. We show that graphs not permitted by Vaiśeṣ ika ontology are not generated by the proposed grammar. Further, we write Interpreter of these graphical structures. This creates computational environment which can be deployed for writing computational applications of Vaiśeṣ ika ontology. We illustrate how this environment can be used to create applications like computing śā bdabodha of sentences.

  13. NeXO Web: the NeXO ontology database and visualization platform

    PubMed Central

    Dutkowski, Janusz; Ono, Keiichiro; Kramer, Michael; Yu, Michael; Pratt, Dexter; Demchak, Barry; Ideker, Trey

    2014-01-01

    The Network-extracted Ontology (NeXO) is a gene ontology inferred directly from large-scale molecular networks. While most ontologies are constructed through manual expert curation, NeXO uses a principled computational approach which integrates evidence from hundreds of thousands of individual gene and protein interactions to construct a global hierarchy of cellular components and processes. Here, we describe the development of the NeXO Web platform (http://www.nexontology.org)—an online database and graphical user interface for visualizing, browsing and performing term enrichment analysis using NeXO and the gene ontology. The platform applies state-of-the-art web technology and visualization techniques to provide an intuitive framework for investigating biological machinery captured by both data-driven and manually curated ontologies. PMID:24271398

  14. Visualization of Large Ontologies in University Education from a Tool Point of View.

    PubMed

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

    2016-01-01

    The realization of ontology visualization requirements in university education is a challenging task and should be supported by appropriate tools. This applies in particular, if the ontology to be visualized is based on a large text corpus that comprises a huge number of concepts, relations and annotations. In SNIK, we developed such an ontology of information management in hospitals in order to support the transfer of knowledge in the context of the university education. The challenge is to identify tools and methods, which are capable to support ontology visualization and usage as efficiently as possible. Related research fields (e.g. bioinformatics) are confronted with similar visualization problems. These tools and methods used could provide a suitable solution in our research field. In total, we assessed eight tools concerning the visualization of large ontologies to evaluate their suitability representing knowledge in the field of medical informatics. PMID:27577402

  15. 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

  16. 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

  17. An Evolutionary Ontology Approach for Community-Based Competency Management

    NASA Astrophysics Data System (ADS)

    de Baer, Peter; Meersman, Robert; Zhao, Gang

    In this article we describe an evolutionary ontology approach that distinguishes between major ontology changes and minor ontology changes. We divide the community in three (possibly overlapping) groups, i.e. facilitators, contributors, and users. Facilitators are a selected group of domain experts who represent the intended community. These facilitators define the intended goals of the ontology and will be responsible for major ontology and ontology platform changes. A larger group of contributors consists of all participating domain experts. The contributors will carry out minor ontology changes, like instantiation of concepts and description of concept instances. Users of the ontology may explore the ontology content via the ontology platform and/or make use of the published ontology content in XML or HTML format. The approach makes use of goal and group specific user interfaces to guide the ontology evolution process. For the minor ontology changes, the approach relies on the wisdom of crowds.

  18. 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. PMID:25490128

  19. 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…

  20. 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. PMID:21366305

  1. 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.

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

    NASA Astrophysics Data System (ADS)

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

    2010-03-01

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

  3. Ontological Model for EHR Interoperability.

    PubMed

    Bouanani-Oukhaled, Zahra; Verdier, Christine; Dupuy-Chessa, Sophie; Fouladi, Karan; Breda, Laurent

    2016-01-01

    The main purpose of this paper is to design a data model for Electronic Health Records which main goal is to enable cooperation of various heterogeneous health information systems. We investigate the interest of the meta-ontologies proposed in [1] by instantiating it with real data. We tested the feasibility of our model on real anonymous medical data provided by the Médibase Systèmes company. PMID:27350489

  4. 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

  5. COMPASS: A Geospatial Knowledge Infrastructure Managed with Ontologies

    NASA Astrophysics Data System (ADS)

    Stock, K.

