Version 155 (modified by val_wood, 9 years ago) (diff)


(January 21st 2013)

Outstanding Action items from November

  • AI Organise a large general "PomBase" banner
  • Demo of curation tool (postponed)
  • Send papers to Paul K.
  • AI Val/curators will start to send out a large number of community curation sessions (postponed until new session management and documenation is in place. Will continue to send out small numbers of papers)
  • AI Sam's data, decided to add "condition" Val will contact Sam, also need to add PMID and chase "quiescence term", then decide where this data should live (decided Kim's ftp directory or pombe-embl svn repository)

New action items from December

  • VW chase up pombe community browser feedback as have not responded to recent requests (DONE, not sure if anyone has responsded still)
    • VW Look into WT grant and forward details to Jürg (DONE, Jurg thinks not appropriate. Val has written application for money for catering for poster session at ISB)
    • Redesign of the PomBase front page.
      • VW open new jira item with mock up (DONE)
      • VW: Source some images of cells that could be used.
      • VW: Highlight specific papers to display on the front page
      • MM: Convert to a multi-column format.
    • MM: Load the transcriptome datasets listed on JIRA
    • MM: Update xref names before running the update annotation scripts.
    • MM takes some time to consider the order of the loading for GO term names and gene names (related to above)
    • PK/DS/MM: EMBL submission files. Work out what is going to happen with these going forward (for this Val will first test how close the current file is )
    • Search:
      • MM: Auto-regenerate the search indexes and get ES to set up a new domain and index the PomBase dumps.
      • MM: Get the simple search to include the orthologues (DONE)
      • All curators: discussion to nail down what search options and behaviour we really want, then update Jira

(DONE see

  • VW to chase up motif search code from Sanger (DONE)
  • VW/MAH to look into where UTR.fasta data came from - DONE
  • KR: Generate v31 Chado dump (DONE)
  • DS/MM: GFF and GTF usage standardisation in ensembl for downloads. Needs assigning.
  • KR: Work on the Session Management for the curation tool.

New Agenda Items

  • wild card searching "Not being able to search on partial gene names or IDs"
  • It is particularly important that the curators know in advance that a particular dataset will be taken

i) to be used in Ensembl and ii) to be hosted as the next version in PomBase?.

just in case we know of any issues with these datasets that we are in the process of fixing etc.etc.

(we also usually do a run, check the logs, fix warnings and do another run)

  • Turnaround time of < 2 months is too long once community curation is launched (version 30 is from 12

November). We should talk about ways to improve this (most MODs update nightly).

  • Gene name synching (e.g. why is mre11 still called rad32…was changed in early November?)
  • What do we need to tell CRUK lab heads to resolve their fire wall problem ?

  • Helpdesk Did anyone answer the GFF/GTF query
    • General helpdesk procedure. ...answer within a couple of days


Updates from various Areas

Curation Update

Phenotype Ontology

  • n phenotype terms
  • anything else

Chado loading

  • anything

Curation tool

  • anything

Review priorities & progress

Current jira status:

Meetings Attended/ Upcoming

  • item


  • item

PI's meeting