Emerging semantics to link phenotype and environment
Identifieur interne : 000247 ( Ncbi/Checkpoint ); précédent : 000246; suivant : 000248Emerging 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
Affiliations:
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</affiliation>
</author>
<author><name sortKey="Walls, Ramona L" sort="Walls, Ramona L" uniqKey="Walls R" first="Ramona L." last="Walls">Ramona L. Walls</name>
<affiliation wicri:level="1"><nlm:aff id="aff-16"><institution>iPlant Collaborative, University of Arizona</institution>
,<addr-line>Tucson, 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>
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</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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</tree>
</affiliations>
</record>
Pour manipuler ce document sous Unix (Dilib)
EXPLOR_STEP=$WICRI_ROOT/Ticri/CIDE/explor/OcrV1/Data/Ncbi/Checkpoint
HfdSelect -h $EXPLOR_STEP/biblio.hfd -nk 000247 | SxmlIndent | more
Ou
HfdSelect -h $EXPLOR_AREA/Data/Ncbi/Checkpoint/biblio.hfd -nk 000247 | SxmlIndent | more
Pour mettre un lien sur cette page dans le réseau Wicri
{{Explor lien |wiki= Ticri/CIDE |area= OcrV1 |flux= Ncbi |étape= Checkpoint |type= RBID |clé= PMC:4690371 |texte= Emerging semantics to link phenotype and environment }}
Pour générer des pages wiki
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