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The vertebrate taxonomy ontology: a framework for reasoning across model organism and species phenotypes

Peter E Midford, Thomas Dececchi, James P Balhoff, Wasila M Dahdul, Nizar Ibrahim, Hilmar Lapp, John G Lundberg, Paula M Mabee, Paul C Sereno, Monte Westerfield, Todd J Vision, David C Blackburn
<span title="">2013</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
Description: As a step towards development of such a resource, and to enable large-scale integration of phenotypic data across vertebrates, we created the Vertebrate Taxonomy Ontology (VTO), a semantically  ...  A hierarchical taxonomy of organisms is a prerequisite for semantic integration of biodiversity data.  ...  Mayden and K. Conway for providing information on the taxonomy of Cypriniformes, M. Sabaj Pérez, M. Coburn, T. Grande, and E.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-4-34">doi:10.1186/2041-1480-4-34</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24267744">pmid:24267744</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4177199/">pmcid:PMC4177199</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/jeagurxhvzhvto23w4szndqa2y">fatcat:jeagurxhvzhvto23w4szndqa2y</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170921233804/https://jbiomedsem.biomedcentral.com/track/pdf/10.1186/2041-1480-4-34?site=jbiomedsem.biomedcentral.com" 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/fa/a2/faa2c08cf74585fad34898637a6f0c1b20ebefb7.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-4-34"> <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/PMC4177199" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

ATOL: The Multi-species Livestock Trait Ontology [chapter]

Wiktoria Golik, Olivier Dameron, Jérôme Bugeon, Alice Fatet, Isabelle Hue, Catherine Hurtaud, Matthieu Reichstadt, Marie-Christine Salaün, Jean Vernet, Léa Joret, Frédéric Papazian, Claire Nédellec (+1 others)
<span title="">2012</span> <i title="Springer Berlin Heidelberg"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/jyopc6cf5ze5vipjlm4aztcffi" style="color: black;">Communications in Computer and Information Science</a> </i> &nbsp;
This paper presents the multi-species Animal Trait Ontology for Livestock (ATOL) and the methodology used for its design.  ...  ATOL has been designed as a reference source for indexing phenotype databases and scientific papers.  ...  was created to provide a standardized vocabulary to facilitate the comparison of trait data within and across vertebrate species.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-35233-1_28">doi:10.1007/978-3-642-35233-1_28</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/vloi43ivjff47aslnd2udwtwz4">fatcat:vloi43ivjff47aslnd2udwtwz4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200309202655/https://prodinra.inra.fr/ft?id=64A59A68-1C8C-4299-84EB-D506268A3166" 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/81/8f/818f62d4e85923c9056cfbb937335cd3bdcd054a.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/978-3-642-35233-1_28"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a>

Phenex: Ontological Annotation of Phenotypic Diversity

James Balhoff, Wasila Dahdul, Cartik Kothari, Hilmar Lapp, John Lundberg, Paula Mabee, Peter Midford, Monte Westerfield, Todd Vision
<span title="2009-12-14">2009</span> <i title="Springer Science and Business Media LLC"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/gfizkffjyzhple2sfhgk46dk2e" style="color: black;">Nature Precedings</a> </i> &nbsp;
Phenotypic differences among species have long been systematically itemized and described by biologists in the process of investigating phylogenetic relationships and trait evolution.  ...  Thus, this rich store of phenotype data has been largely unavailable for statistical and computational comparisons across studies or integration with other biological knowledge.  ...  Acknowledgments We thank the following for their contributions to the development of this software: Chris  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1038/npre.2009.4068.1">doi:10.1038/npre.2009.4068.1</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/r4uhdqwduvd6ti6ocoors4epzq">fatcat:r4uhdqwduvd6ti6ocoors4epzq</a> </span>
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Interoperability between Biomedical Ontologies through Relation Expansion, Upper-Level Ontologies and Automatic Reasoning

