wiki:PombasePlanningMeetingAgenda20130822

PomBase Planning Meeting 22 Aug 2013

Cambridge - Meeting Room B, Sanger Building

Action item review

Postponed Action Items

  • Demo of curation tool (postponed)
  • Mark to liaise with Giulietta to help with making a pombe community curation video (postponed until curators have script)
  • 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.

Completed Action items

Action items in progress, no follow up required

Outstanding action items

New (and continuing) Agenda items

Hosting high throughput datasets

  • Can we send out the e-mail soliciting dataset submission?

...From Nick ...the final assemblies are available for the pombe syntenic octosporus and cryophilus, see details below:

...still waiting on japonicus

Priority Jira tickets

Resolution problem with region in detail view https://www.ebi.ac.uk/panda/jira/browse/PB-1429

Health check required for search problem https://www.ebi.ac.uk/panda/jira/browse/PB-1436

Progress soliciting HTP datasets, Incoming ftp directory need this first (even for testing if not announced) https://www.ebi.ac.uk/panda/jira/browse/PB-1407

Next step for pombe SRA studies https://www.ebi.ac.uk/panda/jira/browse/PB-1405

What to do about SO filter https://www.ebi.ac.uk/panda/jira/browse/PB-1455

Reciprocal physical interaction and target_of annotations

Versioning

What is still to do here? (announce?) ...We should document somewhere the diff between INDSEC 1 & 2

Release pipeline

Is this complete?

Chado

Usage stats

http://tinyurl.com/7qs2zap

Website

Phenotype ontology

Canto

Canto, Gigascience interest http://www.gigasciencejournal.com/about

Other general issues

Helpdesk

Curation

Update on community curation

Literature (triage) status

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

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
2 DNA_binding_specificity
17 cat_act
19 ex_tools
32 pathway
32 subunit_composition
116 m_f_g
153 complementation
225 genome_org
258 misc
411 disease_associated
653 name_description
839 EC numbers
937 sequence
1601 warning
1876 PomBase? family or domain
2002 PSI-MOD
5140 PomBase? gene characterisation status
7016 PomBase? gene products
7807 molecular_function
12350 biological_process
14252 cellular_component
23807 fission_yeast_phenotype
25452 species_dist
28105 gene_ex
Total 133102

Last month was 107654

News and outreach

  • Coordinating news announcements on pombelist, front page, Google plus, twitter, linked in

  • Survey, anything outstanding?

Next priorities

Publications

Meetings

Next planning meeting

AOB

Last modified 7 years ago Last modified on Sep 3, 2013, 1:42:35 PM