    2009-04-01

    COMPASS: A Geospatial Knowledge Infrastructure Managed with Ontologies Dr Kristin Stock Allworlds Geothinking, United Kingdom and EDINA, University of Edinburgh, United Kingdom and Centre for Geospatial Science University of Nottingham Nottingham United Kingdom The research and decision-making process in any discipline is supported by a vast quantity and diversity of scientific resources, including journal articles; scientific models; scientific theories; data sets and web services that implement scientific models or provide other functionality. Improved discovery and access to these scientific resources has the potential to make the process of using and developing scientific knowledge more effective and efficient. Current scientific research or decision making that relies on scientific resources requires an extensive search for relevant resources. Published journal papers may be discovered using web searches on the basis of words that appear in the title or metadata, but this approach is limited by the need to select the appropriate words, and does not identify articles that may be of interest because they use a similar approach, methodology or technique but are in a different discipline, or that are likely to be helpful despite not sharing the same keywords. The COMPASS project is developing a knowledge infrastructure that is intended to enhance the user experience in discovering scientific resources. This is being achieved with an approach that uses ontologies to manage the knowledge infrastructure in two ways: 1. A set of ontologies describe the resources in the knowledge infrastructure (for example, publications and web services) in terms of the domain concepts to which they relate, the scientific theories and models that they depend on, and the characteristics of the resources themselves. These ontologies are provided to users either directly or with assisted search tools to aid them in the discovery process. OWL-S ontologies are being used to describe web

  6. 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

  7. Ontology-Based Analysis of Microarray Data.

    PubMed

    Giuseppe, Agapito; Milano, Marianna

    2016-01-01

    The importance of semantic-based methods and algorithms for the analysis and management of biological data is growing for two main reasons. From a biological side, knowledge contained in ontologies is more and more accurate and complete, from a computational side, recent algorithms are using in a valuable way such knowledge. Here we focus on semantic-based management and analysis of protein interaction networks referring to all the approaches of analysis of protein-protein interaction data that uses knowledge encoded into biological ontologies. Semantic approaches for studying high-throughput data have been largely used in the past to mine genomic and expression data. Recently, the emergence of network approaches for investigating molecular machineries has stimulated in a parallel way the introduction of semantic-based techniques for analysis and management of network data. The application of these computational approaches to the study of microarray data can broad the application scenario of them and simultaneously can help the understanding of disease development and progress. PMID:25971913

  8. Multicriteria analysis of ontologically represented information

    NASA Astrophysics Data System (ADS)

    Wasielewska, K.; Ganzha, M.; Paprzycki, M.; Bǎdicǎ, C.; Ivanovic, M.; Lirkov, I.

    2014-11-01

    Our current work concerns the development of a decision support system for the software selection problem. The main idea is to utilize expert knowledge to help the user in selecting the best software / method / computational resource to solve a computational problem. Obviously, this involves multicriterial decision making and the key open question is: which method to choose. The context of the work is provided by the Agents in Grid (AiG) project, where the software selection (and thus multicriterial analysis) is to be realized when all information concerning the problem, the hardware and the software is ontologically represented. Initially, we have considered the Analytical Hierarchy Process (AHP), which is well suited for the hierarchical data structures (e.g., such that have been formulated in terms of ontologies). However, due to its well-known shortcomings, we have decided to extend our search for the multicriterial analysis method best suited for the problem in question. In this paper we report results of our search, which involved: (i) TOPSIS (Technique for Order Preference by Similarity to Ideal Solution), (ii) PROMETHEE, and (iii) GRIP (Generalized Regression with Intensities of Preference). We also briefly argue why other methods have not been considered as valuable candidates.

  9. 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.

  10. 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

  11. Toward cognitivist ontologies : on the role of selective attention for upper ontologies.

    PubMed

    Carstensen, Kai-Uwe

    2011-11-01

    Ontologies play a key role in modern information society although there are still many fundamental questions regarding their structure to be answered. In this paper, some of these are presented, and it is argued that they require a shift from realist to cognitivist ontologies, with ontology design crucially depending on taking both cognitive and linguistic aspects into consideration. A detailed discussion of central parts of a proposed cognitivist upper ontology based on qualitative representations of selective attention is presented. PMID:21523446

  12. A Pilot Ontology for Healthcare Quality Indicators.

    PubMed

    White, Pam; Roudsari, Abdul

    2015-01-01

    Computerisation of quality indicators for the English National Health Service currently relies primarily on queries and clinical coding, with little use of ontologies. We created a searchable ontology for a diverse set of healthcare quality indicators. We investigated attributes and relationships in a set of 222 quality indicators, categorised by clinical pathway, inclusion and exclusion criteria and US Institute of Medicine purpose. Our pilot ontology could reduce duplication of effort in healthcare quality monitoring. PMID:26262409

  13. Towards a Formal Representation of Processes and Objects Regarding the Delivery of Telehealth Services: The Telehealth Ontology (TEON).

