wiki:PombasePlanningMeetingAgenda20131009

Version 9 (modified by val_wood, 7 years ago) (diff)

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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

http://tinyurl.com/7qs2zap

  • Corrupted stats EVERY month

Versioning

Website

Phenotype ontology

Midori add summary numbers

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:

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

ItemMarch meetingApril meeting May meeting July 3 Aug 18 Oct ??
All publications975597619773 9935 9989 10025
Un-triaged publications042 1 0 0
Curatable publications47354740 4780 4877 4896 4909
Publications with Approved sessions580600 647 674 712 791
Publications with active sessions245247 265 249 246 209
Publications with session needing approval144 416 18 35
community curatable publications - -- 262 351 385
community curated publications with approved sessions- -- 31 58 80

Canto annotations (from 2013-??-??)

nameMarch countApril countMay countJuly countAugust
PSI-MOD7777777878
molecular_function167173182204222
cellular_component211245272353376
biological_process838893927944975
fission_yeast_phenotype35193820387944644971
Total48125208533760436622

All annotation types

namecount
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

News and Outreach

Next planning meeting

AOB

  • students