Version 52 (modified by gomidori, 10 years ago) (diff)


PomBase Technical Meetings

Fortnightly conference calls

26 Aug 2011

  • Mark explain the different Ensembl databases and how they fit together
  • Discuss Interactions from Chado or Intact

9 Sept 2011

  • Intersection_of tags and ontologies/Ensembl (GO/SO/FYPO)
    • ignore in the short term
    • Longer term Mark and Dan will speak to Andy (Ensembl core)
  • Interaction progress
    • Mark in importing interactions directly from Chado
  • Change time of regular slot if long term (not suitable for Jurg and Antonia)
    • Doodle poll will be arranged
  • Timelines and progress (how many Jira items, testing etc)
    • Waiting for go-ahead for testing from Mark
    • Will not get filtered GOA data before Kim leaves, so tentative release data is early November, we will draw up a list of "required for release" items
  • Still need external data to be fully loaded. Kim has done this but he is still working on internal filtering
    • see above
  • Arrange a date for the next "in person" meeting Midori will describe our phenotype model
    • Doodle poll for in around 3 weeks
  • A heads up about annotation extensions (we can probably leave this to the next in person meeting)
    • Add this to next in person meeting
  • Kim's last day!

27th Sept 2011

  • NAR paper accepted
    • Midori will circulate and submit database description
  • Controlled curation are now visible on dev, but without associated references. How soon for the physical/genetic interactions on display on dev. I don't think we fully understand this cycle.
    • Mark explained this again, some fixes (GO totals) will come through when we mirror Ensembl EG 11 (possibly Thursday)
    • dev data (including interactions) will be visible when Mark loads for Preview (probably in the next 2 weeks)

  • Reciprocal links back to "gene overview page" (curated gene page) needs to be much more prominent
    • possibilities discussed
      • i) Make link in menu bar more prominent (and not disappear when page with is small)
      • ii) Add at the top of the right hand menu bar
      • iii) Place a link in the prominent part of the "Ensembl gene summary page" (how would this be worded).
      • Most likely a combination of 2 options will be required as we need to be able to get to this page from anywhere on the Ensembl site, BUT it needs to be VERY prominent on the Ensembl gene summary page,
    • Jurg will ask his lab how obvious it is to get to the gene summary page currently, and where they would like/expect to see this
  • AI from last planning meeting....Ensembl group tell us which format specification for various HTP datasets
    • Mark to send a list of file preferences in order, for each data type which Ensembl can handle (variation, transcriptomics, general chromosomal features (replication origins etc)...etc. From this we can revise/extend until we have full list and can write suitable announcement (request for datasets).
  • Mark has made good progress displaying annotation extensions but there is an upstream issue that can only be addressed by Kim so on hold (suppress on pages for now?)
    • Mark will do a temporary fix and Midori and Val will discuss formatting on the page but this will be suppressed until release and released and announced later (will require some explanation for community so it is better if this isn't buried in the main release)
  • Any progress with the GO totals on pages ? (critical)
    • See above
  • How many critical items remain? How soon should go ahead and ask selected people to look (once we have interactions and correct GO totals?) ....will still be caveat that not all GO data loaded (HTP localization and external annotations), still waiting for Kim's filter
    • Midori will send a summary of critical list in a few days
  • Is it possible to export GFF from Ensembl?
    • GTF is possible, (how does this differ from GFF3)?
    • Need to make sure all current download data (and possibly additional ones) is available on new ftp site, with instruction in FAQ how to get specific data sets, and links from Main PomBase to different download options (Midori?)

