Pombase Planning Meeting Minutes 28 May 2013

EBI 2-4 pm
Present: Antonia, Mark, Dan, Val, Paul
Remote: Kim
Chair: Val
Minutes: Val
Apologies: Midori, Jürg, Steve

Outstanding from April and earlier

  • AI: User documentation on version naming for website, should be 'generatable' from Marks documentation (Midori)
  • AI: Curators and Kim to record curation stats. Should separate staff & community.
  • AI: Curators to ask community for pictures to rotate on the front page.
  • AI Curators to draw up a script for the curation video. What steps do we want to show on the video? Discuss at next curator meeting.

  • AI Mark will do general PomBase poster for Pombe 2013
  • AI Mark to work on automated release pipeline with regression testing. Plan is to have a pipeline ready for the next meeting (Mark - In Progress, see minutes).
  • AI: Document version calling (Mark)
  • AI: User documentation for website, should be copy-pasteable from Marks documentation (Midori)

Postponed Action Items

  • AI Demo of curation tool (postponed)
  • AI 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
  • AI: Take a look at the interaction data and see if some text-linkages can be made between interactor A and B (Mark)
  • AI NAR update paper needs to be in for September. Request beginning of June/July? (Mark).

New issues


( Fill in proposal here)

  • There will be a major version number for the community which will follow chado version numbers 34 etc For each version we will record on a PomBase? documentation page (automatically generated)
    • INSDC assembly (currently 2)
    • gene build 2.1 etc
    • annotation version will be the chado version
    • ensembl software version
    • GO GAF file date
    • Interpro release
    • compara version
    • pombe cerevisiae ortholog table version
    • etc

This means :

  • Users can report chado version for any analysis and other components will be traceable
  • Users can easily check which components other than the functional annotation (which will change every release) have changed, to see if a particular type of analysis is affected. For example analysis which is dependent only on gene structures changes will need to be updated less frequently).

  • For legacy data users can continue to use file date stamp

AI Versioning What is the action item? (MArk/Dan)

Ftp site update

Almost done

  • pep stats length has merged into the charge and mass file
  • AI Check all required files are present and correct on ftp site (Val)

Automated update pipeline

Almost finished but still need testing etc

  • AI standard health checks (Dan)
  • AI Selenium testing (Dan)
  • AI manual smoke testing (Dan)

Chado issue

  • Remove ':pep' from identifiers in cDNA FASTA file (Kim)

Discussed moving to similar schema as for transcripts, so proteins are named systematic_ID.1 .2 matching alternative transcripts and only differentiated by "type" Any changes related to this are postponed until after 2013 which gives us time to think if this is what we really want to do (Kim sounded not keen)

AI :pep val spotted that this item referred to cDNA fasta, which seems sort of odd that it has a pep ID at all? (val check)

ENA linking

This should be resolved in EMBL soon.

  • AI Once the new db_refs are present in the EMBL entries curators should e-mail NCBI to let them know (val)

Supporting the hosting of large scale datasets

Using Juan and Jurgs polyA data as a test case (or any of the other datasets listed on the jira tracker)

  • The BAM files ideally should be in ENA
    • submitting to ENA will be a world of pain for our users
    • To trouble shoot submission EG will submit these test files to ENA
  • AI create an incoming Ftp directory to support hosting incoming large scale datasets (EG)
  • AI Curators document use of ftp directory (file naming, required data etc, but this is on hold until the system is running smoothly ...Paul does not want to announce until tested). At the same time we will document the accptable file formats for each data type

Front page news

  • AI curators should ensure that front page is updated, minimally at release time (curators)

Making Artemis applet available

Kim summarized what is involved

  • use java web start
  • access chromosome file with url from Ensembl server
  • can link to a particular gene starting point relatively easy to implement
  • On hold until after pombe 2013. We will revisit at follow up meeting

PomBase? tag line

General consensus is that we should be a more definite "The scientific resource for fission yeast"

AI change Pombase tagline in database header (mark) AI change Pombase tagline in banner (midori) AI change Pombase tagline in any other publicity material (check flyer etc) (all)

make all genome features available in GFF or GTF file

  • This is in progress for EG generally.
  • In the meantime Dan suggested a RESTFUL interface which can generate this file

AI Report that the GFF "source" column should be the specific data provider (PomBase? not Ensembl) (dan) DONE

Pombe 2013


  • AI Val to circulate pombe 2013 flyer (not will be printed on A5)
  • AI changes for pombe 2013 flyer (mark)
    • i) make PomBase?.org bigger
    • ii) remove or replace FYPO logo
    • iii) slightly reduce size of smart phone swipy image (it still looks large at A5 resolution; should be 2-2.5 cm sq?)
    • iv) Italicise organims
    • v) what did we decide to do about the pombelist URL (omit?)
    • vi) add poster numbers


  • AI Ask Jurg if it is possible to include the twitter #pombe2013 in conference materials (in addition to our leaflet) (val)
  • AI Add link to twitter feed from Pombase (Mark)
  • AI Publicise twitter feed on mailing list just before the meeting (Mark)


  • Paul K will attend the Thursday lunchtime demo to take questions/feedback about the browser or other Ensembl related features
  • AI ask Jurg if the demo sessions can be advertised as 30 min demos. We plan to run the session for 30 mins, and allow people the opportunity to leave, but will stay until the next conference session begins to run discussion and answer questions (val)

Update cycle

Update cycle appears to be running smoothly. This update has been postponed to allow time to include detailed phenotype data from (about 14000 annotations)

  • AI Val liaise with Mark to make sure the update begins with time to get the new phenotype data live for pombe 2013
  • AI Val will get as much of the phenotype data from mapped as possible but won't be able to finalise until Midori includes all of the new population phenotype terms required which may take a few days
  • Minor issue with the last update, some gene lists were missing for specific ontology terms. This was due to the annotation extension term names not being updated with the ontology. Mark has changed this so that everything (ontology terms and extensions0 are updated, so this should not happen in future

Usage stats

We think we are heading for ~ 7000 unique users a month since geneDB shut down, however this has not been possible to check because the stats are not currently being generated

AI Report non generation of web stats (Mark)

New data types in feature qualifiers (mainly SO terms)

AI Mark needs to know when new SO qualifiers (like TR box) are added (open jira item for Kim to generate a list)

Curation update

Number of fully curated papers now 647 (up from 600 in April), a further 265 sessions have active sessions Now have all session management in place to start sending out bulk community curation sessions.

AI Aim to send out ~50 before pombe 2013 (val)

Jira priorities

AI Finalise the ftp updating and aim to get the remaining jira tickets for Version 35 through (Mark) Val is keen for these with the highest priority: (home page revamp) (Merge allele_type and allele columns) The front page revamp will make the resource look a little more exciting The allele type /allele description column merge will improve the presentation of the phenotype data a lot and improve the user experience for this gene page section

Last modified 7 years ago Last modified on May 30, 2013, 10:51:16 PM