Pombase Planning Meeting 29 April 2013

Cambridge - Sanger Building Seminar Room 2-4 pm

Action item review

Action items done

  • Curators and Kim to further discuss the monthly build which will be available on the first Monday of each month - DONE (procedures in place to produce Chado dump as specified)
  • Mark, Dan and Paul to provide an estimate for when they will be able to go live with the build given to them on the first Monday of each month - DONE (details in March meeting minutes)
  • Mark to run checks to find out the exact loading times (DONE; details in March meeting minutes)
  • Val will contact Paul K about EBI site-wide search indexing PomBase - DONE (email sent 2013-03-19)
  • Val will check when Sanger will decommission GeneDB - DONE (email sent 2013-03-19)
  • Val to look into whether phenotype annotation data are missing - DONE (traced to ontology update glitch; blame SourceForge)
  • Val to look into GO slim problems and pinpoint some example missing genes from lists - DONE (see PB-1208 and below)
  • Midori put in jira description what cDNA fasta file formats we require - DONE (in comment on PB-1214)
  • Kim to check if citexplore (references?) can be put into Chado in order to speed up loading (superseded by other work)
  • Val and Kim to see what files Kim could write some code to generate automatically in order to get regular updates (superseded; will be done as part of Ensembl pipeline)

Outstanding action items

  • Organise a large general "PomBase" banner
  • Demo of curation tool (postponed)
  • Val/curators will start to send out a large number of community curation sessions (postponed until new session management and documentation is in place. Will continue to send out small numbers of papers) - getting closer
  • Mark to liaise with Giulietta to help with making a Pombe community curation video.
  • Val to ask CRUK if their firewall is stripping cookies from pages and let Mark know
  • 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?)

New action items from March

  • Mark to work on automated release pipeline with regression testing. Plan is to have a pipeline ready for the next meeting.
  • Load and display RNA/protein expression data from Sam's paper (Mark; slated for v34)
  • Mark to sort out GO slim count anomalies (see PB-1208)
  • Remove ':pep' from identifiers in cDNA FASTA file (Mark or Dan)
  • Find out why Chado uses :pep notation (Val)
  • Mark will do general PomBase poster for Pombe 2013 (especially since old one didn't survive Biocuration 2013 ...)
  • Midori to look into beer mugs and T-shirts (in progress)

New issues


Update cycle

  • Review how to coordinate gene model/sequence feature changes with rest of release pipeline
  • Now showing v33 (7th March; 535 fully curated publications)
  • Chado load done for v34; live yet?
  • Data ready for Kim to do v35 chado load
  • Need ftp site update ASAP after v34 live (even if some has to be done manually)
  • Add Jira fix-versions for next couple chado releases

Usage stats


  • Recent troubles with references & CiteXplore/EuropePMC
    • How confident can we be that missing references or unresolved appearance (PMID:000 vs Author et al. yyyy) problems won't recur?
  • SOAP (and other) errors appearing on gene and static pages, likewise
  • Sam's data - in Chado v34; will it/did it go live with rest of v34?
  • GO slim counts (PB-1208)
  • Can we decouple static Drupal page updates (dev --> www) from data updates, so the former don't get delayed if there are problems with the latter? (PB-1270 done, for which thanks; but what about the general case in future?)
  • ETA/effort estimate for reciprocal interaction annotations (PB-873)?

Other general issues

  • Anything to report on incuding PomBase in EBI site-wide search?

Progress reports


  • Pipeline progress?
    • ftp site updates - all existing and desired new files accounted for?
  • anything not covered for issues & queries above



  • Literature (triage) status
ItemMarch meetingApril meeting
All publications97559761
Un-triaged publications04
Curatable publications47354740
Publications with Approved sessions580600
Publications with active sessions245247
Publications with session needing approval144
  • Canto annotations (from 2013-04-26)
nameMarch countApril count
PomBase annotation extension terms14481605

Phenotype ontology

  • 2016 terms
  • distinguish cell viability and population viability


  • Sam's data loaded for v34
  • GMOD want to incorporate Kim's annotation extension stuff into (central) Chado schema


  • email templates (invitation to curate, session reassignment, etc.)
  • web site improvements - content, linking
  • documentation available for annotation data types
  • GMOD want to include Canto as a GMOD-compliant tool to use with Chado

Next priorities




  • BYG Nottingham (Midori, Antonia)
    • possible community curation leads ... and Bollywood-style dancing
  • Biocuration 2013 (Val, Midori, Antonia)
    • GMOD interest in Chado & Canto, as noted above
    • Interest in Canto, phenotypes, annotation extension usage
  • GO Consortium meeting (Val, Midori, Antonia, Mark)
    • annotation extensions again!
    • GO Galaxy


  • Pombe 2013
    • 13 May curator meeting + curator/programmer conf call devoted to planning our activities, esp. lunchtime demos, tutorials, etc.
    • ideally would like Canto tutorial video ready

Next planning meeting

Wednedsay 29 May, 2-4 pm, at EBI


Last modified 7 years ago Last modified on May 28, 2013, 11:32:37 AM