wiki:PombasePlanningMeetingAgenda20130318

(March 18 2013)

Actions

Outstanding Action items

  • AI Organise a large general "PomBase" banner
  • 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)
  • AI: Mark to liaise with Giulietta to help with making a Pombe community curation video.
  • AI: Val to ask CRUK if their firewall is stripping cookies from pages and let Mark know

New action items from February

  • AI 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)
  • AI 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 (see below).
  • AI Kim to check if citexplore (references?) can be put into Chado in order to speed up loading (out of date)
  • AI Mark to run checks to find out the exact loading times (done see below)
  • AI 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?)
  • AI Val and Kim to see what files Kim could write some code to generate automatically in order to get regular updates (postpoed, will be done as part of Ensembl pipeline)

New Agenda Items

General

  • We are now showing version 31 from 19 December (324 fully curated publications)
    • V32 was skipped because version 31 hasn't gone live (330 fully curated publications)
    • V33 (7th March) (535 fully curated publications) is on stage

File formats and repositories for HTP data

  • Proteomics (Dieter Wolfe)
  • Transcriptomics/RNA seq
  • Poly A sites (Juan Mata) Bam files? GFF with score

We want to put s!ome documentation up about what users need to do

Updates from various Areas

Website update from Mark

  • Present the stats for the difference between the stage site now and the live site as it was when we were having trouble.
    • Talk about the use of Monitor.us (Starter pack is $7.50 per month and can select 3 locations by country (US has 5 of those locations) (25 listed), actual location not listed.)
    • See if it is possible to set something up in Cambridge.
    • Looking at converting the python Selenium tests into Java and then working on expanding the tests that are run.
  • Got the data on Thursday (7th March). I had started working on the ontology db and loading that so they could get the release to us. I have been able to perform the updates and reload the core and ontology

a couple of times to fix a few bugs. v33 is now on the test genomebrowser. I have initiated the stage.pombase.org Drupal server to rebuild the JSON cache. I have also rebuilt the ontology database. If everything is working and the stats look fine we should be able to start to push through to dev on Tuesday and then hopefully on to live on Wednesday.

  • Given the manual run through that I have just done; Val and Kim are you happy going forward with the timeline that I'll take the latest release on the 1st Monday of the Month and then go for release on the third Monday? This gives two weeks for the updates and then do the release on a Monday rather than a Friday?
  • After going through a full release manually I have noted down the procedure I followed, along with subsequent updates. This now needs to be formalised and packed in an automated fashion along with regression testing. My target is to focus on this after the release and hopefully have a pipeline ready for the next meeting.
  • With automation I need to work on the dumping scripts for the stats. These should come in soon after having the main pipeline generated and then I can just plumb them in accordingly.

This discussion will probably cover many of the items below:

  • update on speed and page loading
  • Update on regularity of updates
  • Progress implementing the RNA/protein expression data from Sam's paper
    • (now tabled for V 34, need to load into Chado and get display on gene page sorted)
  • Update on gene name synching (e.g. why is mre11 still called rad32…was changed in early November?)
  • Update on providing files for download
    • At present files are not consistent with version (out of date). Lots of outstanding helpdesk tickets related to this
  • synchronicity issues

http://www.ebi.ac.uk/panda/jira/browse/PB-1208

Helpdesk

  • Quite a lot of open tickets, can everone check
  • Complaint about new site speed and browser

Curation Update

triage and curation

All publications (9755)

  • Un-triaged publications (0)
  • Triaged publications (9755)
    • Curatable publications (4735)
  • 580 approved sessions up from 535 in Feb
  • Publications with active sessions (245)
  • Publications with session needing approval (14)

  • session management and help finishing for Canto (testing and update in progress)
  • Annotation in the curation tool

name count
PSI-MOD 77
molecular_function 167
cellular_component 211
biological_process 838
PomBase annotation extension terms 1448
fission_yeast_phenotype 3519
Total 6260

This brings the CV annotation grand total to 95622 to include the legacy, a lot are from genome wide/or automated (deletion phenotype (~5000), orfeome (~7000), GOA IEA (~5000), species distribution (30,000)

  • Graph (attached) shows increase in amount of curatable info in papers per year (doubled since 1995, excludes genome wide)

Phenotype Ontology

  • 2000 phenotype terms
  • anything else

Chado loading

  • anything to report ?

Curation tool

  • anything to report?

Review next priorities & progress

Current jira status:

  • Data download files
  • Other data hosting

Meetings Attended Upcoming

  • 26 Feb Ontology group at EBI
    • MAH phenotype ontology presentation
    • VW Curation tool presentation
  • 28 Feb-1 March GO cell cycle ontology content meeting ( GO (MGI/TAIR/FlyBase/PomBase/Uniprot and Jacky Hayles/ Takashi Toda and Rob De Bruin)
    • Massive cell cycle overhaul, many changes to terms and annotations, many will be through for version 34/35, will improve cell cycle representation (10% of S. p gene products)
    • VW writing report and paper
  • March 20-22 BYG 2 posters submitted: Antonia (community curation), Midori (phenotypes)
    • this week
    • MAH is doing a FYPO presentation
  • April 7-10 ISB, 4 posters submitted: Val (Annotation QC) Mark (general PomBase), Antonia (community curation), Midori (phenotypes) Mark might want to attend, at least poster sessions?
    • April 10-13 GO meeting is immediately after this meeting, Mark should attend the software sessions

  • Pombe meeting, 3 posters submitted: Val (Annotation QC), Antonia (community curation), Midori (phenotypes)

AOB

Last modified 8 years ago Last modified on Mar 18, 2013, 6:46:38 PM

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