https://wiki.planteome.org/api.php?action=feedcontributions&feedformat=atom&user=Cjmungall 2026-04-05T04:58:04Z User contributions MediaWiki 1.41.1 https://wiki.planteome.org/index.php?title=Ontology_Working_Group_Meeting,_Tuesday_June_23rd,_2015&diff=1622 2015-06-23T02:50:34Z

<p>Cjmungall: </p> <hr /> <div>'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''<br /> <br /> Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/985703701<br /> <br /> * Who will attend: LC, MAL, DWS, PJ, BS, AM<br /> * Others: GG, JE ?<br /> * Regrets: EA, CM<br /> <br /> ==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_June_9th,_2015| June 9th]]: ==<br /> * new [[Crop_Ontology_Pages]] on the wiki (MAL)<br /> * Agrovoc discussion- Part of FAO<br /> * Updates on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)<br /> <br /> == Updates on New Hires, etc==<br /> * '''OSU: New Postdoc Curator has joined the team: Austin Meier'''<br /> ** Austin's Background: <br /> <br /> <br /> * NYBG: - Offer to postdoc candidate has been made, waiting for confirmation, graduate student will be joining to help with the imaging work, and a summer undergrad intern to help with the imaging<br /> <br /> ==Report from Bioversity team: Marie_Angelique==<br /> <br /> ==Mappings from CO to TO: MAL==<br /> From [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015]] :<br /> * Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool<br /> * Import as OWL or OBO, * Needs to make the product using owl files??<br /> * Add mapping to terms, structure or words<br /> <br /> ===Results of mapping to [http://www.cropontology.org/ontology/CO_321/Wheat Wheat Ontology CO:321]===<br /> * The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)<br /> * The manually created '''Xrefs to TO''' can be used to double check the AML mappings (a caution as they were created some time ago- may be out of date) <br /> * The AML tool found about 73 mapping, case independent <br /> * Results on [https://github.com/Planteome/ibp-wheat-traits/tree/master/mappings Github]<br /> <br /> * Results: color coding:<br /> ** Green- Xref and AML in agreement<br /> ** Orange- Xref and AML NOT in agreement<br /> ** No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.<br /> <br /> * Mapping to PO was complicated by the presence of the synonyms, and issue of AML did not want to use the PO terms more than once. <br /> <br /> Examples of lack of agreement:<br /> * CO term: CO:321:0000040 grain size <br /> * Xref to: seed size TO:0000391<br /> * AML maps it to: TO:0000397 grain size (which is correct)<br /> <br /> Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- ''Are these only in the wheat file right now?''<br /> <br /> ==Next Meeting Tuesday July 21st==<br /> <br /> Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page</div>

Cjmungall