Journal article Open Access

The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants

Hoehndorf, Robert; Alshahrani, Mona; Gkoutos, Georgios V.; Gosline, George; Groom, Quentin; Hamann, Thomas; Kattge, Jens; de Oliveira, Sylvia Mota; Schmidt, Marco; Sierra, Soraya; Smets, Erik; Vos, Rutger A.; Weiland, Claus


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  <identifier identifierType="URL">https://zenodo.org/record/167636</identifier>
  <creators>
    <creator>
      <creatorName>Hoehndorf, Robert</creatorName>
      <givenName>Robert</givenName>
      <familyName>Hoehndorf</familyName>
      <nameIdentifier nameIdentifierScheme="ORCID" schemeURI="http://orcid.org/">0000-0001-8149-5890</nameIdentifier>
      <affiliation>Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955–6900, Kingdom of Saudi Arabia</affiliation>
    </creator>
    <creator>
      <creatorName>Alshahrani, Mona</creatorName>
      <givenName>Mona</givenName>
      <familyName>Alshahrani</familyName>
      <affiliation>Computational Bioscience Research Center (CBRC), King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955–6900, Kingdom of Saudi Arabia</affiliation>
    </creator>
    <creator>
      <creatorName>Gkoutos, Georgios V.</creatorName>
      <givenName>Georgios V.</givenName>
      <familyName>Gkoutos</familyName>
      <affiliation>College of Medical and Dental Sciences, Institute of Cancer and Genomic Sciences, Centre for Computational Biology, University of Birmingham, Birmingham, B15 2TT, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Gosline, George</creatorName>
      <givenName>George</givenName>
      <familyName>Gosline</familyName>
      <affiliation>Royal Botanical Gardens, Kew, Richmond, Surrey, TW9 3AB, United Kingdom</affiliation>
    </creator>
    <creator>
      <creatorName>Groom, Quentin</creatorName>
      <givenName>Quentin</givenName>
      <familyName>Groom</familyName>
      <affiliation>Botanic Garden Meise, Nieuwelaan 38, Meise, 1860, Belgium</affiliation>
    </creator>
    <creator>
      <creatorName>Hamann, Thomas</creatorName>
      <givenName>Thomas</givenName>
      <familyName>Hamann</familyName>
      <affiliation>Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Kattge, Jens</creatorName>
      <givenName>Jens</givenName>
      <familyName>Kattge</familyName>
      <affiliation>Max Planck Institute for Biogeochemistry, Hans Knoell Str. 10, Jena, 07745, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>de Oliveira, Sylvia Mota</creatorName>
      <givenName>Sylvia Mota</givenName>
      <familyName>de Oliveira</familyName>
      <affiliation>Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Schmidt, Marco</creatorName>
      <givenName>Marco</givenName>
      <familyName>Schmidt</familyName>
      <affiliation>Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany</affiliation>
    </creator>
    <creator>
      <creatorName>Sierra, Soraya</creatorName>
      <givenName>Soraya</givenName>
      <familyName>Sierra</familyName>
      <affiliation>Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Smets, Erik</creatorName>
      <givenName>Erik</givenName>
      <familyName>Smets</familyName>
      <affiliation>Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Vos, Rutger A.</creatorName>
      <givenName>Rutger A.</givenName>
      <familyName>Vos</familyName>
      <affiliation>Naturalis Biodiversity Center, P.O. Box 9517, Leiden, 2300 RA, The Netherlands</affiliation>
    </creator>
    <creator>
      <creatorName>Weiland, Claus</creatorName>
      <givenName>Claus</givenName>
      <familyName>Weiland</familyName>
      <affiliation>Senckenberg Biodiversity and Climate Research Centre (BiK-F), Senckenberganlage 25, Frankfurt am Main, 60325, Germany</affiliation>
    </creator>
  </creators>
  <titles>
    <title>The flora phenotype ontology (FLOPO): tool for integrating morphological traits and phenotypes of vascular plants</title>
  </titles>
  <publisher>Zenodo</publisher>
  <publicationYear>2016</publicationYear>
  <subjects>
    <subject>Phenotype</subject>
    <subject>Biodiversity</subject>
    <subject>Flora</subject>
    <subject>Botany</subject>
    <subject>Morphological traits</subject>
