Emerging semantics to link phenotype and environment
Identifieur interne : 000090 ( Pmc/Curation ); précédent : 000089; suivant : 000091Emerging semantics to link phenotype and environment
Auteurs : Anne E. Thessen [États-Unis] ; Daniel E. Bunker [États-Unis] ; Pier Luigi Buttigieg [Allemagne] ; Laurel D. Cooper [États-Unis] ; Wasila M. Dahdul [États-Unis] ; Sami Domisch [États-Unis] ; Nico M. Franz [États-Unis] ; Pankaj Jaiswal [États-Unis] ; Carolyn J. Lawrence-Dill [États-Unis] ; Peter E. Midford [États-Unis] ; Christopher J. Mungall [États-Unis] ; Martín J. Ramírez [Argentine] ; Chelsea D. Specht [États-Unis] ; Lars Vogt [Allemagne] ; Rutger Aldo Vos [Pays-Bas] ; Ramona L. Walls [États-Unis] ; Jeffrey W. White [États-Unis] ; Guanyang Zhang [États-Unis] ; Andrew R. Deans [États-Unis] ; Eva Huala [États-Unis] ; Suzanna E. Lewis [États-Unis] ; Paula M. Mabee [États-Unis]Source :
- PeerJ [ 2167-8359 ] ; 2015.
Abstract
Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.
Url:
DOI: 10.7717/peerj.1470
PubMed: 26713234
PubMed Central: 4690371
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<author><name sortKey="Mungall, Christopher J" sort="Mungall, Christopher J" uniqKey="Mungall C" first="Christopher J." last="Mungall">Christopher J. Mungall</name>
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<author><name sortKey="Ramirez, Martin J" sort="Ramirez, Martin J" uniqKey="Ramirez M" first="Martín J." last="Ramírez">Martín J. Ramírez</name>
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</nlm:aff>
<country xml:lang="fr">Argentine</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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<author><name sortKey="Specht, Chelsea D" sort="Specht, Chelsea D" uniqKey="Specht C" first="Chelsea D." last="Specht">Chelsea D. Specht</name>
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,<addr-line>Berkeley, CA</addr-line>
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<author><name sortKey="Vogt, Lars" sort="Vogt, Lars" uniqKey="Vogt L" first="Lars" last="Vogt">Lars Vogt</name>
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</nlm:aff>
<country xml:lang="fr">Allemagne</country>
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<author><name sortKey="Vos, Rutger Aldo" sort="Vos, Rutger Aldo" uniqKey="Vos R" first="Rutger Aldo" last="Vos">Rutger Aldo Vos</name>
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<author><name sortKey="Walls, Ramona L" sort="Walls, Ramona L" uniqKey="Walls R" first="Ramona L." last="Walls">Ramona L. Walls</name>
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</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="White, Jeffrey W" sort="White, Jeffrey W" uniqKey="White J" first="Jeffrey W." last="White">Jeffrey W. White</name>
<affiliation wicri:level="1"><nlm:aff id="aff-17"><institution>US Arid Land Agricultural Research Center, United States Department of Agriculture—ARS</institution>
,<addr-line>Maricopa, AZ</addr-line>
,<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Zhang, Guanyang" sort="Zhang, Guanyang" uniqKey="Zhang G" first="Guanyang" last="Zhang">Guanyang Zhang</name>
<affiliation wicri:level="1"><nlm:aff id="aff-8"><institution>School of Life Sciences, Arizona State University</institution>
,<addr-line>Tempe, AZ</addr-line>
,<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Deans, Andrew R" sort="Deans, Andrew R" uniqKey="Deans A" first="Andrew R." last="Deans">Andrew R. Deans</name>
<affiliation wicri:level="1"><nlm:aff id="aff-18"><institution>Department of Entomology, Pennsylvania State University</institution>
,<addr-line>University Park, PA</addr-line>
,<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Huala, Eva" sort="Huala, Eva" uniqKey="Huala E" first="Eva" last="Huala">Eva Huala</name>
<affiliation wicri:level="1"><nlm:aff id="aff-19"><institution>Phoenix Bioinformatics</institution>
,<addr-line>Redwood City, CA</addr-line>
,<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Lewis, Suzanna E" sort="Lewis, Suzanna E" uniqKey="Lewis S" first="Suzanna E." last="Lewis">Suzanna E. Lewis</name>
<affiliation wicri:level="1"><nlm:aff id="aff-11"><institution>Genomics Division, Lawrence Berkeley National Laboratory</institution>
,<addr-line>Berkeley, CA</addr-line>
,<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
</affiliation>
</author>
