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PomBase Planning Meeting ?? Feb 2015
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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'
- http://genomebrowser.pombase.org/Schizosaccharomyces_pombe/Info/Index
- 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.
- We had a little discussion about this and Mark suggested
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
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