Robert Hoehndorf, Michel Dumontier, Anika Oellrich, Dietrich Rebholz-Schuhmann, Paul N. Schofield, Georgios V. Gkoutos, Ioannis P. Androulakis
<span title="2011-07-18">2011</span> <i title="Public Library of Science (PLoS)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/s3gm7274mfe6fcs7e3jterqlri" style="color: black;">PLoS ONE</a> </i> &nbsp;
Researchers design ontologies as a means to accurately annotate and integrate experimental data across heterogeneous and disparate data-and knowledge bases.  ...  However, many biomedical ontologies do not sufficiently formalize the semantics of their relations and are therefore limited with respect to automated reasoning for large scale data integration and knowledge  ...  Author Contributions Conceived and designed the experiments: RH. Performed the experiments: RH. Analyzed the data: RH GG PS DRS MD. Contributed reagents/ materials/analysis tools: AO RH.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1371/journal.pone.0022006">doi:10.1371/journal.pone.0022006</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21789201">pmid:21789201</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3138764/">pmcid:PMC3138764</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/3zijjpuvurdktbiwooj4ocoup4">fatcat:3zijjpuvurdktbiwooj4ocoup4</a> </span>
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An ontology-based comparative anatomy information system

Ravensara S. Travillian, Kremena Diatchka, Tejinder K. Judge, Katarzyna Wilamowska, Linda G. Shapiro
<span title="">2011</span> <i title="Elsevier BV"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/7zekrk5bkbglxhzdjmkpl6hksq" style="color: black;">Artificial Intelligence in Medicine</a> </i> &nbsp;
differences across species; (2) the design of the structure of a mapping between the anatomical models of two different species and its application to information about specific structures in humans,  ...  the analysis of genotype-phenotype relationships among various animal models in support of a wide array of clinical and scientific initiatives.  ...  We have developed a cross-species model that provides a formalized ontological framework for the analysis of structural phenotype comparison, as well as application of the model's foundational principles  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.artmed.2010.10.001">doi:10.1016/j.artmed.2010.10.001</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/21146377">pmid:21146377</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3055271/">pmcid:PMC3055271</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/scrm4hs4ebfddiwzuvrnhj4kb4">fatcat:scrm4hs4ebfddiwzuvrnhj4kb4</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170808083103/http://people.cs.vt.edu/tkjudge/Papers/Journals/OntologyBasedComparativeAnatomySystem.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/3e/ee/3eee34b36c6b3b0abd73e8a7bb0a1979bcf11f7b.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.artmed.2010.10.001"> <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/PMC3055271" 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 reference ontology for biomedical informatics: the Foundational Model of Anatomy

Cornelius Rosse, José L.V. Mejino
<span title="">2003</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;
The Foundational Model of Anatomy (FMA), initially developed as an enhancement of the anatomical content of UMLS, is a domain ontology of the concepts and relationships that pertain to the structural organization  ...  We propose the FMA as a reference ontology in biomedical informatics for correlating different views of anatomy, aligning existing and emerging ontologies in bioinformatics ontologies and providing a structure-based  ...  Model of Anatomy over a nearly 10 year period.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2003.11.007">doi:10.1016/j.jbi.2003.11.007</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/14759820">pmid:14759820</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/goicxldsajfbxfupwr635ml5py">fatcat:goicxldsajfbxfupwr635ml5py</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180722042057/http://sigpubs.biostr.washington.edu/archive/00000135/01/jbi-fma.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/a2/1e/a21ec1217fe29c37050267a46a3d0ce0a609b8e4.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1016/j.jbi.2003.11.007"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> elsevier.com </button> </a>

Phenotype Ontology Research Coordination Network meeting report: creating a community network for comparing and leveraging phenotype-genotype knowledge across species