    PubMed

    Santana, Filipe; Schulz, Stefan; Campos, Amadeu; Novaes, Magdala A

    2015-01-01

    This study introduces ontological aspects concerning the Telehealth Ontology (TEON), an ontology that represents formal-ontological content concerning the delivery of telehealth services. TEON formally represents the main services, actors and other entity types relevant to telehealth service delivery. TEON uses the upper level ontology BioTopLite2 and reuses content from the Ontology for Biomedical Investigations (OBI). The services embedded in telehealth services are considered as essential as the common services provided by the health-related practices. We envision TEON as a service to support the development of telehealth systems. TEON might also enable the integration of heterogeneous telehealth systems, and provide a base to automatize the processing of telehealth-related content. PMID:26262407

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

    SciTech Connect

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

    2006-01-23

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

  15. 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

  16. Ontology Driven Analysis of Spatio-temporal Phenomena, Aimed At Spatial Planning And Environmental Forecasting

    NASA Astrophysics Data System (ADS)

    Iwaniak, A.; Łukowicz, J.; Strzelecki, M.; Kaczmarek, I.

    2013-10-01

    Spatial planning is a crucial area for balancing civilization development with environmental protection. Spatial planning has a multidisciplinary nature. It must take into account the dynamics of the processes, which could affect the integrity of the environmental system. That is why we need a new approach to modelling phenomena occurring in space. Such approach is offered by ontologies, based on Description Logic (DL) and related to inference systems. Ontology is a system for the knowledge representation, including conceptual scheme and based on this scheme representation of reality. Ontologies can be enriched with additional logical systems. The authors present a way of building domain ontologies for spatial planning, including the representation of spatio-temporal phenomena. Description Logic is supplemented by structures of temporal logic. As a result, the analysis for exploring the topological relations between spatial objects will be extended to include temporal relationships: coincidence, precedence and succession, cause and effect relationship. Spatio-temporal models with temporal logic structures, encoded in ontologies, could be a subject of inference process, performed by semantic reasoners (reasoner engines). Spatio-temporal representations are offered, by so-called upper ontologies, such as GFO, BFO, OCHRE and others. Temporal structures provided in such ontologies, are useful for the analysis of data obtained from environmental and development monitoring systems and for description and representation of historical phenomena. They allow creating the models and scenarios of expected spatial transformation. They will support analysis for spatial development design, decision-making in spatial planning and forecasting of environmental impact.

  17. Ontology of Serious Games

    ERIC Educational Resources Information Center

    Prayaga, Lakshmi; Rasmussen, Karen L.

    2008-01-01

    Computer games are no longer just for entertainment; they have also become a useful instructional strategy for acquiring knowledge. When games are used for purposes other than strict entertainment they become serious games. The goal of serious games is to enable the player to learn a task, master a strategy or develop a skill. Serious games can be…

  18. Dermal and inhalation exposure to methylene bisphenyl isocyanate (MDI) in iron foundry workers.

    PubMed

    Liljelind, I; Norberg, C; Egelrud, L; Westberg, H; Eriksson, K; Nylander-French, L A

