Science.gov

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. 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).

  12. 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

  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. 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

  16. 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

  17. 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…

  18. 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.

  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. 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

  2. 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

  3. 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

  4. 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

  5. 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.

  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. 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

  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. 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.

  11. 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

  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. 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

  19. 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

  20. 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.

  1. 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.

  2. 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

  3. 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.

  4. 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

  5. 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

  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. 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

  16. 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

  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. 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

  19. 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…

  20. 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

  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. 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.

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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.

  9. 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.

  10. 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

  11. 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

  12. 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

  13. 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

  14. 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

  15. 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.

  16. 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…

  17. 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…

  18. 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

  19. 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

  20. 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)

  1. 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)

  2. 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

  3. 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

  4. 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.

  5. 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.

  6. 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

  7. 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

  8. 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...

  9. 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

  10. 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

  11. 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.

  12. 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.

  13. 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.

  14. 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 ...

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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.

  20. 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.

  1. 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

  2. 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.

  3. 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.

  4. 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…

  5. 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.

  6. 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.

  7. 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.

  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. 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

  13. 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

  14. 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.

  15. 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

  16. 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

  17. 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

  18. 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.

  19. 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

  20. 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

  1. 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

  2. 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…

  3. 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.

  4. 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

  5. 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.

  6. 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

  7. 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

  8. How granularity issues concern biomedical ontology integration.

    PubMed

    Schulz, Stefan; Boeker, Martin; Stenzhorn, Holger

    2008-01-01

    The application of upper ontologies has been repeatedly advocated for supporting interoperability between domain ontologies in order to facilitate shared data use both within and across disciplines. We have developed BioTop as a top-domain ontology to integrate more specialized ontologies in the biomolecular and biomedical domain. In this paper, we report on concrete integration problems of this ontology with the domain-independent Basic Formal Ontology (BFO) concerning the issue of fiat and aggregated objects in the context of different granularity levels. We conclude that the third BFO level must be ignored in order not to obviate cross-granularity integration. PMID:18487840

  9. 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.

  10. 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…

  11. 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

  12. 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.

  13. 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...

  14. 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.

  15. 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.

  16. 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.

  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. 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.

  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. 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

  2. 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

  3. 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…

  4. 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

  5. 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).

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

    PubMed

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

    2016-06-01

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

  7. 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

  8. 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

  9. 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

  10. 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

  11. Final Scientific Report Steel Foundry Refractory Lining Optimization

    SciTech Connect

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

    2002-12-02

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

  12. 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.

  13. 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

  14. 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

  15. 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

  16. 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.

  17. 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

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

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

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

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

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

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

  20. 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

  1. 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

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

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

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

  3. 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

  4. 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

  5. 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.

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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

  11. 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

  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. 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

  14. 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

  15. 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

  16. 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...

  17. 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…

  18. 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…

  19. 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

  20. 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

  1. 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.

  2. 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.

  3. 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.

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

    PubMed

    Dönitz, Jürgen; Wingender, Edgar

    2012-01-01

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

  5. 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…

  6. 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.

  7. 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.

  8. 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.

  9. 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.

  10. 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.

  11. 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.

  12. 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

  13. 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

  14. 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…

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

    NASA Astrophysics Data System (ADS)

    Raskin, R.

    2005-12-01

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

  16. 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

  17. 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

  18. 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…

  19. 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

  20. Kuhn's Ontological Relativism.

    ERIC Educational Resources Information Center

    Sankey, Howard

    2000-01-01

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

  1. 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.

  2. 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

  3. Gene Ontology annotations and resources.

    PubMed

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

    2013-01-01

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

  4. 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

  5. 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.

  6. 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

  7. 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.

  8. 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…

  9. 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…

  10. 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.

  11. 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

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

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

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

  13. 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

  14. 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

  15. 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

  16. 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

  17. 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

  18. 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

  19. 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

  20. 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

  1. 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

  2. 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

  3. 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...

  4. 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…

  5. 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

  6. 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.

  7. 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

  8. 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

  9. 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

  10. 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

  11. The Gene Ontology: enhancements for 2011.

    PubMed

    2012-01-01

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

  12. The Gene Ontology: enhancements for 2011

    PubMed Central

    2012-01-01

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

  13. 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

  14. 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

  15. 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.

  16. 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.

  17. 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

  18. 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.

  19. 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.

  20. "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…

  1. 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

  2. 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.

  3. 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.

  4. 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

  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. 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

  7. Ontological Modeling for Integrated Spacecraft Analysis

    NASA Technical Reports Server (NTRS)

    Wicks, Erica

    2011-01-01

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

  8. AmiGO: online access to ontology and annotation data

    SciTech Connect

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

    2009-01-15

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

  9. 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

  10. 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.