Report Open Access

Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species

Matentzoglu, Nicolas; Balhoff, James P.; Bello, Susan M.; Boerkoel, Cornelius F.; Bradford, Yvonne M.; Carmody, Leigh C.; Cooper, Laurel D.; Grove, Christian A.; Harris, Nomi L.; Köhler, Sebastian; Laporte, Marie-Angélique; Laulederkind, Stanley L.F.; Lee, Raymond; Mazandu, Gaston K.; McMurry, Julie A.; Mungall, Chris; Osumi-Sutherland, David; Pilgrim, Clare; Rageth, Kayli; Robb, Sofia M.C.; Robinson, Peter N.; Segerdell, Erik; Thessen, Anne; Vasilevsky, Nicole; Zhang, Xingmin A.; Haendel, Melissa A.


MARC21 XML Export

<?xml version='1.0' encoding='UTF-8'?>
<record xmlns="http://www.loc.gov/MARC21/slim">
  <leader>00000nam##2200000uu#4500</leader>
  <datafield tag="041" ind1=" " ind2=" ">
    <subfield code="a">eng</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">phenomics</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">deep phenotyping</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">ontologies</subfield>
  </datafield>
  <datafield tag="653" ind1=" " ind2=" ">
    <subfield code="a">phenotype ontologies</subfield>
  </datafield>
  <controlfield tag="005">20200120152716.0</controlfield>
  <datafield tag="500" ind1=" " ind2=" ">
    <subfield code="a">Funding: This workshop was supported by an NIH conference grant "Forums for Integrative phenomics" to Melissa Haendel and Peter Robinson: 1U13CA221044.</subfield>
  </datafield>
  <controlfield tag="001">2382757</controlfield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Renaissance Computing Institute, University of North Carolina at Chapel Hill</subfield>
    <subfield code="0">(orcid)0000-0002-8688-6599</subfield>
    <subfield code="a">Balhoff, James P.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">The Jackson Laboratory, Bar Harbor, ME, USA</subfield>
    <subfield code="0">(orcid)0000-0003-4606-0597</subfield>
    <subfield code="a">Bello, Susan M.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Sanford Imagenetics, Sanford Health, Sioux Falls, SD, USA</subfield>
    <subfield code="a">Boerkoel, Cornelius F.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">University of Oregon, Institute of Neuroscience</subfield>
    <subfield code="0">(orcid)0000-0002-9900-7880</subfield>
    <subfield code="a">Bradford, Yvonne M.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA</subfield>
    <subfield code="0">(orcid)0000-0001-7941-2961</subfield>
    <subfield code="a">Carmody, Leigh C.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Department of Botany and Plant Pathology, Oregon State University</subfield>
    <subfield code="0">(orcid)0000-0002-6379-8932</subfield>
    <subfield code="a">Cooper, Laurel D.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">California Institute of Technology</subfield>
    <subfield code="0">(orcid)0000-0001-9076-6015</subfield>
    <subfield code="a">Grove, Christian A.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA</subfield>
    <subfield code="0">(orcid)0000-0001-6315-3707</subfield>
    <subfield code="a">Harris, Nomi L.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Charité Centrum für Therapieforschung, Charité - Universitätsmedizin Berlin Corporate Member of Freie Universität Berlin, Humboldt-Universität zu Berlin, and Berlin Institute of Health, Berlin, 10117, Germany</subfield>
    <subfield code="0">(orcid)0000-0002-5316-1399</subfield>
    <subfield code="a">Köhler, Sebastian</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Bioversity International</subfield>
    <subfield code="0">(orcid)0000-0002-8461-9745</subfield>
    <subfield code="a">Laporte, Marie-Angélique</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Marquette University, Medical College of Wisconsin</subfield>
    <subfield code="0">(orcid)0000-0001-5356-4174</subfield>
    <subfield code="a">Laulederkind, Stanley L.F.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Wormbase, www.wormbase.org</subfield>
    <subfield code="0">(orcid)0000-0002-8151-7479</subfield>
    <subfield code="a">Lee, Raymond</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Human Genetics, University of Cape Town, SA</subfield>
    <subfield code="a">Mazandu, Gaston K.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Linus Pauling institute, Oregon State University, Corvallis OR, USA</subfield>
    <subfield code="0">(orcid)0000-0002-9353-5498</subfield>
    <subfield code="a">McMurry, Julie A.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Environmental Genomics and Systems Biology, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA</subfield>
    <subfield code="0">(orcid)0000-0002-6601-2165</subfield>
    <subfield code="a">Mungall, Chris</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK</subfield>
    <subfield code="0">(orcid)0000-0002-7073-9172</subfield>
    <subfield code="a">Osumi-Sutherland, David</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">FlyBase, Department of Genetics, University of Cambridge, Downing Street, Cambridge, UK</subfield>
    <subfield code="0">(orcid)0000-0002-1373-1705</subfield>
    <subfield code="a">Pilgrim, Clare</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Sanford Imagenetics, Sanford Health, Sioux Falls, SD, USA</subfield>
    <subfield code="a">Rageth, Kayli</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Stowers Institute for Medical Research, Kansas City, MO</subfield>
    <subfield code="0">(orcid)0000-0002-3528-5267</subfield>
    <subfield code="a">Robb, Sofia M.C.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA</subfield>
