Version 9 (modified by val_wood, 8 years ago) (diff)


PomBase Planning Meeting 22 Jan 2014

Cambridge - ????????

Action item review

Postponed Action Items

None, all are now on relevant trackers

Outstanding action items carried forward from previous meeting

None, all are now on relevant trackers

Action items from Nov

  • AI: Ensembl to look toward a better format to represent data which is presented at the single nucleotide level and cannot be indexed
  • AI: Mark put the contig/gene view above the above the data tracks
  • AI: Mark to zoom out detail browser view once to include context around gene
  • 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)
  • 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
  • AI: Val to Summarize tasks need to be done for the grant proposal.

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)

  • Are we still not doing somthing we are supposed to. (Re e-mail Mark was surprised about ne features appearing, I think we were supposed to give prior notice, but I don't think there are procedures in place for this?

  • 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"

"I've seen nasty GFF files which do this by having the same ID for

the gene and CDS records (etc), which I think is invalid and wrong" ...I think we do this (at least we have always used the same IDs for both historically)

  • Problems with overnight synching of drupal site. Are these resolved?
  • multiple alignment related
    • is it possble to generate alignements on the sequence set selected only
    • what is used to generate the multiple alignements?
  • UniProt? trying to generate uniprot -> pombase mappings using PomBAse, this is NOT going to work.

...Need to liaise with UniProt? to figure out what they are trying to do.

4 helpdesk tickets:

  • Query from a user we can't answer:
    • "Resolved: definition of feature types"
    • basically appear to be reporting problems with the gff file

  • Speed
    • (ETA around a month?) a new track loader where data is combined so that loading is quicker. (progess?)

  • Drupal changes, what are they?


  • 1. Val start to contact users for support letters. Also need specific letters from japonicas, Octosporus and cryptococcus neoformans communities, and WT funded researchers.

Draft requests

  • 2. Antonia/Kim? update curation increase per paper graph, generate paper curation rate graph
  • 3. 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
  • 4. Val, create a list of the Intermine features which will be immediately useful for PomBase? users
  • 5. Val contact Reactome (Peter D'Eustachio)


  • 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?
  • 6. discuss network and pathway data visualization
    • i) low resolution (PPI data)
    • ii) medium resolution (summarising GO data)- separate project?
    • iii) high resolution, pathway curation

(slides to demo)

  • 7. Curators and Mark . Document enhancements to existing gene page displays.

  • 8. Curators, mockup of graphical display of modifications and mutations in sequence context

Hosting high throughput datasets

Quite a few datasets now uploaded ready to host

Priority Jira tickets

27 tickets open for V 40

  • We should go through these and assess
  • Mark to explain drupal work


  • Nothing of note

Usage stats

  • Nov 10859 unique users
  • Dec 8512 unique users



Phenotype ontology


  • Paper submitted
  • GMOD compliance granted
  • video preontation at GMOD meeting well received
  • presenting demo to some plant communities this week possibly?

Other general issues



Update on community curation

  • Sent the second reminders for teh first batch of communiyt 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)

Literature (triage) status

ItemMarch meetingApril meeting May meeting July 3 Aug 18 Oct ??Nov 20 Jan 20
All publications975597619773 9935 9989 10025 1012010133
Un-triaged publications042 1 0 0 0 3
Curatable publications47354740 4780 4877 4896 4909 4951 4963
Publications with Approved sessions580600 647 674 712 791 884 928
Publications with active sessions245247 265 249 246 209 225 228
Publications with session needing approval144 416 18 35 23 20
community curatable publications - -- 262 351 385 433 446
community curated publications with approved sessions- -- 31 58 80 94 110
curatable publications without sessions----3730?3542 3515
  • aiming to keep "curatable publications without sessions" in decline

Canto annotations (from 2013-??-??)

nameMarch countApril countMay countJuly count
PomBase annotation extension terms1448160516511938

All annotation types

EC numbers
PomBase family or domain
PomBase gene characterisation status
PomBase gene products
PomBase annotation extension terms

(last month's total was )

Next priorities



News and Outreach

Next planning meeting