    2010-01-01

    Diisocyanates are a group of chemically reactive agents, which are used in the production of coatings, adhesives, polyurethane foams, and parts for the automotive industry and as curing agents for cores in the foundry industry. Dermal and inhalation exposure to methylene bisphenyl isocyanate (MDI) is associated with respiratory sensitization and occupational asthma. However, limited research has been performed on the quantitative evaluation of dermal and inhalation exposure to MDI in occupationally exposed workers. The objective of this research was to quantify dermal and inhalation exposure levels in iron foundry workers. Workers involved in mechanized moulding and mechanized production of cores were monitored: 12 core makers, 2 core-sand preparers, and 5 core installers. Personal breathing-zone levels of MDI were measured using impregnated filter sampling. Dermal exposure to MDI was measured using a tape-strip technique. Three or five consecutive tape-strip samples were collected from five exposed skin areas (right and left forefingers, left and right wrists, and forehead). The average personal air concentration was 0.55 microg m(-3), 50-fold lower than the Swedish occupational exposure limit of 30 microg m(-3). The core makers had an average exposure of 0.77 microg m(-3), which was not significantly different from core installers' and core-sand preparers' average exposure of 0.16 microg m(-3) (P = 0.059). Three core makers had a 10-fold higher inhalation exposure than the other core makers. The core makers' mean dermal exposure at different skin sites varied from 0.13 to 0.34 microg while the two other groups' exposure ranged from 0.006 to 0.062 microg. No significant difference was observed in the MDI levels between the skin sites in a pairwise comparison, except for left forefinger compared to left and right wrist (P < 0.05). In addition, quantifiable but decreasing levels of MDI were observed in the consecutive tape strip per site indicating MDI penetration

  19. Foundry sands as low-cost adsorbent material for Cr (VI) removal.

    PubMed

    Campos, I; Alvarez, J A; Villar, P; Pascual, A; Herrero, L

    2013-01-01

    The potential of foundry sands, industrial waste from the iron foundry industry, was evaluated for the removal of Cr (VI) using discontinuous assays. Chemical foundry sands are composed of fine silica sand, furanic resins as binder, chemical catalyst and residual iron particles. The influence ofpH, agitation rate and metal concentration on the removal process was investigated. Kinetic and equilibrium tests were conducted to determine Cr (VI) removal from aqueous solutions at a temperature range of 25-55 degrees C. Cr (VI) removal of 40-100% for a range of pH 6-1.6 was obtained. This removal was attributed to the presence of a large number of protonated silanol and aluminol groups. Cr (VI) adsorption in foundry sands follows a pseudo-second-order kinetic reaction (Ho model, r2 > 0.999) reaching kinetic constants of 0.341, 0.551, 0.775 and 0.920 g/mg h at 25, 35, 45 and 55 degrees C, respectively. The adsorption data were fitted to the Langmuir adsorption isotherm model (r > 0.99) obtaining adsorption capacities (q(max)) of 1.99, 2.40, 2.50, and 3.14 mg Cr (VI)/g sand at 25, 35, 45 and 55 degrees C, respectively. Calculated Gibbs free energy change (deltaG0), adsorption energy (E) and activation energy (E(a)) values indicate that a physisorption mechanism governs Cr (VI) adsorption process in foundry sands. PMID:24191460

  20. Arthrogryposis as a Syndrome: Gene Ontology Analysis.

    PubMed

    Hall, Judith G; Kiefer, Jeff

    2016-07-01

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

  1. Self-organizing ontology of biochemically relevant small molecules

    PubMed Central

    2012-01-01

    Background The advent of high-throughput experimentation in biochemistry has led to the generation of vast amounts of chemical data, necessitating the development of novel analysis, characterization, and cataloguing techniques and tools. Recently, a movement to publically release such data has advanced biochemical structure-activity relationship research, while providing new challenges, the biggest being the curation, annotation, and classification of this information to facilitate useful biochemical pattern analysis. Unfortunately, the human resources currently employed by the organizations supporting these efforts (e.g. ChEBI) are expanding linearly, while new useful scientific information is being released in a seemingly exponential fashion. Compounding this, currently existing chemical classification and annotation systems are not amenable to automated classification, formal and transparent chemical class definition axiomatization, facile class redefinition, or novel class integration, thus further limiting chemical ontology growth by necessitating human involvement in curation. Clearly, there is a need for the automation of this process, especially for novel chemical entities of biological interest. Results To address this, we present a formal framework based on Semantic Web technologies for the automatic design of chemical ontology which can be used for automated classification of novel entities. We demonstrate the automatic self-assembly of a structure-based chemical ontology based on 60 MeSH and 40 ChEBI chemical classes. This ontology is then used to classify 200 compounds with an accuracy of 92.7%. We extend these structure-based classes with molecular feature information and demonstrate the utility of our framework for classification of functionally relevant chemicals. Finally, we discuss an iterative approach that we envision for future biochemical ontology development. Conclusions We conclude that the proposed methodology can ease the burden of

  2. Hybrid Ontology for Semantic Information Retrieval Model Using Keyword Matching Indexing System

    PubMed Central

    Uthayan, K. R.; Anandha Mala, G. S.

