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Quality control for terms and definitions in ontologies and taxonomies

Jacob Köhler, Katherine Munn, Alexander Rüegg, Andre Skusa, Barry Smith
<span title="2006-04-19">2006</span> <i title="Springer (Biomed Central Ltd.)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/n5zrklrhlzhtdorf4rk4rmeo3i" style="color: black;">BMC Bioinformatics</a> </i> &nbsp;
Our methods provide reliable indications of the quality of terms and definitions in ontologies and taxonomies.  ...  By automatically aligning GO with other ontologies and taxonomies we were able to propose alternative synonyms and definitions for some of these problematic terms.  ...  Acknowledgements All Authors wish to thank Martin Urban, Steve Thomas, Tully Yates and Jan Taubert for the evaluation of the indexes.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-7-212">doi:10.1186/1471-2105-7-212</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/16623942">pmid:16623942</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC1482721/">pmcid:PMC1482721</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/wuxo67shuzht5ovmq65xxq7n3e">fatcat:wuxo67shuzht5ovmq65xxq7n3e</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20190501185418/https://bmcbioinformatics.biomedcentral.com/track/pdf/10.1186/1471-2105-7-212" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/04/36/04360c9836edd4c64a2321633be51d6a68bc027a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/1471-2105-7-212"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC1482721" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Vocabularies and Retrieval Tools in Biomedicine: Disentangling the Terminological Knot

Klaar Vanopstal, Robert Vander Stichele, Godelieve Laureys, Joost Buysschaert
<span title="2009-11-12">2009</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jyvyntri6rhjfd33rbhr3cl2yu" style="color: black;">Journal of medical systems</a> </i> &nbsp;
Terms like "thesaurus", "taxonomy", "classification", "glossary", "ontology" and "controlled vocabulary" can be used in diverse contexts, causing confusion and vagueness about their denotation.  ...  We examined some important (bio)medical systems for their compatibility with the definitions proposed in the first part of this paper.  ...  Introduction Terms such as thesaurus, taxonomy, ontology and controlled vocabulary, and even glossary, dictionary and lexicon at first sight seem to be unambiguous terms.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10916-009-9389-z">doi:10.1007/s10916-009-9389-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20703537">pmid:20703537</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5v3osykxozfxha4vcf3dqlx4oq">fatcat:5v3osykxozfxha4vcf3dqlx4oq</a> </span>
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Special issue on fuzzy ontologies and fuzzy markup language applications

Giovanni Acampora, Chang-Shing Lee
<span title="2011-11-06">2011</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/e5brmbb4nne2bb6o5whxervgii" style="color: black;">Soft Computing - A Fusion of Foundations, Methodologies and Applications</a> </i> &nbsp;
Loia and S. Senatore introduces an OWL-based upper ontology, called OWL-FC (Ontology Web Language for Fuzzy Control), capable of supporting a semantic definition of fuzzy control.  ...  Indeed, fuzzy set theory may extend the conventional ontology idea with a collection of fuzzy or vague terms like ''creamy'', ''hot'', ''large'', for which a clear and precise definition is not possible  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s00500-011-0785-1">doi:10.1007/s00500-011-0785-1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ubmuvalk2zbudnzrdv4ynosot4">fatcat:ubmuvalk2zbudnzrdv4ynosot4</a> </span>
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An Ontology to Standardize Research Output of Nutritional Epidemiology: From Paper-Based Standards to Linked Content

Yang, Ambayo, Baets, Kolsteren, Thanintorn, Hawwash, Bouwman, Bronselaer, Pattyn, Lachat
<span title="2019-06-08">2019</span> <i title="MDPI AG"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ztxgyntcovcxnht5g4vkoge5ka" style="color: black;">Nutrients</a> </i> &nbsp;
Methods: Firstly, a scoping review was conducted to identify existing ontology terms for reuse in ONE.  ...  The terms used in the standards were summarized and listed separately in a taxonomic hierarchy.  ...  Quality characteristics of selected ontologies for nutritional epidemiology. Appendix A Nutrients 2019, 11, 1300  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/nu11061300">doi:10.3390/nu11061300</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/31181762">pmid:31181762</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6628051/">pmcid:PMC6628051</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/m4lz6fhl7vbtllaiofxoywrkje">fatcat:m4lz6fhl7vbtllaiofxoywrkje</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200306140907/https://publications.tno.nl/publication/34634282/ZGPEyj/yang-2019-ontology.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/26/21/2621b9e90fc4bbd7e4866a8f4c985f3c397bbdf1.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.3390/nu11061300"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> mdpi.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC6628051" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

