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
  • AI: Mark needs to know when new SO qualifiers (like TR box) are added (open jira item for Kim to generate a list) ( 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,

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 rest is in
  • 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
  • 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


Started tidying code and documenting for GMOD acceptance.

  • We need to release the code that loads Canto data into Chado so it can be mentioned in the Canto paper.
  • Currently the code works for us but we need to split the PomBase specific code from the more general code.

Usage stats

  • Corrupted stats EVERY month



  • User reported intermittent browser speed issues
  • Mark demo reciprocal "targetis" annotation

Phenotype ontology

2700 terms; cell cycle phenotypes overhauled


Improved the documentation ready for the Canto paper, small bug fixes and small features/additions.


Antonia add summary op open ticket status


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:


  • Decide overall grant aims

Other general issues


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 countAugustSept

All annotation types

cv_name count
DNA_binding_specificity 2
cat_act 17
ex_tools 19
pathway 32
subunit_composition 42
m_f_g 116
complementation 167
genome_org 225
misc 258
disease_associated 412
name_description 669
EC numbers 839
sequence 940
warning 1603
PSI-MOD 1769
PomBase? family or domain 1881
PomBase? gene characterisation status 5142
PomBase? gene products 7018
molecular_function 8439
biological_process 12317
cellular_component 14205
gene_ex 24488
species_dist 25463
fission_yeast_phenotype 26056
TOTAL 132119

Last month was 133102

Next priorities


  • Canto paper nearly ready for submission
  • Annotation extensions (Racheal Huntley et al) nearly ready for submission


  • Val attnded GO meeting
    • feedback on "regulates" relationship

News and Outreach

Next planning meeting


  • students
Last modified 7 years ago Last modified on Oct 9, 2013, 2:09:37 PM