<author><name sortKey="Mabee, Paula M" sort="Mabee, Paula M" uniqKey="Mabee P" first="Paula M." last="Mabee">Paula M. Mabee</name>
<affiliation wicri:level="1"><nlm:aff id="aff-6"><institution>Department of Biology, University of South Dakota</institution>
,<addr-line>Vermillion, SD</addr-line>
,<country>United States</country>
</nlm:aff>
<country xml:lang="fr">États-Unis</country>
<wicri:regionArea># see nlm:aff country strict</wicri:regionArea>
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</analytic>
<series><title level="j">PeerJ</title>
<idno type="eISSN">2167-8359</idno>
<imprint><date when="2015">2015</date>
</imprint>
</series>
</biblStruct>
</sourceDesc>
</fileDesc>
<profileDesc><textClass></textClass>
</profileDesc>
</teiHeader>
<front><div type="abstract" xml:lang="en"><p>Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.</p>
</div>
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<pmc article-type="research-article"><pmc-dir>properties open_access</pmc-dir>
<front><journal-meta><journal-id journal-id-type="nlm-ta">PeerJ</journal-id>
<journal-id journal-id-type="iso-abbrev">PeerJ</journal-id>
<journal-id journal-id-type="pmc">PeerJ</journal-id>
<journal-id journal-id-type="publisher-id">PeerJ</journal-id>
<journal-title-group><journal-title>PeerJ</journal-title>
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<issn pub-type="epub">2167-8359</issn>
<publisher><publisher-name>PeerJ Inc.</publisher-name>
<publisher-loc>San Francisco, USA</publisher-loc>
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<article-meta><article-id pub-id-type="pmid">26713234</article-id>
<article-id pub-id-type="pmc">4690371</article-id>
<article-id pub-id-type="publisher-id">1470</article-id>
<article-id pub-id-type="doi">10.7717/peerj.1470</article-id>
<article-categories><subj-group subj-group-type="heading"><subject>Biodiversity</subject>
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<subj-group subj-group-type="heading"><subject>Bioinformatics</subject>
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</article-categories>
<title-group><article-title>Emerging semantics to link phenotype and environment</article-title>
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</name>
<xref ref-type="aff" rid="aff-13">13</xref>
</contrib>
<contrib id="author-14" contrib-type="author"><name><surname>Vogt</surname>
<given-names>Lars</given-names>
</name>
<xref ref-type="aff" rid="aff-14">14</xref>
</contrib>
<contrib id="author-15" contrib-type="author"><name><surname>Vos</surname>
<given-names>Rutger Aldo</given-names>
</name>
<xref ref-type="aff" rid="aff-15">15</xref>
</contrib>
<contrib id="author-16" contrib-type="author"><name><surname>Walls</surname>
<given-names>Ramona L.</given-names>
</name>
<xref ref-type="aff" rid="aff-16">16</xref>
</contrib>
<contrib id="author-17" contrib-type="author"><name><surname>White</surname>
<given-names>Jeffrey W.</given-names>
</name>
<xref ref-type="aff" rid="aff-17">17</xref>
</contrib>
<contrib id="author-18" contrib-type="author"><name><surname>Zhang</surname>
<given-names>Guanyang</given-names>
</name>
<xref ref-type="aff" rid="aff-8">8</xref>
</contrib>
<contrib id="author-19" contrib-type="author"><name><surname>Deans</surname>
<given-names>Andrew R.</given-names>
</name>
<xref ref-type="aff" rid="aff-18">18</xref>
</contrib>
<contrib id="author-20" contrib-type="author"><name><surname>Huala</surname>
<given-names>Eva</given-names>
</name>
<xref ref-type="aff" rid="aff-19">19</xref>
</contrib>
<contrib id="author-21" contrib-type="author"><name><surname>Lewis</surname>
<given-names>Suzanna E.</given-names>
</name>
<xref ref-type="aff" rid="aff-11">11</xref>
</contrib>
<contrib id="author-22" contrib-type="author"><name><surname>Mabee</surname>
<given-names>Paula M.</given-names>
</name>
<xref ref-type="aff" rid="aff-6">6</xref>
</contrib>
<aff id="aff-1"><label>1</label>
<institution>Ronin Institute for Independent Scholarship</institution>
,<addr-line>Monclair, NJ</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-2"><label>2</label>
<institution>The Data Detektiv</institution>
,<addr-line>Waltham, MA</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-3"><label>3</label>
<institution>Department of Biological Sciences, New Jersey Institute of Technology</institution>
,<addr-line>Newark, NJ</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-4"><label>4</label>
