View source for Ontology Working Group Meeting, Tuesday June 23rd, 2015

'''Time: 8:15am PDT (GMT-7:00) Pacific Time (US and Canada)'''
Connection details: Join from PC, Mac, iOS or Android: https://zoom.us/j/985703701
* In attendance: LC, MAL, DWS, PJ, BS, AM, JE
* Regrets: EA, CM

* Link to recording- Video: File:  [[File:Ontology WG 6-23-15 video.mp4|thumbnail|Ontology WG 6-23-15 video.mp4]]
* Link to recording- Audio: File: [[File:Ontology WG 6-23-15 audio.m4a|thumbnail|Ontology WG 6-23-15 audio.m4a]]

==Summary from last meeting [[Ontology_Working_Group_Meeting,_Tuesday_June_9th,_2015| June 9th]]: ==
* new [[Crop_Ontology_Pages]] on the wiki (MAL)
* Agrovoc discussion- Part of FAO
* Updates on Plant Disease Ontology and future plans for Plant Stress Ontology (Laurel)

== Updates on New Hires, etc==
* '''OSU: New Postdoc Curator has joined the team: Austin Meier'''
** Austin's Background:  
***Born: Omaha, NE
***Undergraduate:  BS biology (genetics): University of Iowa, Iowa City
***internship: Monsanto, Huxley IA
***Graduate:  PhD Plant Breeding, Plant Genetics:  University of Wisconsin, Madison.
 
* 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

==Report from Bioversity team: Marie_Angelique==
Notes from premeeting: 
* MAL needs the updated owl version of the ontologies for the mapping.  Can obtain owl version from SVN for PO, EO and PDO.  TO has been moved to Github so the OWL chron job is no longer running- need to talk with JE about.

Link to OWL files on SVN: 
* PO: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/OWL_format/plant_ontology.owl?view=log plant_ontology.owl]- 
** Note: this is out of date, not updating automatically?

* TO: Need to set up at Github [https://github.com/Planteome/plant-trait-ontology plant-trait-ontology]
** Need to set up automatic conversion to OWL

* PDO: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_disease/ plant_disease]
** Need to set up automatic conversion to OWL
** Need to clean up the SVN folder

* EO: [http://palea.cgrb.oregonstate.edu/viewsvn/Poc/trunk/ontology/collaborators_ontology/plant_environment/ plant-environment]
** Automatic conversion to OWL??

* Repo names for CO vocabs have been changed at Github- "IBP-rice-traits"
* Name or number spaces discussion- not resolved yet

* Note: Xref Links CO trait definitions which are mapped to Gramene right have been changed to the Planteome page- 
** These need to be updated in the actual OBO file in Github, rather than just on the CO website- refs exist in wheat and maize files only? Need to check.

==Mappings from CO to TO: MAL==
From [[Ontology_Working_Group_Meeting,_Tuesday_May_26th,_2015]] :
* Marie-Angelique is testing Mapping to TO using the program Agreement Maker Light (AML) (http://agreementmaker.org/) tool
* Import as OWL or OBO, * Needs to make the product using owl files??
* Add mapping to terms, structure or words

===Results of mapping to [http://www.cropontology.org/ontology/CO_321/Wheat Wheat Ontology CO:321]===
* The Wheat Ontology CO:321 has 240 trait terms, with 46 xrefs to the TO (done by Rosemary Shrestha)
* 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)  
* The AML tool found about 73 mapping, case independent 
* Results on [https://github.com/Planteome/ibp-wheat-traits/tree/master/mappings Github]

* Results: color coding:
** Green- Xref and AML in agreement
** Orange- Xref and AML NOT in agreement
** No color- new mapping that the AML tool found- about 30 new ones identified, need to be verified.

* 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. 

Examples of lack of agreement:
* CO term:  CO:321:0000040 grain size 
* Xref to: seed size TO:0000391
* AML maps it to: TO:0000397 grain size (which is correct)

===Test of a new algorithm developed at LASIGE in Lisbon===
* Compound matching [http://ceur-ws.org/Vol-1317/om2014_poster2.pdf Poster]
* We ran first tests with TO-PO-PATO and COWheat-PO-PATO. The idea is to only look at the top results first to check if the things are ok. 
** The top results were good for TO-PO-PATO. But we did not get result for COWheat-PO-PATO. Therefore we are working on that

==Next Meeting Tuesday July 28th==

Back to the [[Planteome_Ontology_Development_and_Coordination_Working_Group]] page