An Evolutive Process to Convert Glossaries into Ontologies

José R. Hilera, Carmen Pagés, J. Javier Martínez, J. Antonio Gutiérrez, Luis De-Marcos
<span title="2010-12-01">2010</span> <i title="Boston College University Libraries"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ttpgthsdzrdozieu3cxrhiaipy" style="color: black;">Information Technology and Libraries</a> </i> &nbsp;
an ontology that may be used to index or search for information resources and documents stored in libraries or on the Semantic Web.  ...  This paper describes a method to generate ontologies from glossaries of terms.  ...  This research is co-funded by the Spanish Ministry of Industry, Tourism and Commerce PROFIT program (grant TSI-020100-2008-23).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6017/ital.v29i4.3130">doi:10.6017/ital.v29i4.3130</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3a2l5mlu5jfqzf474s4tbjpj7q">fatcat:3a2l5mlu5jfqzf474s4tbjpj7q</a> </span>
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Taxonomy and Ontology Management Tools: A General Explanation [chapter]

Sukumar Mandal
<span title="2019-10-03">2019</span> <i title="IntechOpen"> Ontology in Information Science [Working Title] </i> &nbsp;
This paper has selected the matured level open-source tools for management of taxonomy and ontology in semantic web environment.  ...  Apart from this it also presents some important snapshot available in an online environment for designing and developing the taxonomy and ontology.  ...  export in RDF format, complete export in txt, scope notes, historical and bibliographical notes, user management, terms and user supervision, duplicates terms control, free terms control, quality assurance  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5772/intechopen.88606">doi:10.5772/intechopen.88606</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/i2kgd35dwvbe5oy5aqinj6bpku">fatcat:i2kgd35dwvbe5oy5aqinj6bpku</a> </span>
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Behavior change interventions: the potential of ontologies for advancing science and practice

Kai R. Larsen, Susan Michie, Eric B. Hekler, Bryan Gibson, Donna Spruijt-Metz, David Ahern, Heather Cole-Lewis, Rebecca J. Bartlett Ellis, Bradford Hesse, Richard P. Moser, Jean Yi
<span title="2016-08-01">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/lcknn27sbzdslll7sgcu5dobtu" style="color: black;">Journal of behavioral medicine</a> </i> &nbsp;
In information science, an ontology is a systematic method for articulating a "controlled vocabulary" of agreed-upon terms and their inter-relationships.  ...  ; see Table 1 for key terms used in this article).  ...  For example, MeSH terms are a controlled vocabulary organized into a taxonomy.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10865-016-9768-0">doi:10.1007/s10865-016-9768-0</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27481101">pmid:27481101</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6kfheajckfeazbopgjh3y7m3oa">fatcat:6kfheajckfeazbopgjh3y7m3oa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180723231731/http://discovery.ucl.ac.uk/1508938/1/Michie_Larsen%20et%20al%2C%20BCI%20Ontologies%202016_updatedKGv2.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/97/4f/974fb90ae9072d64d12bec2d35ece02212cb2445.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s10865-016-9768-0"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Complex overlapping concepts: An effective auditing methodology for families of similarly structured BioPortal ontologies

Ling Zheng, Yan Chen, Gai Elhanan, Yehoshua Perl, James Geller, Christopher Ochs
<span title="2018-05-28">2018</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
In previous research, we have demonstrated for a number of ontologies that structurally complex concepts (for different definitions of "complex") in an ontology are more likely to exhibit errors than other  ...  We demonstrate quality assurance results for both of them. Furthermore, in this paper we observe two novel, important, and useful phenomena during quality assurance of "overlapping concepts."  ...  The content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2018.05.015">doi:10.1016/j.jbi.2018.05.015</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/29852316">pmid:29852316</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC6609446/">pmcid:PMC6609446</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/itsh3cctojhgdovevm7xtpqcie">fatcat:itsh3cctojhgdovevm7xtpqcie</a> </span>
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IrGO: Iranian traditional medicine General Ontology and knowledge base