<institution>HGF-MPG Group for Deep Sea Ecology and Technology, Alfred-Wegener-Institut, Helmholtz-Zentrum für Polar-und Meeresforschung</institution>
,<addr-line>Bremerhaven</addr-line>
,<country>Germany</country>
</aff>
<aff id="aff-5"><label>5</label>
<institution>Department of Botany and Plant Pathology, Oregon State University</institution>
,<addr-line>Corvallis, OR</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-6"><label>6</label>
<institution>Department of Biology, University of South Dakota</institution>
,<addr-line>Vermillion, SD</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-7"><label>7</label>
<institution>Department of Ecology and Evolutionary Biology, Yale University</institution>
,<addr-line>New Haven, CT</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-8"><label>8</label>
<institution>School of Life Sciences, Arizona State University</institution>
,<addr-line>Tempe, AZ</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-9"><label>9</label>
<institution>Departments of Genetics, Development and Cell Biology and Agronomy, Iowa State University</institution>
,<addr-line>Ames, IA</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-10"><label>10</label>
<addr-line>Richmond, VA</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-11"><label>11</label>
<institution>Genomics Division, Lawrence Berkeley National Laboratory</institution>
,<addr-line>Berkeley, CA</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-12"><label>12</label>
<institution>Division of Arachnology, Museo Argentino de Ciencias Naturales–CONICET</institution>
,<addr-line>Buenos Aires</addr-line>
,<country>Argentina</country>
</aff>
<aff id="aff-13"><label>13</label>
<institution>Departments of Plant and Microbial Biology & Integrative Biology, University of California</institution>
,<addr-line>Berkeley, CA</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-14"><label>14</label>
<institution>Institut für Evolutionsbiologie und Ökologie, Universität Bonn</institution>
,<addr-line>Bonn</addr-line>
,<country>Germany</country>
</aff>
<aff id="aff-15"><label>15</label>
<institution>Naturalis Biodiversity Center</institution>
,<addr-line>Leiden</addr-line>
,<country>The Netherlands</country>
</aff>
<aff id="aff-16"><label>16</label>
<institution>iPlant Collaborative, University of Arizona</institution>
,<addr-line>Tucson, AZ</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-17"><label>17</label>
<institution>US Arid Land Agricultural Research Center, United States Department of Agriculture—ARS</institution>
,<addr-line>Maricopa, AZ</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-18"><label>18</label>
<institution>Department of Entomology, Pennsylvania State University</institution>
,<addr-line>University Park, PA</addr-line>
,<country>United States</country>
</aff>
<aff id="aff-19"><label>19</label>
<institution>Phoenix Bioinformatics</institution>
,<addr-line>Redwood City, CA</addr-line>
,<country>United States</country>
</aff>
</contrib-group>
<contrib-group><contrib id="editor-1" contrib-type="editor"><name><surname>Crandall</surname>
<given-names>Keith</given-names>
</name>
</contrib>
</contrib-group>
<pub-date pub-type="epub" date-type="pub" iso-8601-date="2015-12-14"><day>14</day>
<month>12</month>
<year iso-8601-date="2015">2015</year>
</pub-date>
<pub-date pub-type="collection"><year>2015</year>
</pub-date>
<volume>3</volume>
<elocation-id>e1470</elocation-id>
<history><date date-type="received" iso-8601-date="2015-07-15"><day>15</day>
<month>7</month>
<year iso-8601-date="2015">2015</year>
</date>
<date date-type="accepted" iso-8601-date="2015-11-12"><day>12</day>
<month>11</month>
<year iso-8601-date="2015">2015</year>
</date>
</history>
<permissions><copyright-statement>© 2015 Thessen et al.</copyright-statement>
<copyright-year>2015</copyright-year>
<copyright-holder>Thessen et al.</copyright-holder>
<license xlink:href="http://creativecommons.org/licenses/by/4.0/"><license-p>This is an open access article distributed under the terms of the <ext-link ext-link-type="uri" xlink:href="http://creativecommons.org/licenses/by/4.0/">Creative Commons Attribution License</ext-link>
, which permits unrestricted use, distribution, reproduction and adaptation in any medium and for any purpose provided that it is properly attributed. For attribution, the original author(s), title, publication source (PeerJ) and either DOI or URL of the article must be cited.</license-p>