    2015-01-01

    Ontology is the process of growth and elucidation of concepts of an information domain being common for a group of users. Establishing ontology into information retrieval is a normal method to develop searching effects of relevant information users require. Keywords matching process with historical or information domain is significant in recent calculations for assisting the best match for specific input queries. This research presents a better querying mechanism for information retrieval which integrates the ontology queries with keyword search. The ontology-based query is changed into a primary order to predicate logic uncertainty which is used for routing the query to the appropriate servers. Matching algorithms characterize warm area of researches in computer science and artificial intelligence. In text matching, it is more dependable to study semantics model and query for conditions of semantic matching. This research develops the semantic matching results between input queries and information in ontology field. The contributed algorithm is a hybrid method that is based on matching extracted instances from the queries and information field. The queries and information domain is focused on semantic matching, to discover the best match and to progress the executive process. In conclusion, the hybrid ontology in semantic web is sufficient to retrieve the documents when compared to standard ontology. PMID:25922851

  3. What is nature capable of? Evidence, ontology and speculative medical humanities.

    PubMed

    Savransky, Martin; Rosengarten, Marsha

    2016-09-01

    Expanding on the recent call for a 'critical medical humanities' to intervene in questions of the ontology of health, this article develops a what we call a 'speculative' orientation to such interventions in relation to some of the ontological commitments on which contemporary biomedical cultures rest. We argue that crucial to this task is an approach to ontology that treats it not as a question of first principles, but as a matter of the consequences of the images of nature that contemporary biomedical research practices espouse when they make claims to evidence, as well as the possible consequences of imagining different worlds in which health and disease processes partake. By attending to the implicit ontological assumptions involved in the method par excellence of biomedical research, namely the randomised controlled trial (RCT), we argue that the mechanistic ontology that tacitly informs evidence-based biomedical research simultaneously authorises a series of problematic consequences for understanding and intervening practically in the concrete realities of health. As a response, we develop an alternative ontological proposition that regards processes of health and disease as always situated achievements. We show that, without disqualifying RCT-based evidence, such a situated ontology enables one to resist the reduction of the realities of health and disease to biomedicine's current forms of explanation. In so doing, we call for medical humanities scholars to actively engage in the speculative question of what nature may be capable of. PMID:27222529

  4. 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.

  5. 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.

  6. 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. PMID:25922851

  7. 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

  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. 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.

  10. A Proposal for a Bohmian Ontology of Quantum Gravity

    NASA Astrophysics Data System (ADS)

    Vassallo, Antonio; Esfeld, Michael

    2014-01-01

    The paper shows how the Bohmian approach to quantum physics can be applied to develop a clear and coherent ontology of non-perturbative quantum gravity. We suggest retaining discrete objects as the primitive ontology also when it comes to a quantum theory of space-time and therefore focus on loop quantum gravity. We conceive atoms of space, represented in terms of nodes linked by edges in a graph, as the primitive ontology of the theory and show how a non-local law in which a universal and stationary wave-function figures can provide an order of configurations of such atoms of space such that the classical space-time of general relativity is approximated. Although there is as yet no fully worked out physical theory of quantum gravity, we regard the Bohmian approach as setting up a standard that proposals for a serious ontology in this field should meet and as opening up a route for fruitful physical and mathematical investigations.

  11. 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

    ... Five-Year (``Sunset'') Review, 76 FR 74775 (December 1, 2011). \\2\\ See Foundry Coke Products from the... FR 20788 (April 6, 2012) and accompanying Issues and Decision Memorandum. \\3\\ See Foundry Coke Products from China Determination, 77 FR 32998 (June 4, 2012), and USITC Publication 4326 (May 29,...

  12. 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 ...

  13. 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,...

  14. 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,...

  15. 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,...

  16. 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,...

  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, 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,...