Ayeh Naghizadeh, Mahdi Salamat, Donya Hamzeian, Shaghayegh Akbari, Hossein Rezaeizadeh, Mahdi Alizadeh Vaghasloo, Reza Karbalaei, Mehdi Mirzaie, Mehrdad Karimi, Mohieddin Jafari
<span title="2021-04-16">2021</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
extracted terms; (2) arranging the classes in a taxonomy; (3) determining object and data properties; (4) specifying annotation properties including ID, labels (English and Persian), alternative terms  ...  , and definitions (English and Persian); (5) ontology evaluation.  ...  They both commented on the revised manuscript and helped in evaluating the ontology. All authors read and approved the final manuscript.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-021-00237-1">doi:10.1186/s13326-021-00237-1</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/33863373">pmid:33863373</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cmjxqqx4nnb73oeihtf75ra5dm">fatcat:cmjxqqx4nnb73oeihtf75ra5dm</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20210419191055/https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/s13326-021-00237-1.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/db/ac/dbac39d323c67a1ab38aeb5215204f7632f53ff3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-021-00237-1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> springer.com </button> </a>

Semi-automated ontology generation within OBO-Edit

Thomas Wächter, Michael Schroeder
<span title="2010-06-01">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4r72gbmtcrde5no3fwwogjs3cu" style="color: black;">Computer applications in the biosciences : CABIOS</a> </i> &nbsp;
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.  ...  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.  ...  ACKNOWLEDGEMENTS We gratefully acknowledge Götz Fabian, Marcel Hanke and Atif Iqbal for their support developing the GUI; the OBO Edit Working i95  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq188">doi:10.1093/bioinformatics/btq188</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20529942">pmid:20529942</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2881373/">pmcid:PMC2881373</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jlb4hyxrjzbg3dy3i3ddixhnge">fatcat:jlb4hyxrjzbg3dy3i3ddixhnge</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20111111115712/http://bioinformatics.oxfordjournals.org.ezproxy.lib.utah.edu/content/26/12/i88.full.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/b2/ad/b2ad55437e7ce951c42683adab4c265d1c21245e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bioinformatics/btq188"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> oup.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2881373" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Community Development of the SWEET Semantic System for Earth and Environmental Data - A Call for Interest [article]

Robert J. Rovetto
<span title="2022-02-03">2022</span> <i title="ESIP"> figshare.com </i> &nbsp;
The Jan 19, 2022 session presentation on the SWEET ontologies, at the ESIP January Meeting.  ...  as SME Quality control of descriptions/definitions of terms (e.g., for your subject expertise), both natural language, and computable• Takeaway points • Time-permitting: Demo: -Open SWEET online: Github  ...  updates via SemTech: merge their domain ontology, in order to create innovating 🡪 SME focus on a topic, term or concept • Verify definitions dispatch via the ESIP Community Ontology Repository [5], and  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.18866780.v1">doi:10.6084/m9.figshare.18866780.v1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/cz63fw5onnbxxdwwtoyiksw2em">fatcat:cz63fw5onnbxxdwwtoyiksw2em</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20220207100517/https://s3-eu-west-1.amazonaws.com/pstorage-esip-59238749823042/33677501/SWEET_Session_19Jan2022_Rovetto_v1.pdf?X-Amz-Algorithm=AWS4-HMAC-SHA256&amp;X-Amz-Credential=AKIAIQ5OITBVR63NL6XA/20220207/eu-west-1/s3/aws4_request&amp;X-Amz-Date=20220207T100516Z&amp;X-Amz-Expires=10&amp;X-Amz-SignedHeaders=host&amp;X-Amz-Signature=d31c36e1d573dd86990374f1bee6b41e8d164fb0b7236bf49230d235497c9a92" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/19/3e/193eabdd618fc21449310ac4fb44c23671a8f294.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.6084/m9.figshare.18866780.v1"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="unlock alternate icon" style="background-color: #fb971f;"></i> figshare.com </button> </a>

MiDas: automatic extraction of a common domain of discourse in sleep medicine for multi-center data integration