Paula Mabee, Andrew Deans, Eva Huala, Suzanna E Lewis
<span title="2012-07-20">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/5xcscx7glffihaolts5vo2ioaa" style="color: black;">Standards in Genomic Sciences</a> </i> &nbsp;
A recent meeting of the Phenotype Research Coordination Network (RCN) aimed to coordinate and leverage current efforts.  ...  Representing phenotype in a way that can be linked to thousands of molecular genetic and environmental databases is an unresolved research challenge.  ...  We also wish to thank our hosts for this meeting, the National Evolutionary Synthesis Center (NESCent), for providing such a superb venue and support staff.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.4056/sigs.2926219">doi:10.4056/sigs.2926219</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/23409218">pmid:23409218</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3558964/">pmcid:PMC3558964</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/62pwf4mucjddbjugcpbfsw2jai">fatcat:62pwf4mucjddbjugcpbfsw2jai</a> </span>
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The Teleost Anatomy Ontology: Anatomical Representation for the Genomics Age

Wasila M. Dahdul, John G. Lundberg, Peter E. Midford, James P. Balhoff, Hilmar Lapp, Todd J. Vision, Melissa A. Haendel, Monte Westerfield, Paula M. Mabee
<span title="2010-03-29">2010</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/joedkitv5rgjbedvcdqnnoemkq" style="color: black;">Systematic Biology</a> </i> &nbsp;
This noncomputable format has also precluded linkage to the large knowledgebase of genomic, genetic, developmental, and phenotype data in model organism databases.  ...  features across species.  ...  ACKNOWLEDGMENTS We are grateful to the following for their contributions to ontology development, mostly at NESCent working groups and Phenoscape data jamborees: G.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/sysbio/syq013">doi:10.1093/sysbio/syq013</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/20547776">pmid:20547776</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2885267/">pmcid:PMC2885267</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/v2kaej7yh5dafeitupyxd54yfy">fatcat:v2kaej7yh5dafeitupyxd54yfy</a> </span>
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Evaluation of research in biomedical ontologies

R. Hoehndorf, M. Dumontier, G. V. Gkoutos
<span title="2012-09-08">2012</span> <i title="Oxford University Press (OUP)"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/op7ztx4fhvairowgqifu7dnvsi" style="color: black;">Briefings in Bioinformatics</a> </i> &nbsp;
To support the development of effective research methodologies for applied ontology, we critically discuss the question how its research results should be evaluated.  ...  the objective evaluation and comparison of research results in applied ontology.  ...  For example, the development of formal definitions for phenotype ontologies [86] can be quantitatively evaluated by using these definitions to integrate multiple model organism databases and analyse  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1093/bib/bbs053">doi:10.1093/bib/bbs053</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22962340">pmid:22962340</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3888109/">pmcid:PMC3888109</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/lyepy5en5vfpzgbq6uaaxr7aiu">fatcat:lyepy5en5vfpzgbq6uaaxr7aiu</a> </span>
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An ontology for major histocompatibility restriction

Randi Vita, James A. Overton, Emily Seymour, John Sidney, Jim Kaufman, Rebecca L. Tallmadge, Shirley Ellis, John Hammond, Geoff W. Butcher, Alessandro Sette, Bjoern Peters
<span title="2016-01-11">2016</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
No consistent nomenclature exists across different vertebrate species.  ...  Conclusions: Overall, representing MHC molecules provides a challenging and practically important test case for ontology building, and could serve as an example of how to integrate other ontology building  ...  Acknowledgements We wish to thank Kirsten Fischer Lindahl and Lutz Walter for their kind assistance with the mouse and rat MHC molecule nomenclatures, respectively.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-016-0045-5">doi:10.1186/s13326-016-0045-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/26759709">pmid:26759709</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4709943/">pmcid:PMC4709943</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/6h5naahrg5hbpoyrmebzatv2ha">fatcat:6h5naahrg5hbpoyrmebzatv2ha</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20171016182943/http://publisher-connector.core.ac.uk/resourcesync/data/Springer-OA/pdf/9d7/aHR0cDovL2xpbmsuc3ByaW5nZXIuY29tLzEwLjExODYvczEzMzI2LTAxNi0wMDQ1LTUucGRm.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/d8/26/d826c1bf17010513cdcf7fbd5e75eba52f3657a3.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/s13326-016-0045-5"> <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/PMC4709943" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The NIFSTD and BIRNLex Vocabularies: Building Comprehensive Ontologies for Neuroscience