  • If time maybe Mark can explain this item, if now we can chat to him offline later...
    • This will go away

11 October 2011

Present: Val, Midori, Antonia, Steve, Paul, Mark, Dan

  • The advanced search (aka query builder) has continued to point to EG10 for more than a week after the EG11 release, and therefore hasn't been working the whole time. I think Mark has a plan to write scripts that will speed (and automate?) the changeover for future EG updates, so this agenda item is mainly to establish that the new system MUST be in place for to proceed beyond preview. Even a one-day lag will be unacceptable once is fully live (genedb redirecting to pombase), unless something literally catches fire. (added 2011-10-07 MAH)
    • Noted and logged. Mark will fix www and dev for now; this required a manual code change.
    • For future EG updates, Mark has written and will deploy an admin interface that will simplify the change (and that he can use from home or delegate if necessary).
    • Established EG testing and release procedures will include PomBase once it's in production.
  • Any comments on the draft email to ask the community for datasets? (note that only list members can see the archive)
    • Paul et al. at EBI will comment on draft in next couple days. Once everyone is happy with the content, we'll decide exactly when to send it to pombelist (want to get it out sooner rather than later, but it's probably worth waiting until all GO data are in so people aren't distracted by missing data if they visit the pombase site).
  • Any progress on setting up focused user testing?
    • Not yet; Paul will follow up this week.
  • AOB
    • Val asked about suggesting changes to the Ensembl browser that would affect Ensembl generally. All confirmed that we should make suggestions on the PomBase Jira tracker, and Mark or Paul can forward them on as necessary (i.e. no change from procedure agreed after last planning meeting).

25 October 2011

  • Mark has 4/5 critical/blocker items outstanding and is working through these
  • still waiting on final GO load from Kim, with filters, we will try to speed this up by doing a prefilter before the database load for one step, and only filtering the redundant annotations within Chado.
  • Val will start sorting press releases
  • Dates for i) moving to preview ii) removing preview label iii) official launch

22 November 2011

From last time:

  • Mark continuing to work through open Jira items; good progress
  • Mark using chado load from about a month ago
    • Kim has filtered GO annotations where IEAs less specific than manual; next load will also filter IEAs at same specificity as manual
    • Not enough time to reload before Monday announcements, but no restriction on when to update thereafter
  • Press releases are with relevant press offices, which should get final versions to us by Friday, ready for release Monday 28 Nov.
  • We'll have to see how long it'll take to "graduate" from preview

New items:

  • left hand menu update
    • Mark will remove the stuff we don't want cluttering the page (Midori will find or create Jira item for specifics)
  • Some discussion of possible appearance tweaks for header/tab bar
    • darker shade of grey for text
    • trim whitespace borders
    • decided not to merge Submit and Download into single 'data' tab

6 December 2011

  • Launch and press releases went out on Monday 28 Nov. as planned
  • Call postponed until next week due to lack of agenda

16 20 December 2011

Present: Val, Steve, Jürg, Midori, Mark

  • Usage statistics (curators)
    • Did usage increase after the 28 Nov. announcements?
      • Yes! Mark has access to stats for visits, unique visitors, pages, and hits (and will enquire about meaning and distinction between pages and hits). Table below.
      • Many more visits and pages than Ensembl Fungi, but apples-oranges comparison
      • We can stop worrying (and close the Jira item) about traffic level
    • Need convenient link for PomBase people (essentially, the pombase-internal list members) to see usage stats (without EBI login)
    • Need to make suitable subset of usage stats available to users, SAB, funders, etc. -- preferably via publicly-accessible link
      • Mark will look into what stats can be made visible outside EBI, and how
  • Sub-domain for the curation tool - (KMR)
    • Mark hasn't heard anything yet. Needs input from Paul, and probably will involve EBI External Services. Carry item over to next call.
  • Criteria and procedure for preview phase to end (MAH)
    • Val & Midori to circulate list of things needed/conditions to meet, and who will do what
      • Items include new chado load (Kim & Mark), data sync & update improvements (Mark), page validation (Mark), filling in missing data (Val, Kim Mark; new chado load should address much of this)
      • Jürg will ask lab members whether there's anything they can't do on PomBase, and note anything especially urgent.
    • Evaluate progress in late January; reasonable to expect it will be ready then
    • Still plan to redirect Genedb gene pages upon pombase "preview" removal

Usage June 2011 onwards:

Monthunique visits
Dec. 1-202061

Now around 100,000 pages and 126,000 hits per month

3 January 2012

No call. Happy New Year!

17 January 2012

  • item (carried over from 20 Dec.)

Add items to discuss next time here

  • Jan. 17 or Jan. 31 (or both, if necessary): review "post-preview" criteria & progress