Ontology meeting 2016-08-25: Difference between revisions

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===TG freeform===
Following up on last week's discussion (see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#TG_freeform), these were the action items:
"FreeForm is currently broken so needs to be closed down. But could still be useful if fixed, e.g. for protein complexes (better for Birgit to add). AI: Chris to post ticket detailing problems and to look into whether there is some easy way to fix."
Chris - could you update us please? In the meantime, shall I (Paola) send another reminder to go-consortium NOT to use the tool?
===Daily report of terms and stats===
See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?
===Metadata update===
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md


===Modified proteins===
===Modified proteins===
Line 54: Line 73:
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]
NTR: population of unicellular-organism process terms [[https://github.com/geneontology/go-ontology/issues/12614]]


===TG freeform===
Following up on last week's discussion (see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#TG_freeform), these were the action items:
"FreeForm is currently broken so needs to be closed down. But could still be useful if fixed, e.g. for protein complexes (better for Birgit to add). AI: Chris to post ticket detailing problems and to look into whether there is some easy way to fix."
Chris - could you update us please? In the meantime, shall I (Paola) send another reminder to go-consortium NOT to use the tool?
===Daily report of terms and stats===


See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats
Chris, is there a quick fix to reinstate this please, or should a ticket be filed?
===Metadata update===
*GOREF plan - e.g. https://github.com/geneontology/go-site/blob/issue-214/metadata/gorefs/goref-0000002.md





Revision as of 11:20, 25 August 2016

Attendees:

Regrets:

Minutes: Paola


xref error

These keep coming in at commit:

ERROR: valid-id-space: bad xref: :develops_from Line: xref: :develops_from
ERROR: valid-id-space: bad xref: :part_of Line: xref: :part_of

TG freeform

Following up on last week's discussion (see http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#TG_freeform), these were the action items:

"FreeForm is currently broken so needs to be closed down. But could still be useful if fixed, e.g. for protein complexes (better for Birgit to add). AI: Chris to post ticket detailing problems and to look into whether there is some easy way to fix."

Chris - could you update us please? In the meantime, shall I (Paola) send another reminder to go-consortium NOT to use the tool?

Daily report of terms and stats

See http://wiki.geneontology.org/index.php/Ontology_meeting_2016-08-18#Daily_report_of_terms_and_stats

Chris, is there a quick fix to reinstate this please, or should a ticket be filed?

Metadata update


Modified proteins

There have recently been a few GH items about modified proteins particularly with respect to binding. We should reopen this discussion and formulate a proposal for the meeting at USC. [[1]] [[2]] [[3]]

Protein complexes

https://github.com/geneontology/go-ontology/issues/12574#issuecomment-242399346

Val says "many people use the "protein complex" term, and would expect that to retrieve complexes like the ribosome and the spliceosome and telomerase (I suspect)

Is it possible to define a protein complex as a complex which has only proteins, or protein and RNA components?

so protein complex --ribonucleoprotein complex

Would that be crazy? then everything can go under protein complex, unless we know that it has an RNA component, then it moves down...

This way people will retrieve all protein complexes with the protein complex term.

Similarly protein-DNA complex (telosome), which is currently not retrieved by a "protein complex" search. I doubt there are any biologists who would not describe the telosome as a 'protein complex' https://en.wikipedia.org/wiki/Shelterin

but you would not currently retrieve it with a protein complex search.."


FAO update

  • FAO now has a home on github
  • We have a partial axiomatization of some fungal CCs and BPs using FAO - now in import chain

New high level terms for fungal processes (population of unicellular organisms vs. multicellular organism)

Please read ahead of meeting, I needed a little time to wrap my head around this. (Tanya)

NTR: population of unicellular-organism process terms [[4]]