  </subjects>
  <dates>
    <date dateType="Issued">2016-11-14</date>
  </dates>
  <resourceType resourceTypeGeneral="Text">Journal article</resourceType>
  <alternateIdentifiers>
    <alternateIdentifier alternateIdentifierType="url">https://zenodo.org/record/167636</alternateIdentifier>
  </alternateIdentifiers>
  <relatedIdentifiers>
    <relatedIdentifier relatedIdentifierType="DOI" relationType="IsIdenticalTo">10.1186/s13326-016-0107-8</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/ecfunded</relatedIdentifier>
    <relatedIdentifier relatedIdentifierType="URL" relationType="IsPartOf">https://zenodo.org/communities/fp7-bmc</relatedIdentifier>
  </relatedIdentifiers>
  <rightsList>
    <rights rightsURI="http://creativecommons.org/licenses/by/4.0/legalcode">Creative Commons Attribution 4.0 International</rights>
    <rights rightsURI="info:eu-repo/semantics/openAccess">Open Access</rights>
  </rightsList>
  <descriptions>
    <description descriptionType="Abstract">&lt;p&gt;&lt;strong&gt;Background: &lt;/strong&gt;The systematic analysis of a large number of comparable plant trait data can support investigations into phylogenetics and ecological adaptation, with broad applications in evolutionary biology, agriculture, conservation, and the functioning of ecosystems. Floras, i.e., books collecting the information on all known plant species found within a region, are a potentially rich source of such plant trait data. Floras describe plant traits with a focus on morphology and other traits relevant for species identification in addition to other characteristics of plant species, such as ecological affinities, distribution, economic value, health applications, traditional uses, and so on. However, a key limitation in systematically analyzing information in Floras is the lack of a standardized vocabulary for the described traits as well as the difficulties in extracting structured information from free text.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Results: &lt;/strong&gt;We have developed the Flora Phenotype Ontology (FLOPO), an ontology for describing traits of plant species found in Floras. We used the Plant Ontology (PO) and the Phenotype And Trait Ontology (PATO) to extract entity-quality relationships from digitized taxon descriptions in Floras, and used a formal ontological approach based on phenotype description patterns and automated reasoning to generate the FLOPO. The resulting ontology consists of 25,407 classes and is based on the PO and PATO. The classified ontology closely follows the structure of Plant Ontology in that the primary axis of classification is the observed plant anatomical structure, and more specific traits are then classified based on parthood and subclass relations between anatomical structures as well as subclass relations between phenotypic qualities.&lt;/p&gt;&lt;p&gt;&lt;strong&gt;Conclusions: &lt;/strong&gt;The FLOPO is primarily intended as a framework based on which plant traits can be integrated computationally across all species and higher taxa of flowering plants. Importantly, it is not intended to replace established vocabularies or ontologies, but rather serve as an overarching framework based on which different application- and domain-specific ontologies, thesauri and vocabularies of phenotypes observed in flowering plants can be integrated.&lt;/p&gt;</description>
  </descriptions>
  <fundingReferences>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/284443/">284443</awardNumber>
      <awardTitle>European Plant Phenotyping Network</awardTitle>
    </fundingReference>
    <fundingReference>
      <funderName>European Commission</funderName>
      <funderIdentifier funderIdentifierType="Crossref Funder ID">10.13039/501100000780</funderIdentifier>
      <awardNumber awardURI="info:eu-repo/grantAgreement/EC/FP7/312848/">312848</awardNumber>
      <awardTitle>Coordination and policy development in preparation for a European OpenBiodiversity Knowledge Management System, addressing Acquisition,Curation, Synthesis, Interoperability and Dissemination</awardTitle>
    </fundingReference>
  </fundingReferences>
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