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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 PomBase? 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 relevant 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 progress 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
- Maybe this isn't an issue. I think what people really need are feature pages for non gene features ...we can now see the features in the context view from the gene pages: http://www.pombase.org/spombe/result/SPAP7G5.06 *The next stage is to create pages for them and have the feature IDs linked from the adjacent features.
- 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
- 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
- Discuss what people think of making "review" versions of curated sessions accessible from literature section ? useful or not?
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
Usage stats
- 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 |
| 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 |
- 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
170515