Satya S Sahoo, Chimezie Ogbuji, Lingyun Luo, Xiao Dong, Licong Cui, Susan S Redline, Guo-Qiang Zhang
<span title="2011-10-22">2011</span> <i title="American Medical Informatics Association"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/g6q27b56yzeupjryv6lby2r2pa" style="color: black;">AMIA Annual Symposium Proceedings</a> </i> &nbsp;
Clinical studies often use data dictionaries with controlled sets of terms to facilitate data collection, limited interoperability and sharing at a local site.  ...  Using the Multi-Modality, Multi-Resource Environment for Physiological and Clinical Research (Physio-MIMI) multi-center project in sleep medicine as a use case, we demonstrate the use of MiDas in extracting  ...  This research was supported in part by the Physio-MIMI project (NCRR-94681DBS78) and Case Western Reserve University/Cleveland Clinic & CTSA Grant (UL1 RR024989).  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22195180">pmid:22195180</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3243207/">pmcid:PMC3243207</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tazkidfxlncn5lb3tfwmcfqpfa">fatcat:tazkidfxlncn5lb3tfwmcfqpfa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200209193311/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC3243207&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/24/a3/24a3426ede02c086bc4506aa49707667707f1354.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3243207" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

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

Christopher Ochs, James Geller, Yehoshua Perl, Mark A. Musen
<span title="">2016</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/p4kk6lusgrhyxecgig72iasi5q" style="color: black;">Journal of Biomedical Informatics</a> </i> &nbsp;
In this paper, we describe the Ontology Abstraction Framework (OAF), a unified framework and software system for deriving, visualizing, and exploring partialarea taxonomy abstraction networks.  ...  In previous work, we have introduced different kinds of abstraction networks to provide a theoretical foundation for ontology quality assurance tools.  ...  The authors thank David Kaufmann and Stephanie Furniss for their work on the preliminary OAF user evaluations.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2016.06.008">doi:10.1016/j.jbi.2016.06.008</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/27345947">pmid:27345947</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4987206/">pmcid:PMC4987206</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/aetz22yux5aftoxywhu4x44gzi">fatcat:aetz22yux5aftoxywhu4x44gzi</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20191028223603/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4987206&amp;blobtype=pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/21/7e/217eb075d6d9c6a322b98e2013053fc0db906142.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2016.06.008"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4987206" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

Knowledge Domain Navigation in Interdisciplinary Digital Landscapes

Arjun Sabharwal
<span title="">2011</span> <i title="Informa UK Limited"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4jnfyoqdq5babjkc6toi6h7c2i" style="color: black;">Journal of Library Metadata</a> </i> &nbsp;
Subject metadata fields are especially suited to controlled vocabularies organized in taxonomies.  ...  The conceptual framework for knowledge domain navigation has two dimensions: epistemological and ontological.  ...  control and content standards, clearly stating conditions and terms for use, support-long-term preservation, and having "the qualities of good objects including authority, authenticity, archivability,  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/19386389.2011.570655">doi:10.1080/19386389.2011.570655</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/tqmm45brk5ctvhqu3t4zsbniu4">fatcat:tqmm45brk5ctvhqu3t4zsbniu4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20160328014421/http://web.simmons.edu:80/~weigle/INTERO_METADATA_LANGU/Sabharwal_KnowledgeDomainNavigation.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/48/06/4806bf8088eaea084b943ae18bd553e3769c58bb.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1080/19386389.2011.570655"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> tandfonline.com </button> </a>

Ontology-Driven Automated Generation of Data Entry Interfaces to Databases [chapter]

Alan Cannon, Jessie B. Kennedy, Trevor Paterson, Mark F. Watson
<span title="">2004</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/2w3awgokqne6te4nvlofavy5a4" style="color: black;">Lecture Notes in Computer Science</a> </i> &nbsp;
By constraining the data entered to a term definition ontology and utilising appropriate defined domain terminology the quality of the collected data can be improved.  ...  This paper discusses an ontology based approach for the automatic generation of data entry interfaces to databases.  ...  The ontology is composed of 'Defined Terms' (terms with associated definitions and citations) and relationships between these terms.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-27811-5_15">doi:10.1007/978-3-540-27811-5_15</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ptajsvd3kncjpkrjogoh46aesa">fatcat:ptajsvd3kncjpkrjogoh46aesa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170923000654/http://www.soc.napier.ac.uk/~prometheus/prometheus_2/publications/Cannon_etal_BNCOD.pdf" title="fulltext PDF download" data-goatcounter-click="serp-fulltext" data-goatcounter-title="serp-fulltext"> <button class="ui simple right pointing dropdown compact black labeled icon button serp-button"> <i class="icon ia-icon"></i> Web Archive [PDF] <div class="menu fulltext-thumbnail"> <img src="https://blobs.fatcat.wiki/thumbnail/pdf/c8/e5/c8e5cf51b46b5991a4b24f90a1222948dcf8fa9e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-540-27811-5_15"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>
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