  18. Characterization of physical and chemical properties of spent foundry sands pertinent to beneficial use in manufactured soils

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Of 2,000 United States foundries, 93% produce ferrous or aluminum castings, generating 9.4 million tons of non-hazardous spent foundry sand (SFS) annually, of which only 28% is beneficially used. The U.S. EPA Resource Conservation Challenge identifies SFS as a priority material for beneficial use a...

  19. The characterization of trace metals and organics in spent foundry sands over a one-year period

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Millions of tons of spent sand, used to create metalcasting molds, are generated by the foundry industry each year in the United States. Not surprisingly, spent foundry sands (SFSs) are an excellent substitute for virgin sands that are currently used in manufactured soils and geotechnical applicati...

  20. 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. PMID:25389077

  1. Using ontologies to improve semantic interoperability in health data.

    PubMed

    Liyanage, Harshana; Krause, Paul; De Lusignan, Simon

    2015-01-01

    The present-day health data ecosystem comprises a wide array of complex heterogeneous data sources. A wide range of clinical, health care, social and other clinically relevant information are stored in these data sources. These data exist either as structured data or as free-text. These data are generally individual person-based records, but social care data are generally case based and less formal data sources may be shared by groups. The structured data may be organised in a proprietary way or be coded using one-of-many coding, classification or terminologies that have often evolved in isolation and designed to meet the needs of the context that they have been developed. This has resulted in a wide range of semantic interoperability issues that make the integration of data held on these different systems changing. We present semantic interoperability challenges and describe a classification of these. We propose a four-step process and a toolkit for those wishing to work more ontologically, progressing from the identification and specification of concepts to validating a final ontology. The four steps are: (1) the identification and specification of data sources; (2) the conceptualisation of semantic meaning; (3) defining to what extent routine data can be used as a measure of the process or outcome of care required in a particular study or audit and (4) the formalisation and validation of the final ontology. The toolkit is an extension of a previous schema created to formalise the development of ontologies related to chronic disease management. The extensions are focused on facilitating rapid building of ontologies for time-critical research studies. PMID:26245245

  2. 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. PMID:23304354

  3. 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.

  4. [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. PMID:7732197

  5. Simulating the deformation of dies in the foundry

    NASA Astrophysics Data System (ADS)

    Chabod, A.; Longa, Y.; Dracon, J. M.; Chailler, K.; Hairy, P.; Da Silva, A.

    2012-07-01

    Digital simulation (QuikCAST, ProCAST) is already used extensively when designing metallic dies for founding, in particular to design filling and gating systems. Simulation of the steady-state temperature cycles of dies has also been mastered. With large castings, the temperature gradient induced between the moulding surface and the rear surfaces of the die leads to deformations that may be large enough to measure, and incompatible with the required dimensional accuracy. The temperature gradient also creates thermal fatigue stresses that cause crazing of the die surface. In the study conducted by CTIF, aimed at measuring tooling deformations, various ways of measuring displacements at high temperatures (with and without contact) were investigated in order to evaluate their capabilities and limitations. An experimental device was designed - a test bench combining a metallic die having a simple geometry, in which an aluminium part could be cast, and instrumentation (temperature and displacement sensors). The deformations of the die were measured during first cycles of temperature homogenization. Concurrently, thermomechanical calculations were carried out on the same geometry using PROCAST. The calculation results are well correlated with the experimental measurements and validate the tools and the calculation methods. This thermomechanical approach makes it possible to optimize die design in the foundry and to predict high-temperature deformations as early as the design stage. Knowledge of these deformations makes it possible in turn to anticipate the geometrical and dimensional variations undergone by the castings themselves and so to improve their accuracy. The designer can act on the temperature of the die or the design of the casting, or create a die in which the expected thermal deformation is reversed so as to produce a casting having the correct dimensions. In short, thermomechanical simulation can be applied to this problem to achieve a better understanding

  6. 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.

  7. 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

  8. An Ontology-Based Collaborative Design System

    NASA Astrophysics Data System (ADS)

    Su, Tieming; Qiu, Xinpeng; Yu, Yunlong

    A collaborative design system architecture based on ontology is proposed. In the architecture, OWL is used to construct global shared ontology and local ontology; both of them are machine-interpretable. The former provides a semantic basis for the communication among designers so as to make the designers share the common understanding of knowledge. The latter which describes knowledge of designer’s own is the basis of design by reasoning. SWRL rule base comprising rules defined based on local ontology is constructed to enhance the reasoning capability of local knowledge base. The designers can complete collaborative design at a higher level based on the local knowledge base and the global shared ontology, which enhances the intelligence of design. Finally, a collaborative design case is presented and analyzed.

