Feb 18th, 2016 Ontology Working Group Meeting: Difference between revisions

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''Currently, only the is_a, part_of and occurs_in relations are being displayed''
''Currently, only the is_a, part_of and occurs_in relations are being displayed''
* See Tracker: [https://github.com/Planteome/planteome-ontology-browsers/issues/20 Relations are not being recognized and displayed in AmiGO 2.0 #20]
* See Tracker: [https://github.com/Planteome/planteome-ontology-browsers/issues/20 Relations are not being recognized and displayed in AmiGO 2.0 #20]
* CM: its a priority for GO as well and they are working on it, although they have been short-handed
* CM: its a priority for GO as well and they are working on it, although they have been short-handed, but are making it a priority for Planteome this month.
** Could browse on OLS-beta: http://www.ebi.ac.uk/ols/beta/ontologies/to (''Note that this is only the live version to.owl- cannot view the crop specific ontologies there'')  
** Could browse on OLS-beta: http://www.ebi.ac.uk/ols/beta/ontologies/to (''Note that this is only the live version to.owl- cannot view the crop specific ontologies there'')  
 
*''Can we point the OLS and others like Bioportal to 'to-basic.obo'?  Looks weird with the BFO and PLANTCHEBIROLE terms.''
''Can we point the OLS and others like Bioportal to 'to-basic.obo'?  Looks weird with the BFO and PLANTCHEBIROLE terms.''


* The annotations should be moving correctly through the relations in the graph, even if they are not displayed
* The annotations should be moving correctly through the relations in the graph, even if they are not displayed
** CM: This is why the relations
** CM: This is why the relations are being filtered. The old AmiGO would propagate everything, but now it can be set in the Planteome AmiGO 2.0 configuration. Generally, you only want the gene expression to propagate up through is_a and part_of
are being filtered.
''Need to look at the other PO relations such as has_part, participates_in, has_participant and for the TO, inheres_in and occurs_in and any others''
 


* Display of CO terms with dash or colon (''did not discuss this week'')
* Display of CO terms with dash or colon (''did not discuss this week'')

Revision as of 22:15, 18 February 2016

Planteome Ontology WG Zoom Meeting

  • Date: Thursday Feb 18th, 2016
  • Time: 8:15am PST (GMT-8)
  • Connection details: Join from PC, Mac, Linux, iOS or Android: https://zoom.us/j/627445291
  • Attendees: AM, LC, CM, PJ, MAL, EA, GK, JE

Agenda:

Amigo 2.0 issues

  • Display of relations

Currently, only the is_a, part_of and occurs_in relations are being displayed

  • The annotations should be moving correctly through the relations in the graph, even if they are not displayed
    • CM: This is why the relations are being filtered. The old AmiGO would propagate everything, but now it can be set in the Planteome AmiGO 2.0 configuration. Generally, you only want the gene expression to propagate up through is_a and part_of

Need to look at the other PO relations such as has_part, participates_in, has_participant and for the TO, inheres_in and occurs_in and any others

  • Display of CO terms with dash or colon (did not discuss this week)

Eg Cassava scale terms

  • Status of the Biocuration presentation and possible ICBO paper: Comparison of ontology mapping techniques to map traits (MAL)
    • bottleneck: needs of a collaborative revision of the design patterns
  • Revisons to the equivalence axioms
  • occurs_in, Inheres_in
  • how to describe "number_of"


    • agreement on a timeline
  • Display of the Crop Ontologies in amiGO2
    • crop specific names
  • Visit to IRRI: 7-11 March: TD revision and data annotation
  • Status of second year funding??
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