William J. Bug, Giorgio A. Ascoli, Jeffrey S. Grethe, Amarnath Gupta, Christine Fennema-Notestine, Angela R. Laird, Stephen D. Larson, Daniel Rubin, Gordon M. Shepherd, Jessica A. Turner, Maryann E. Martone
<span title="">2008</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/u22dt24i4vfrpip5iefcgkkzbi" style="color: black;">Neuroinformatics</a> </i> &nbsp;
A critical component of the Neuroscience Information Framework (NIF) project is a consistent, flexible terminology for describing and retrieving neurosciencerelevant resources.  ...  ontology for neuroscience with sufficient granularity to describe and access a diverse collection of information became obvious.  ...  the original author(s) and source are credited.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12021-008-9032-z">doi:10.1007/s12021-008-9032-z</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/18975148">pmid:18975148</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC2743139/">pmcid:PMC2743139</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/5xu3gqt2hndotmmjru4xwnwaqu">fatcat:5xu3gqt2hndotmmjru4xwnwaqu</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170829091741/https://www.bioontology.org/sites/default/files/NIFSTD.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/de/6c/de6c55176e36f7b95859686dd2973b93e0fadfe8.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1007/s12021-008-9032-z"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> springer.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2743139" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The ontology of craniofacial development and malformation for translational craniofacial research

J.F. Brinkley, C. Borromeo, M. Clarkson, T.C. Cox, M.J. Cunningham, L.T. Detwiler, C.L. Heike, H. Hochheiser, J.L.V. Mejino, R.S. Travillian, L.G. Shapiro
<span title="2013-10-04">2013</span> <i title="Wiley"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/ljnx2e2nyjc7ddewul7pus5jqa" style="color: black;">American Journal of Medical Genetics. Part C, Seminars in Medical Genetics</a> </i> &nbsp;
We introduce the Ontology of Craniofacial Development and Malformation (OCDM) as a mechanism for representing knowledge about craniofacial development and malformation, and for using that knowledge to  ...  The OCDM is based on the Foundational Model of Anatomy (FMA), our comprehensive ontology of canonical human adult anatomy, and includes modules to represent adult and developmental craniofacial anatomy  ...  To provide a framework for this large and diverse amount of information we organize the OCDM primarily around human adult and developmental anatomy, as provided by our Foundational Model of Anatomy (FMA  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/ajmg.c.31377">doi:10.1002/ajmg.c.31377</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/24124010">pmid:24124010</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC4041627/">pmcid:PMC4041627</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/krlolzm72vdcpmu3g5n5jvzxkq">fatcat:krlolzm72vdcpmu3g5n5jvzxkq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20200208064818/http://europepmc.org/backend/ptpmcrender.fcgi?accid=PMC4041627&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/0a/14/0a14c670c4f4360edf449202679f2e0fa8144f2e.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1002/ajmg.c.31377"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> wiley.com </button> </a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4041627" title="pubmed link"> <button class="ui compact blue labeled icon button serp-button"> <i class="file alternate outline icon"></i> pubmed.gov </button> </a>

The Ontology for Parasite Lifecycle (OPL): towards a consistent vocabulary of lifecycle stages in parasitic organisms

