Difference between revisions of "Ontology meeting 2013-11-20"

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(Moving logical defs into the editors obo file)
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===viral cross-products (bumped to next week)===
+
===viral cross-products===
  
 
*We need a better way to represent viral modulation of cell activity. We've used has_particiapnt for now:
 
*We need a better way to represent viral modulation of cell activity. We've used has_particiapnt for now:
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===Follow-up: TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE) (bumped to next week)===
+
===Follow-up: TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE)===
  
 
See latest discussion: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-11-07#Follow-up:_TG_TEMPLATE_FOR_ORGANELLE_PART_.28LUMEN.2C_MEMBRANE.29
 
See latest discussion: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-11-07#Follow-up:_TG_TEMPLATE_FOR_ORGANELLE_PART_.28LUMEN.2C_MEMBRANE.29
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===Review of template requests in Jira (bumped to next week)===
+
===Review of template requests in Jira===
  
 
* https://www.ebi.ac.uk/panda/jira/browse/GO-58
 
* https://www.ebi.ac.uk/panda/jira/browse/GO-58
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===New TG template for 'cell migration'? (bumped to next week)===
+
===New TG template for 'cell migration'?===
  
 
Note that 'cell chemotaxis' is_a 'cell migration', which is fine based on their definitions. However, both 'cell chemotaxis' and 'cell migration' terms have logical defs based on alters_location_of, e.g.
 
Note that 'cell chemotaxis' is_a 'cell migration', which is fine based on their definitions. However, both 'cell chemotaxis' and 'cell migration' terms have logical defs based on alters_location_of, e.g.
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Chris says: "It would be good to use a more generic relation, but this depends on the hierarchy being disjoint with other classes using the same relation with a different genus.."
 
Chris says: "It would be good to use a more generic relation, but this depends on the hierarchy being disjoint with other classes using the same relation with a different genus.."
 +
  
 
=== Review proposed fixes to terms for extracellular & extra-organismal region terms - including  status of 'other organism' ===
 
=== Review proposed fixes to terms for extracellular & extra-organismal region terms - including  status of 'other organism' ===
  
 
See: https://www.ebi.ac.uk/panda/jira/browse/GO-216
 
See: https://www.ebi.ac.uk/panda/jira/browse/GO-216
 +
  
 
=== Moving logical defs into the editors obo file ===
 
=== Moving logical defs into the editors obo file ===
  
 
* https://www.ebi.ac.uk/panda/jira/browse/GO-223
 
* https://www.ebi.ac.uk/panda/jira/browse/GO-223
 +
  
 
==== Testing of OE catalogs ====
 
==== Testing of OE catalogs ====
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** don't save relations
 
** don't save relations
 
** Do a diff of the output
 
** Do a diff of the output
 +
  
 
==== Downstream changes ====
 
==== Downstream changes ====
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* Reconfigure TG to write all-in-one
 
* Reconfigure TG to write all-in-one
 
* Change pipeline, at first just emulate existing pipeline
 
* Change pipeline, at first just emulate existing pipeline
 +
  
 
=== Taxon constraints ===
 
=== Taxon constraints ===
  
 
* https://www.ebi.ac.uk/panda/jira/browse/GO-217
 
* https://www.ebi.ac.uk/panda/jira/browse/GO-217

Revision as of 14:17, 19 November 2013

Attendees:

Minutes: Tanya


viral cross-products

  • We need a better way to represent viral modulation of cell activity. We've used has_particiapnt for now:
[Term]
id: GO:0039671 ! evasion by virus of host natural killer cell activity
intersection_of: GO:0030683 ! evasion or tolerance by virus of host immune response
intersection_of: has_participant CL:0000623 ! natural killer cell

but what we really need to do is say e.g. natural killer cell activity = some biological process has_participant natural killer cell and this process is the regulation of that activity.

Also CL:0000451 ! dendritic cell term

  • We've got lots of terms that reference a specific host protein, where the virus modulates one or more functions of that protein e.g.
id: GO:0039548
name: suppression by virus of host IRF3 activity

IRF3 has multiple activities so we wouldn't make an MF term 'IRF3 activity' but we need it somewhere to be able to say the virus modulates it.

  • Processes where the differentia is that it involves a virus e.g.
id: GO:0039699
name: viral mRNA cap methylation

has_participant is wrong here...need to say has_participant some protein encoded_by virus


Follow-up: TG TEMPLATE FOR ORGANELLE PART (LUMEN, MEMBRANE)

See latest discussion: http://wiki.geneontology.org/index.php/Ontology_meeting_2013-11-07#Follow-up:_TG_TEMPLATE_FOR_ORGANELLE_PART_.28LUMEN.2C_MEMBRANE.29

Do we have action items/time-frames for them?


Stemming from question of adding 'luteinizing hormone' in GO (bumped to next week)

See email thread. Chris says: "GO eds - we will want to switch IDs in the production logical definitions before this, to check the inferences. That's another external ontology imports file - not a big deal. Discuss on thursday?"


Review of template requests in Jira


New TG template for 'cell migration'?

Note that 'cell chemotaxis' is_a 'cell migration', which is fine based on their definitions. However, both 'cell chemotaxis' and 'cell migration' terms have logical defs based on alters_location_of, e.g.

[Term]

id: GO:0072676 ! lymphocyte migration

intersection_of: GO:0016477 ! cell migration

intersection_of: alters_location_of CL:0000542 ! lymphocyte

Chris says: "It would be good to use a more generic relation, but this depends on the hierarchy being disjoint with other classes using the same relation with a different genus.."


Review proposed fixes to terms for extracellular & extra-organismal region terms - including status of 'other organism'

See: https://www.ebi.ac.uk/panda/jira/browse/GO-216


Moving logical defs into the editors obo file


Testing of OE catalogs

Can all editors test the OE beta?

  • Day-to-day editing. OK? Should be unaffected
  • Loading combined file: go_write_test.obo in editors directory
    • Save filter (advanced save):
    • ID starts-with "GO:"
    • don't save relations
    • Do a diff of the output


Downstream changes

  • Reconfigure TG to write all-in-one
  • Change pipeline, at first just emulate existing pipeline


Taxon constraints