    <subfield code="a">Robinson, Peter N.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Institute of Ecology and Evolution, University of Oregon, Eugene, OR</subfield>
    <subfield code="0">(orcid)0000-0002-9611-1279</subfield>
    <subfield code="a">Segerdell, Erik</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Linus Pauling institute, Oregon State University, Corvallis OR, USA</subfield>
    <subfield code="a">Thessen, Anne</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Oregon Health &amp; Science University, Portland, OR 97217</subfield>
    <subfield code="0">(orcid)0000-0001-5208-3432</subfield>
    <subfield code="a">Vasilevsky, Nicole</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">The Jackson Laboratory for Genomic Medicine, Farmington CT 06032, USA</subfield>
    <subfield code="0">(orcid)0000-0002-7284-3950</subfield>
    <subfield code="a">Zhang, Xingmin A.</subfield>
  </datafield>
  <datafield tag="700" ind1=" " ind2=" ">
    <subfield code="u">Linus Pauling institute, Oregon State University, Corvallis OR, USA</subfield>
    <subfield code="0">(orcid)0000-0001-9114-8737</subfield>
    <subfield code="a">Haendel, Melissa A.</subfield>
  </datafield>
  <datafield tag="856" ind1="4" ind2=" ">
    <subfield code="s">186926</subfield>
    <subfield code="z">md5:e7722994b47097a5ff7b8d42f711541b</subfield>
    <subfield code="u">https://zenodo.org/record/2382757/files/potato2018_workshop_report.pdf</subfield>
  </datafield>
  <datafield tag="542" ind1=" " ind2=" ">
    <subfield code="l">open</subfield>
  </datafield>
  <datafield tag="260" ind1=" " ind2=" ">
    <subfield code="c">2018-12-20</subfield>
  </datafield>
  <datafield tag="909" ind1="C" ind2="O">
    <subfield code="p">openaire</subfield>
    <subfield code="p">user-isb</subfield>
    <subfield code="o">oai:zenodo.org:2382757</subfield>
  </datafield>
  <datafield tag="100" ind1=" " ind2=" ">
    <subfield code="u">European Bioinformatics Institute (EMBL-EBI), Wellcome Trust Genome Campus, Cambridge, UK</subfield>
    <subfield code="0">(orcid)0000-0002-7356-1779</subfield>
    <subfield code="a">Matentzoglu, Nicolas</subfield>
  </datafield>
  <datafield tag="245" ind1=" " ind2=" ">
    <subfield code="a">Phenotype Ontologies Traversing All The Organisms (POTATO) workshop aims to reconcile logical definitions across species</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">user-isb</subfield>
  </datafield>
  <datafield tag="540" ind1=" " ind2=" ">
    <subfield code="u">https://creativecommons.org/licenses/by/4.0/legalcode</subfield>
    <subfield code="a">Creative Commons Attribution 4.0 International</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2="7">
    <subfield code="a">cc-by</subfield>
    <subfield code="2">opendefinition.org</subfield>
  </datafield>
  <datafield tag="650" ind1="1" ind2=" ">
    <subfield code="a">Phenotype</subfield>
    <subfield code="0">(url)http://purl.obolibrary.org/obo/UPHENO_0001001</subfield>
  </datafield>
  <datafield tag="520" ind1=" " ind2=" ">
    <subfield code="a">&lt;p&gt;Logical definitions, in particular those following the Entity-Quality approach, are increasingly used to drive automated classification of phenotypes and integrate phenotypes across species semantically. Over the years, the lack of consistent and widespread use of common standards resulted in conceptually equivalent or similar phenotypes with logically divergent definitions. Recently, pattern-based approaches such as Dead Simple Ontology Design Patterns (DOSDP) have emerged as a way to reconcile such divergent definitions on a large scale. To facilitate the widespread adoption of DOSDP-based phenotype ontology development and to organise the reconciliation process involving key model organism communities, we have established the Phenotype Ontologies Traversing All The Organisms (POTATO) Workshop Series. These workshops are part of the NIH-funded &amp;ldquo;Forums for Integrative Phenomics&amp;rdquo; conference award, which provide a venue for phenotype ontology developers and phenomics informaticians to align their goals and technical approaches. The first POTATO workshop, in August 2018, provided training in cutting-edge tools and techniques for developing and releasing ontologies using design patterns and automated imports. This workshop also featured collaborative exercises in reconciling divergent logical definitions drawn from major phenotype ontologies that resulted in a set of general recommendations for how to improve phenotype ontologies and their development as well as a set of reconciled definitions. As a result of the workshop, many of the attendees have joined a phenotype ontology reconciliation effort, aimed at developing and implementing common design patterns across a range of phenotype ontologies. We thus plan to hold additional POTATO workshops.&lt;/p&gt;</subfield>
  </datafield>
  <datafield tag="773" ind1=" " ind2=" ">
    <subfield code="n">doi</subfield>
    <subfield code="i">isVersionOf</subfield>
    <subfield code="a">10.5281/zenodo.2382756</subfield>
  </datafield>
  <datafield tag="024" ind1=" " ind2=" ">
    <subfield code="a">10.5281/zenodo.2382757</subfield>
    <subfield code="2">doi</subfield>
  </datafield>
  <datafield tag="980" ind1=" " ind2=" ">
    <subfield code="a">publication</subfield>
    <subfield code="b">report</subfield>
  </datafield>
</record>
456
232
views
downloads
All versions This version
Views 456458
Downloads 232232
Data volume 43.4 MB43.4 MB
Unique views 386388
Unique downloads 209209

Share

Cite as