wiki:PombasePlanningMeetingMinutes20140122

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

  • AI: Monitor UniProt item on tracker, Ensembl (Paul?) will create mapping, Val will check https://www.ebi.ac.uk/panda/jira/browse/PB-1738
  • AI: Re user gff query the new file appears to contain LTRs , UTRs and the correct number of CDS, Mark to send file/ close ticket
  • AI: Val circulate list of proposed PIs and other groups for support letters for additional suggestions. Draft letter
  • AI: Val create a list of the Intermine features which will be useful for PomBase? users
  • AI: Re gene page revisions to deal with increasing page length Val to a) document b) make mock ups b) ask for community feedback on proposal
  • AI: Problem with Paco's data. Mark to contact Paco/Luis/Ignacio?
  • AI: Val to make curation tool videos for pombelist/FAQ

New (and continuing) Agenda items

  • Kim asked if it is possible for every access to curation.pombase.org 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, we were supposed to give prior notice, are there are procedures in place for this?
    • In future curators should curate a jira ticket to alert Mark when new features are created
  • It was 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 causes 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 possible to generate alignments on the sequence set selected only
    • What is used to generate the multiple alignments?
      • 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 contain 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

Grant

  • 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 increasing 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 looks largely suitable.
    • 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
  • Val 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

Last modified 7 years ago Last modified on Jan 22, 2014, 8:35:30 PM