{"id":107,"date":"2014-11-22T23:20:10","date_gmt":"2014-11-22T22:20:10","guid":{"rendered":"http:\/\/ist.blogs.inra.fr\/wdi\/?page_id=107"},"modified":"2015-09-21T14:36:28","modified_gmt":"2015-09-21T13:36:28","slug":"use-case","status":"publish","type":"page","link":"https:\/\/ist.blogs.inrae.fr\/wdi\/use-case\/","title":{"rendered":"Query Phenotype Trials to build integrative dataset for phenotype or genetic analysis."},"content":{"rendered":"<p>The objective is to get a multitrial Phenotype dataset for a given set of plant material \/ genotype possibly filtered by trait and environment. This dataset can be used for a phenotype metaanalysis or, by adding relevant genotyping information, for a genetic study.<\/p>\n<p>Challenges:<\/p>\n<ul>\n<li>Plant material (or germplasm) can be searched identified by taxon, accession, panel, collection. We need unambiguous ID for all germplasms\n<ul>\n<li>Synonym handling: cimmyt\/2341 == inra\/986 (Open Linked Data)<\/li>\n<li>Germplasm alignment: all germplasm must receive the same ID with a fusion of synonyms list<\/li>\n<li>URIs are very good candidates here<\/li>\n<\/ul>\n<\/li>\n<li>Observed Variables \/ Traits in search results (data matrix)\n<ul>\n<li>case 1: All trials use the same ontologies\n<ul>\n<li>No alignment needed, integration is straightforward<\/li>\n<\/ul>\n<\/li>\n<li>case 2: Trials use different ontologies. They are mapped to each other.\n<ul>\n<li>There is a possible integration if protocols are compatible. This information must be encoded in the ontologies<\/li>\n<\/ul>\n<\/li>\n<li>case 3: Trials use different ontologies. They are not mapped to each other.\n<ul>\n<li>No integration possible. The Trait must be presented as different columns with sufficient metadata and traceability data to allow curation.<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<\/li>\n<li>Observed Variables \/ Traits as search parameters\n<ul>\n<li>find all possible correspondences through ontology traversing and propose the near match to the user: \u201cgrain yield\u201d\/protocol:cimmyt is equivalent to \u201cyield\u201d\/protocol:inra. Do you agree?<\/li>\n<\/ul>\n<\/li>\n<li>Markers: We also need unambiguous identification. This is likely to be very problematic.\n<ul>\n<li>URIs?<\/li>\n<li>Synonyms<\/li>\n<li>Mapping between different sources \/ platform<\/li>\n<li>Computed by genomic positioning comparison<\/li>\n<li>Stored as synonyms (Open Linked Data)<\/li>\n<\/ul>\n<\/li>\n<\/ul>\n<p><span style=\"color: #33aabd\">Written by:<\/span>\u00a0Cyril Pommier<br \/>\n<span style=\"color: #33aabd\">Published on:<\/span>\u00a002 October 2014<\/p>\n","protected":false},"excerpt":{"rendered":"<p>The objective is to get a multitrial Phenotype dataset for a given set of plant material \/ genotype possibly filtered by trait and environment. This dataset can be used for a phenotype metaanalysis or, by adding relevant genotyping information, for a genetic study. Challenges: Plant material (or germplasm) can be searched identified by taxon, accession, [&hellip;]<\/p>\n","protected":false},"author":11,"featured_media":0,"parent":0,"menu_order":0,"comment_status":"open","ping_status":"open","template":"","meta":{"footnotes":""},"class_list":["post-107","page","type-page","status-publish","hentry"],"_links":{"self":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages\/107","targetHints":{"allow":["GET"]}}],"collection":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages"}],"about":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/types\/page"}],"author":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/users\/11"}],"replies":[{"embeddable":true,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/comments?post=107"}],"version-history":[{"count":0,"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/pages\/107\/revisions"}],"wp:attachment":[{"href":"https:\/\/ist.blogs.inrae.fr\/wdi\/wp-json\/wp\/v2\/media?parent=107"}],"curies":[{"name":"wp","href":"https:\/\/api.w.org\/{rel}","templated":true}]}}