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PomBase Planning Meeting 09 Oct 2013
Cambridge - Meeting Room ???, EBI
Action item review
Postponed Action Items
- Demo of curation tool (postponed)
- Dan and Mark to see what files downloadable from PomBase? have previously been generated by Ensembl. These should be easy to create automatic updates for (In progress?)
- making Artemis applet available
- Sort out display for gene captions/summaries on gene pages (Mark)
- Paul to see to that the restriction enzyme mappings get calculated (if REBASE doesn’t work out) and/or get included as a track.
Outstanding action items carried forward from previous meeting
- AI Curators to draw up a script for the curation video. What steps do we want to show on the video? Discuss at next curator meeting. (Part Done)
- AI: Need to document how users can visualize their data privately (Ensembl https://www.ebi.ac.uk/panda/jira/browse/PB-1409)
- AI: Mark needs to know when new SO qualifiers (like TR box) are added (open jira item for Kim to generate a list) (https://www.ebi.ac.uk/panda/jira/browse/PB-1343).. also NOTE: TR box is a gene feature not a transcript feature
- AI:? Discussed moving to similar schema for proteins as for transcripts, so proteins are named systematic_ID.1 .2 matching alternative transcripts and only differentiated by "type" Any changes related to this are postponed until after 2013 which gives us time to think if this is what we really want to do (Kim sounded not keen)
- AI: Val to find assembly files pre-dating 2007, https://sourceforge.net/p/pombase/curation-tasks/24/
Action items from
- AI: send instructions to Val about how to submit data to ftp site? (Mark) (what file format for what data-types. Using accession numbers or uploading data files, genome assembly date, PMID) (Ensembl https://www.ebi.ac.uk/panda/jira/browse/PB-1411) rest is in https://www.ebi.ac.uk/panda/jira/browse/PB-1407)
- AI: Sort out display of reciprocal interactions, this should be done post-chado (as part of loading into ensembl), at the moment they are just mirrored (?) so take care with assymetrical ones (Mark)
- AI: find examples for phenotype graph relations missing (Val) relationships for graph generation, actions rolled into https://www.ebi.ac.uk/panda/jira/browse/PB-1311
- AI: do next step for SRA studies (Val)
- AI: Discussion about grant, Preproposal deadline 2 Dec, arrange meeting with WT
New (and continuing) Agenda items
Hosting high throughput datasets
- Mark demo htp data sets from Marc Bühler DAM 1 D data (discuss display pulled through to PomBase? page, and details displayed)
- ditto Juan's poly A data
Chado
Kim add a summary of changes (loader for phenotype screens etc)
Usage stats
- Corrupted stats EVERY month
Versioning
Website
- User reported intermittent browser speed issues
- Mark demo reciprocal "targetis" annotation
Phenotype ontology
2700 terms; cell cycle phenotypes overhauled
Canto
Kim add summary update
Helpdesk
Antonia add summary op open ticket status
Survey
Survey, look at results so far and address related jira priorities (many moans are ticketed)
Priority Jira tickets and setting priorities for next couple of releases
Based on survey feedback we should look at browser and blast related issues:
- Resolution problem with region in detail view https://www.ebi.ac.uk/panda/jira/browse/PB-1429
- add others
Grant
- Decide overall grant aims
Other general issues
Curation
Update on community curation
- Good quality curation, usually improving for second papers
- Some users providing annotation extensions
Literature (triage) status
Item | March meeting | April meeting | May meeting | July 3 | Aug 18 | Oct ?? |
All publications | 9755 | 9761 | 9773 | 9935 | 9989 | 10025 |
Un-triaged publications | 0 | 4 | 2 | 1 | 0 | 0 |
Curatable publications | 4735 | 4740 | 4780 | 4877 | 4896 | 4909 |
Publications with Approved sessions | 580 | 600 | 647 | 674 | 712 | 791 |
Publications with active sessions | 245 | 247 | 265 | 249 | 246 | 209 |
Publications with session needing approval | 14 | 4 | 4 | 16 | 18 | 35 |
community curatable publications | - | - | - | 262 | 351 | 385 |
community curated publications with approved sessions | - | - | - | 31 | 58 | 80 |
Canto annotations (from 2013-??-??)
name | March count | April count | May count | July count | August |
PSI-MOD | 77 | 77 | 77 | 78 | 78 |
molecular_function | 167 | 173 | 182 | 204 | 222 |
cellular_component | 211 | 245 | 272 | 353 | 376 |
biological_process | 838 | 893 | 927 | 944 | 975 |
fission_yeast_phenotype | 3519 | 3820 | 3879 | 4464 | 4971 |
Total | 4812 | 5208 | 5337 | 6043 | 6622 |
All annotation types
name | count |
DNA_binding_specificity | |
cat_act | |
ex_tools | |
pathway | |
subunit_composition | |
m_f_g | |
complementation | |
genome_org | |
misc | |
disease_associated | |
name_description | |
EC numbers | |
sequence | |
warning | |
PomBase? family or domain | |
PSI-MOD | |
PomBase? gene characterisation status | |
PomBase? gene products | |
molecular_function | |
biological_process | |
cellular_component | |
fission_yeast_phenotype | |
species_dist | |
gene_ex | |
Total |
Last month was 133102
Next priorities
Publications
- Canto nearly ready for submission
- Annotation extensions (Racheal Huntley et al) nearly ready for submission
Meetings
- Val attnded GO meeting
- feedback on "regulates" relationship
News and Outreach
Next planning meeting
AOB
- students