PomBase Planning Meeting 2 2015

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Action item review

Outstanding action items carried forward from previous meeting

Action items from

New (and continuing) Agenda items

• Versioning....
  • ​http://www.pombase.org/about/version-history (need Mark's help to get this file up to date)
  • Problem: For example FungiDB use a descriptions  gff file from PomBase?, as the main input but this only records the Schizosaccharomyces_pombe.ASM294v2.25.gff3.gz which does not change even thought the annotation changes between PomBase? versions as time goes on the gene build becomes more static but the annotation changes more. Need a way to capture the annotation version in the gff versioning.
  • From Midori: the build number in the table has never corresponded to the number embedded in the GFF file names. According to the Jira ticket, "2.1" was the build number for at least chado versions 38-40, and the GFF files nearest those dates include 2.20 and 2.21.
  • How does someone get from Schizosaccharomyces_pombe.ASM294v2.25 to know which gene build?
    • i.e where is the historical data about the on the Ensembl site about the gene build that was used in a specific release?
  • figuring the numbering of releases before 32 ( I think maybe we just used a data stamp for these?)
  • It seems that .25 is <eg_version>
  • The gff file should be renamed to capture
  • PomBase? sequence assembly version
  • gene build version
  • annotation version

• Display of wild strains, see previous minutes
  • Need to discuss what we can feasibly display in the light of the volume and scope of the data
  • should we just attach the phenotype trait data to the SNP?

• Discuss what people think of making "review" versions of curated sessions accessible from literature section ? useful or not?
  • Curation attribution
  • Can flag if a paper is curated or not
  • Raises visibility of what a 'curation session' looks like
  • Can see all annotation from a paper simultaneously

• When will usage stats be back?
  • IS it possible to provide a list of most frequently accessed pages?

Hosting high throughput datasets

• None pending at high priority
  • Carr lab replication origins
  • Gx data (postponed waiting for user0
  • Runge lab, pending (transposon insertions?)

Next Priority Jira tickets

• 1. Finalising any gene page display issues related to summary views etc (phenotype, GO and multi-gene phenotype). Tickets related to this are now collected at Chado future 1 (6 tickets).

• 2. Query builder related tickets especially to handle GO annotation extensions, phenotype conditions and alleles, multi gene phenotypes and sequence features.
  • Curators need to discuss, and then with Kim and Mark, should have done this before meeting

• 3. Refining the Query builder results download for the above new query types (and the others which had previously been identified - downloading physical interactions or GO terms associated with a gene list).

• 4. Other tickets related to the term suggestion behaviour.

• Then tickets in Chado future 3 which appear to be stalled

Chado

Usage stats

​http://tinyurl.com/7qs2zap

• Is it possible to get lists of the most frequently accessed gene pages?

Versioning

Website

Phenotype ontology

Canto

• Kim is finalising multi gene phenotypes (and their storage in Canto), many annotation transfer speed ups.
  • We have a large volume of multi gene phenotype data ready to input so this will be the issues to tackle immediately after the compact display. *There are related tickets already for how this should look on the gene pages.

Other general issues

Helpdesk

Curation

Update on community curation

Literature (triage) status

Item	March 2013	April 2013	May 2013	Aug 2013	May7 2014	July 23 2014	Oct 2014	March 2015
All publications	9755	9761	9773	9989	10356	10400	10522	10693
Curatable publications	4735	4740	4780	4896	5017	5070	4873	4974
Publications with Approved sessions	580	600	647	712	1083	1187	1598	1983
Publications with active sessions	245	247	265	246	220	246	225	146
Publications with session needing approval	14	4	4	18	6	11	19	4
community curatable publications	-	-	-	351	526	613	733	859
community curated publications with approved sessions	-	-	-	58	159	178	207	253
curatable publications without sessions	-	-	-	3730	3256	3177	2518	2413

• numbers of annotatable papers have dropped due to re-triage and classification of some papers that are probably of low value for curation.

All annotation types

172764 increased from 170515 in Oct

Next priorities

Publications

Meetings

News and Outreach

Next planning meeting

AOB