PomBase Planning Meeting ?? Feb 2015

?????

Action item review

Outstanding action items carried forward from previous meeting

Action items from

New (and continuing) Agenda items

• Steve mentioned that it is not easy to find PomABse from the EBI website, and when/if you do eventually get to the EG PomBase? page, it looks as though PomBAse is a funding body not a database
  • ​http://genomebrowser.pombase.org/Schizosaccharomyces_pombe/Info/Index
    • (Also, I have mentioned in the past but a lot of the stuff on this page is not relevent to PomBAse, we should have our own 'skin'

• Has the new Ensembl Web-person person been appointed? Is the browser overhaul in progress? (Re Paul will ensure that that the Ensembl browser developers get the PomBase?? suggestions before the browser overhaul)

• Compact display progess and outstanding

• exporting GO and FYPO data in EMBl /Genbank files

• I still don't see the centromere feature, what was the outcome of this Q? check minutes

Centromere feature is not visible on region in detail view. Do we think it should be? ​http://genomebrowser.pombase.org/Schizosaccharomyces_pombe/Location/View?r=I:3735820-3807289;site=ensemblunit

• Document update procedure and time taken (Mark) Done on Confluence (Q how long is this?)

• ​https://www.ebi.ac.uk/panda/jira/browse/PB-1802 is it best to combine repeats, and ask for average datasets?

• EsyN update

• 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

• Do Ensembl have any plans how to handle chromosome interaction data ​http://nar.oxfordjournals.org/content/42/20/12585.full
  • We had a little discussion about this and Mark suggested
    • In the supplementary file there is an image of the all against all for the likelihood of interaction. It would be possible to have a track that would be a frequency of interaction (irrespective of target), which could be displayed as a gradient track. Then have 3 tracks for each phase of the cell cycle that they analysed
    • Your other option would be a custom display on the PomBase? site using a chord style diagram for regions using colour and thickness to represent the frequency of interaction between 2 positions (eg Chr1:X0-X1==Chr1:Y0-Y1 or Chr1:A0-A1==Chr2:B0-B1). Then have a representation for each phase measured. This would have the advantage of representing a flattened 3D structure and act to give context to the user.

Hosting high throughput datasets

• None pending at high priority (Carr lab replication origins and Gx data)

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

• priority ticket ​https://sourceforge.net/p/pombase/chado/390/

Usage stats

​http://tinyurl.com/7qs2zap

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
All publications	9755	9761	9773	9989	10356	10400	10522
Curatable publications	4735	4740	4780	4896	5017	5070	4873
Publications with Approved sessions	580	600	647	712	1083	1187	1598
Publications with active sessions	245	247	265	246	220	246	225
Publications with session needing approval	14	4	4	18	6	11	19
community curatable publications	-	-	-	351	526	613	733
community curated publications with approved sessions	-	-	-	58	159	178	207
curatable publications without sessions	-	-	-	3730	3256	3177	2518

• numvers of annotatable papers have dropped due to retriage and classification of some papers that are probably of low value for curation.

All annotation types

170515

Next priorities

Publications

Meetings

News and Outreach

Next planning meeting

AOB