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

Health check required for search problem

Progress soliciting HTP datasets, Incoming ftp directory need this first (even for testing if not announced)

Next step for pombe SRA studies

What to do about SO filter

Reciprocal physical interaction and target_of annotations


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

Release pipeline

Is this complete?


Usage stats


Phenotype ontology


Canto, Gigascience interest

Other general issues



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

All annotation types

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



Next planning meeting


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