Manager Call 2016-01-20: Difference between revisions

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Attendees: Melanie, David, Kimberly, Huaiyu, Paola, Judy (briefly) [The GO grant is due Jan 25th, so attendance was limited]
=Agenda=
=Agenda=
==Annotation Files Available for Download==
==Annotation Files Available for Download==
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=Minutes=
=Minutes=
==Annotation Files Available for Download==
Melanie discussed this with Tony. Here are her notes:
1. Us [GOA] vs MODs (eg Pombase)
- we don't take IEAs
- we don't take things we can't map back to UniProt accessions
- if there are problems with the AEs we may drop them (i.e., keeping the annotation but dropping the AE)
One other potential difference between our species-specific files and those provided by MODs is that we do some filtering of the annotations to reduce redundancy:
- we do parent/child filtering of IEA annotations
- if we have essentially the same annotation from multiple sources / with multiple evidence codes, we'll retain the one that we consider to be of the highest quality (where "quality" is based on the evidence code and who supplied the annotation)
2. Us [GOA] vs GO files
Pipeline: The gene_association_goa_human file is checked into the GO SVN under geneontology.org/geneassociations/submissions. GO scripts are then run and they move the file under the /geneassociations/ directory. Those scripts do some filtering including syntax checking and removing annotations to those species for which we are not the authoritative source (e.g. mouse, rat, arabidopsis, zebrafish...)
We [GOA] do not scrape automatically the GO SVN to get files, though most of our external source files are retrieved from the /geneassociations/ directory (i.e., post-submission processing)






[[Category:GO Managers Meetings]]
[[Category:GO Managers Meetings]]

Revision as of 13:25, 20 January 2016

Attendees: Melanie, David, Kimberly, Huaiyu, Paola, Judy (briefly) [The GO grant is due Jan 25th, so attendance was limited]

Agenda

Annotation Files Available for Download

GOC Meetings for 2016

  • I think there's some confusion amongst curators about when the next site-wide consortium meeting is and what the aims of the post-ISB Geneva meeting are.
  • Geneva agenda includes discussion of protein complex annotation. Any other agenda items yet?
  • Any thoughts on when and where there might be a meeting after Geneva in April?
  • The schedule for the Geneva GOC meeting says that on Saturday April 16, "Meeting will run from 9am to 1pm." and "Optional break out groups may follow.". To book flights, we'd need to know if we should stay for the Sat afternoon or not please.

Minutes

Annotation Files Available for Download

Melanie discussed this with Tony. Here are her notes:

1. Us [GOA] vs MODs (eg Pombase)

- we don't take IEAs

- we don't take things we can't map back to UniProt accessions

- if there are problems with the AEs we may drop them (i.e., keeping the annotation but dropping the AE)

One other potential difference between our species-specific files and those provided by MODs is that we do some filtering of the annotations to reduce redundancy:

- we do parent/child filtering of IEA annotations

- if we have essentially the same annotation from multiple sources / with multiple evidence codes, we'll retain the one that we consider to be of the highest quality (where "quality" is based on the evidence code and who supplied the annotation)

2. Us [GOA] vs GO files

Pipeline: The gene_association_goa_human file is checked into the GO SVN under geneontology.org/geneassociations/submissions. GO scripts are then run and they move the file under the /geneassociations/ directory. Those scripts do some filtering including syntax checking and removing annotations to those species for which we are not the authoritative source (e.g. mouse, rat, arabidopsis, zebrafish...)

We [GOA] do not scrape automatically the GO SVN to get files, though most of our external source files are retrieved from the /geneassociations/ directory (i.e., post-submission processing)