  9. 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. PMID:26244889

  10. [Towards a structuring fibrillar ontology].

    PubMed

    Guimberteau, J-C

    2012-10-01

    Over previous decades and centuries, the difficulty encountered in the manner in which the tissue of our bodies is organised, and structured, is clearly explained by the impossibility of exploring it in detail. Since the creation of the microscope, the perception of the basic unity, which is the cell, has been essential in understanding the functioning of reproduction and of transmission, but has not been able to explain the notion of form; since the cells are not everywhere and are not distributed in an apparently balanced manner. The problems that remain are those of form and volume and also of connection. The concept of multifibrillar architecture, shaping the interfibrillar microvolumes in space, represents a solution to all these questions. The architectural structures revealed, made up of fibres, fibrils and microfibrils, from the mesoscopic to the microscopic level, provide the concept of a living form with structural rationalism that permits the association of psychochemical molecular biodynamics and quantum physics: the form can thus be described and interpreted, and a true structural ontology is elaborated from a basic functional unity, which is the microvacuole, the intra and interfibrillar volume of the fractal organisation, and the chaotic distribution. Naturally, new, less linear, less conclusive, and less specific concepts will be implied by this ontology, leading one to believe that the emergence of life takes place under submission to forces that the original form will have imposed and oriented the adaptive finality. PMID:22921289

  11. Clustering of gene ontology terms in genomes.

    PubMed

    Tiirikka, Timo; Siermala, Markku; Vihinen, Mauno

    2014-10-25

    Although protein coding genes occupy only a small fraction of genomes in higher species, they are not randomly distributed within or between chromosomes. Clustering of genes with related function(s) and/or characteristics has been evident at several different levels. To study how common the clustering of functionally related genes is and what kind of functions the end products of these genes are involved, we collected gene ontology (GO) terms for complete genomes and developed a method to detect previously undefined gene clustering. Exhaustive analysis was performed for seven widely studied species ranging from human to Escherichia coli. To overcome problems related to varying gene lengths and densities, a novel method was developed and a fixed number of genes were analyzed irrespective of the genome span covered. Statistically very significant GO term clustering was apparent in all the investigated genomes. The analysis window, which ranged from 5 to 50 consecutive genes, revealed extensive GO term clusters for genes with widely varying functions. Here, the most interesting and significant results are discussed and the complete dataset for each analyzed species is available at the GOme database at http://bioinf.uta.fi/GOme. The results indicated that clusters of genes with related functions are very common, not only in bacteria, in which operons are frequent, but also in all the studied species irrespective of how complex they are. There are some differences between species but in all of them GO term clusters are common and of widely differing sizes. The presented method can be applied to analyze any genome or part of a genome for which descriptive features are available, and thus is not restricted to ontology terms. This method can also be applied to investigate gene and protein expression patterns. The results pave a way for further studies of mechanisms that shape genome structure and evolutionary forces related to them. PMID:24995610

  12. 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

  13. 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

  14. Fabrication of NMOS capacitors with a low-voltage coefficient at a silicon foundry

    NASA Astrophysics Data System (ADS)

    Helms, W. J.

    1985-01-01

    The custom integrated circuit design technic pioneered by Mead and Conway (1980) is often used for moderately complex digital systems. The fabrication is carried out at a foundry where a standard NMOS process is applied to the design. In this note, the Mead-Conway technique has been applied to analog circuits with the goal of producing a reasonable quality switched capacitor filter with as few process modifications as possible. Seven chip runs have been carried out at two separate foundries with good and consistent results.

  15. Geo-Ontologies Are Scale Dependent

    NASA Astrophysics Data System (ADS)

    Frank, A. U.

    2009-04-01

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

  16. 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

  17. 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.

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

    PubMed Central

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

    2010-01-01

    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. PMID:21347086

  19. 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. PMID:25254240

  20. 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