</license>
</permissions>
<self-uri xlink:href="https://peerj.com/articles/1470"></self-uri>
<abstract><p>Understanding the interplay between environmental conditions and phenotypes is a fundamental goal of biology. Unfortunately, data that include observations on phenotype and environment are highly heterogeneous and thus difficult to find and integrate. One approach that is likely to improve the status quo involves the use of ontologies to standardize and link data about phenotypes and environments. Specifying and linking data through ontologies will allow researchers to increase the scope and flexibility of large-scale analyses aided by modern computing methods. Investments in this area would advance diverse fields such as ecology, phylogenetics, and conservation biology. While several biological ontologies are well-developed, using them to link phenotypes and environments is rare because of gaps in ontological coverage and limits to interoperability among ontologies and disciplines. In this manuscript, we present (1) use cases from diverse disciplines to illustrate questions that could be answered more efficiently using a robust linkage between phenotypes and environments, (2) two proof-of-concept analyses that show the value of linking phenotypes to environments in fishes and amphibians, and (3) two proposed example data models for linking phenotypes and environments using the extensible observation ontology (OBOE) and the Biological Collections Ontology (BCO); these provide a starting point for the development of a data model linking phenotypes and environments.</p>
</abstract>
<kwd-group kwd-group-type="author"><kwd>Phenotype</kwd>
<kwd>Environment</kwd>
<kwd>Ontology</kwd>
<kwd>Semantic web</kwd>
<kwd>Biodiversity</kwd>
<kwd>Data integration</kwd>
</kwd-group>
<funding-group><award-group id="fund-1"><funding-source>US National Science Foundation</funding-source>
<award-id>DEB-0956049</award-id>
<award-id>IOS:0822201</award-id>
<award-id>IOS:1127112</award-id>
<award-id>IOS:1340112</award-id>
<award-id>DEB 1208666</award-id>
</award-group>
<award-group id="fund-2"><funding-source>European Union’s Seventh Framework Programme</funding-source>
<award-id>287589</award-id>
</award-group>
<award-group id="fund-3"><funding-source>German Research Foundation DFG</funding-source>
<award-id>DO 1880/1-1</award-id>
</award-group>
<award-group id="fund-4"><funding-source>National Science Foundation Award</funding-source>
<award-id>DBI-0735191</award-id>
<award-id>DBI-1265383</award-id>
</award-group>
<award-group id="fund-5"><funding-source>Office of Science, Office of Basic Energy Sciences</funding-source>
<award-id>R24OD011883</award-id>
</award-group>
<award-group id="fund-6"><funding-source>US Department of Energy</funding-source>
<award-id>DE-AC02-05CH11231</award-id>
</award-group>
<award-group id="fund-7"><funding-source>Phenoscape project NSF grants</funding-source>
<award-id>DBI-1062404</award-id>
<award-id>DBI-1062542</award-id>
</award-group>
<funding-statement>The scientific meeting from which this review arose was organized by the Phenotype Research Coordination Network, which is funded by the US National Science Foundation, grant number DEB-0956049. PLB’s work on this project is supported through the Micro B3 project, funded by the European Union’s Seventh Framework Programme (Joint Call OCEAN.2011-2: marine microbial diversity—new insights into marine ecosystems functioning and its biotechnological potential) under the grant agreement no 287589. SD received funding from the German Research Foundation DFG (grant DO 1880/1-1). PJ and LDC received funding from the US National Science Foundation (NSF IOS:0822201, IOS:1127112, IOS:1340112). CDS received funding from the US National Science Foundation grant number DEB 1208666. RLW was supported by the iPlant collaborative as part of the National Science Foundation Award Numbers DBI-0735191 and DBI-1265383. CJM and SEL were supported by R24OD011883 and by the Director, Office of Science, Office of Basic Energy Sciences, of the US Department of Energy under Contract No. DE-AC02-05CH11231. PMM and WMD were supported through by Phenoscape project (NSF grants DBI-1062404 and DBI-1062542). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.</funding-statement>
</funding-group>
</article-meta>
</front>
</pmc>
</record>
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