Version 5 (modified by val_wood, 8 years ago) (diff)


PomBase Planning Meeting 22 Jan 2014

Action item review

  • AI: Ensembl to look toward a better format to represent data which is presented at the single nucleotide level and cannot be indexed
    • Dan is speaking to Eugene tomorrow, will use BigWIG with a different display

  • AI: Mark Add NCBI blast link with protein sequence submission side by side with Ensembl blast (at least until a usable blast facility is available)
    • On jira
  • AI: Midori to email to ask for data resubmissions (DONE).
  • AI: Val to email Paco for nucleosome positioning data (DONE).
  • AI: Val ask Paul Thomas /CJM to explain details of modular/LEGO annotation (later)
  • AI: Val to Summarize tasks need to be done for the grant proposal. (see below)

Collected Action items Jan

New (and continuing) Agenda items

  • Kim asked if it is possible for every access to to go (transparently) via an EBI server which could show a message if sysbiol/oliver0 is offline (more detail from Kim)
    • we will revisit this next time there is scheduled down time
  • Are we still not doing something we are supposed to? (Re e-mail Mark was surprised about new features appearing, I think we were supposed to give prior notice, but I don't think there are procedures in place for this?
    • In future curators should curate a jira ticket to alert Mark when new features are created
  • In noticed in a thread about gff3 specification "Can anyone think of a valid case where multiple feature lines might have the same ID, but different SO types"
    • This was just a heads up. We will revisit if it cuases problems

  • Problems with overnight synching of drupal site. Are these resolved?
    • Seems OK right now, and Mark can now run the Crontab

  • multiple alignment related
    • is it possble to generate alignements on the sequence set selected only
    • what is used to generate the multiple alignements?
      • In progress as a broader Ensembl item

  • Query from a user we can't answer: "Resolved: definition of feature types" basically appear to be reporting problems with the gff file
    • AI, Re user gff query the new file appears to contian LTRs , UTRs and the correct number of CDS, Mark to send file/ close ticket

  • Speed (ETA around a month?) a new track loader where data is combined so that loading is quicker. (progess?)
    • still in progress, soon
  • Drupal changes, what are they?
    • Mark needs to refactor some code to future proof


  • Val start to contact users for support letters. Also need specific letters from japonicas, Octosporus and cryptococcus neoformans communities, and WT funded researchers.
    • AI, Val circulate list of proposed PIs and other groups for support letters for additional suggestions. Draft letter
  • Antonia/Kim? update curation increase per paper graph, generate paper curation rate graph
    • DONE
  • Val speaking to Intermine and Rafael to make sure no overlap in proposal and aim to share workload. Meeting with Gos planned for mid Feb
    • AI Val, create a list of the Intermine features which will be immediately useful for PomBase? users
  • Val contacted Reactome (Peter D'Eustachio)

Proposal: It should be possible for pathways can be curated by curators, students as part of specific projects or the community (using Reactome or cell designer) Pathways will be hosted in a Reactome instance and linked to from PomBase? gene pages. also are there any widgets?

  • Discussed network and pathway data visualization
    • i) low resolution (PPI data)
    • ii) medium resolution (summarising GO data)- separate project?
    • iii) high resolution, pathway curation
  • We will propose in grant to
    • i) represent physical and geentic interactions on gene pages with cytoscape graphic (and ability to extend into larger network)
    • ii) Pathway curation using GO data to seed networks, using Cell designer and Reactome
  • Curators and Mark . Document enhancements to existing gene page displays.
    • Pages are getting VERY long (see mcm2 for e.g.) have a proposal for page configuration (cookies), and allowing users to toggle between: a) concise (non-redundant biological summary) and complete (all terms, evidences and refs) of annotation views b) Ability to sort data on all columns (terms alleles etc)

AI Re gene page revisions to deal with increasng page length Val to a) document b) make mock ups b) ask for community feedback on proposal

  • Curators, mockup of graphical display of modifications and mutations in sequence context
    • Paul showed us the Ensembl variation display which will largely do the trick.
    • We would additionally like to be able to filter display for specific phenotypes of interest

Hosting high throughput datasets

Quite a few datasets now uploaded ready to host

Priority Jira tickets

Sorted lots of unscheduled tickets

Update on community curation

  • Sent the first reminders for the first batch of community curation sessions, resulted in an increase in submitted sessions. Curators are still approving these.
  • Once we have on top of this I'll send out more reminders, and more new sessions
  • Will make video for community shortly (in next couple of weeks, now have egs. and script)

AI Val to make curation tool videos for pombelist/FAQ