Priti P Parikh, Jie Zheng, Flora Logan-Klumpler, Christian J Stoeckert, Christos Louis, Pantelis Topalis, Anna V Protasio, Amit P Sheth, Mark Carrington, Matthew Berriman, Satya S Sahoo
<span title="">2012</span> <i title="Springer Nature"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/iasjcyzzyncgnohh3aitx65bhq" style="color: black;">Journal of Biomedical Semantics</a> </i> &nbsp;
OPL is primarily designed to serve as a reference ontology for parasite life cycle stages that can be used for database annotation purposes and in the lab for data integration or information retrieval  ...  In addition, the ontology also models necessary contextual details, such as host information, vector information, and anatomical locations.  ...  We also thank Christopher Thomas and Cory Henson at the Kno.e.sis Center for scientific discussion on modeling of the ontology. We thank Dr.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-3-5">doi:10.1186/2041-1480-3-5</a> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/22621763">pmid:22621763</a> <a target="_blank" rel="external noopener" href="https://pubmed.ncbi.nlm.nih.gov/PMC3488002/">pmcid:PMC3488002</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ecdztyc355be5awos42kd43bwa">fatcat:ecdztyc355be5awos42kd43bwa</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20141011233431/http://www.jbiomedsem.com/content/pdf/2041-1480-3-5.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/5e/af/5eaf69241de41413e3ec631b242817dbc23dfdd0.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.1186/2041-1480-3-5"> <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/PMC3488002" 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 Survey on Usage of Ontology in Different Domain

N. MaduraiMeenachi, M. Sai Baba
<span title="2012-09-12">2012</span> <i title="Foundation of Computer Science"> International Journal of Applied Information Systems </i> &nbsp;
ONTOLOGY DEVELOPED IN THE DOMAIN OF AGRICULTURE AGROVOC is used for agriculture controlled-vocabulary searching in various systems throughout the Food and Agriculture Organization (FAO) [6] .  ...  A summary of the available ontology developed in various domains is given and no attempt has been made to evaluate them.  ...  ACKNOWLEDGEMENTS It is a pleasure to acknowledge the encouragement of Shri S.C. Chetal, Director, IGCAR. We also acknowledge the colleagues of SIRD, RMG for their participation and support.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/ijais12-450666">doi:10.5120/ijais12-450666</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/ga22ry4k3bexlcyl7fp3a453hq">fatcat:ga22ry4k3bexlcyl7fp3a453hq</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20180602220502/https://research.ijais.org/volume4/number2/ijais12-450666.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/7e/db/7edb453e39c4117ba22af7b74ad623b8d7cea7a6.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a> <a target="_blank" rel="external noopener noreferrer" href="https://doi.org/10.5120/ijais12-450666"> <button class="ui left aligned compact blue labeled icon button serp-button"> <i class="external alternate icon"></i> Publisher / doi.org </button> </a>

The role of foundational relations in the alignment of biomedical ontologies

Barry Smith, Cornelius Rosse
<span title="">2004</span> <i title="IOS Press"> <a target="_blank" rel="noopener" href="https://fatcat.wiki/container/4ju2ftoebbcvrjj6lqnnbh42wq" style="color: black;">Studies in Health Technology and Informatics</a> </i> &nbsp;
This scheme also provides a template for modeling pathology, physiological function and genotype-phenotype correlations, and it can thus serve as a reference ontology in biomedical informatics.  ...  Here we articulate the need for formally clarifying the is-a and part-of relations in the FMA and similar ontology and terminology systems.  ...  for male vs. female human beings, for human beings at various developmental stages, and for organisms in other species.  ... 
<span class="external-identifiers"> <a target="_blank" rel="external noopener" href="https://www.ncbi.nlm.nih.gov/pubmed/15360852">pmid:15360852</a> <a target="_blank" rel="external noopener" href="https://fatcat.wiki/release/4chvjequpncjfegig7fjifvh6m">fatcat:4chvjequpncjfegig7fjifvh6m</a> </span>
<a target="_blank" rel="noopener" href="https://web.archive.org/web/20170812180805/https://philpapers.org/archive/SMITRO-15.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/33/bc/33bc95c015c6b9dd39dacc94a32fc8ad9bf36c92.180px.jpg" alt="fulltext thumbnail" loading="lazy"> </div> </button> </a>
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