wiki:PomBasePlanningMeetingMinutes20120501

Planning Meeting Tuesday 1 May 2012 - Minutes


Agenda for this meeting


Tuesday 1 May, 15:00, EBI A2-01

Present: Val, Midori, Antonia, Mark, Dan, Paul
Apologies: Steve, Jurg, Kim
Chair: Val
Minutes: Midori

Previous Action Items

  • Desktop sharing: Curators + Kim have used join.me succesfully. No further need for recurring agenda item
  • OLS webservice: Henning not in 2012-05-01; carry over
  • ArrayExpress accession numbers for PMID:18488015: carry over; still of interest as track

DONE (Val)

  • Conrad's data: Dan aware, but no progress yet.
  • Curation subdomain - now active; should also now "know" current PomBase server IP
  • Selenium testing/server: see loading speed item below
  • Genome browser - want all links/features present on all genome browser tabs
    • should be able to make this change
  • Links and genomic regions:
    • this is about going to a gene overview page from genome browser
      • Mark trying to have location-based list of links
      • also want link to PomBase from gene pop-up - priority (new action item for Mark)
    • Matters arising: also brought up link from BLAST results, which also needs some work
    • Matters arising: also still plan to do mock-ups for better link "back" to gene page (in header; maybe additional link within gene tab?)
  • Link to PSI-BLAST: carry over; long term
  • Version of Ensembl help optimized for PomBase
    • Paul et al. to pare down help links to those relevant to PomBase - new action item
    • Matters arising: Do similar for the Tools and Downloads pages linked in genome browser header
  • A number of items that are in Jira, and so won't need further representation in meeting action items (barring unforessen troubles with any):
  • PomBase website speed (esp. gene page loading): The move to the London datacentre is under way even as we meet. Eagerly awaiting outcome. If all is good and fast thereafter, sorted; otherwise, Mark, Dan, et al. will know they need to investigate further.
  • Interaction between PomBase and EBI External Services: still on Paul's to-do list

General

  • Usage stats - down a little (possibly not significantly) since last meeting
    • suspect we've reached the "early adopter" plateau
    • expect increase again when "preview" label goes
    • curators will announce that there will be no further updates to GeneDB content
  • FTP site migration: On Val's to-do list, but loose ends to tie up before migrating; revisit next mtg
  • Data on genome browser tracks
    • Test case for external dataset incorporation: Buck et al. nucleosome localization
      • Mark has BAM files, but not sure about policy - do we house the data? point to data housed externally? some of each? etc.
      • should be able to get data into ENA as reference BAM - will need BAM search to find it; then can find anything at coordinates - this is the preferred longer-term approach; in meantime, preload into PomBase (i.e. host internally)
      • we can ask users for data, explain procedure; not likely to have data deluge before good way to handle it
      • data in ArrayExpress - RNAseq data should also be in ENA as reads, and can be aligned to genome
    • further discussion of what people might provide, and how it would be handled and displayed
      • Val - people have asked to see raw data because experiments quite different
      • Paul - technically feasible to have separate tracks for different expts; but need a better way to navigate through many (hundreds?) of possible tracks; also need to choose default "on" set carefully
        • default is to do alignment in-house; does that ignore processing done in paper? yes, but can show both
        • Quick explanation of "wiggle track"; Val notes that for pombe, RNAseq data will cover almost entire genome!
      • need ENA accessions for datasets of interest
        • most will have been submitted to AE or GEO rather than ENA/GenBank/DDBJ
        • AE -> ENA pipeline clear; not so obvious for GEO
    • Action item: Val to send RNAseq data screenshots
    • Action-ish: Have goal to map datasets from ENA onto PomBase genome periodically - every n releases (Dan lead)
    • Action item: Find ENA accessions for initial datasets; load them by standard EG procedure, which will put RNAseq into one track. Can also consider specific datasets to go on specific tracks. (Mark, Dan)
    • Action item: Chat about datasets inclusion & display with Jurg's group at next meeting (at UCL) (all)
    • Note: the foregoing is an incomplete, and probably unevenly representative, summary of extensive discussions. Additions, clarifications, or corrections welcome. -Midori
  • Improving communication between curators and programmers
    • Val - rationale: good to know of holdups so curators can plan tasks effectively (esp. how much time to devote to website testing)
    • Action item: Dan to forward relevant portions of the Friday-afternoon summary of "what we did and what we plan for next week", esp. for Mark.
    • Continue to set broader timeframe at planning meetings.

GO Regulation

  • Recent email from Jane Lomax is a little ambiguous about molecular function vs. biological process, but on the issue of propagating over 'regulates' relations, indicates that GO (a) does still plan to offer both options and (b) is leaning towards default being not to propagate
  • Action item: Ensembl request for new feature - option to propagate over 'regulates' (curators to open item)
  • Action item: Adjust GO slim to take reg handling into account (curators) DONE action item on jira
  • Curators will also continue to hash out annotation policy with GO

Curation Update

  • As in agenda, plus: soon ready to invite selected individuals to curate papers

User Experience Testing

  • London session - similar conclusions from Cambridge
    • still no success turning tracks on/off
  • raised question of what to call the advanced search, given subtle distinctions among "advanced search
    • Antonia - not a big deal; it's very clear once you try it, and "advanced search" is good
    • leave as is until/unless we think of something better
  • Might be good te change home page to add space to highlight new features, tips & examples, etc.
    • Another possibility: how-to emails based on user queries (Paul - WB do this)
    • Could also showcase FAQ on home page
  • Action item: Mark to type up notes from 2nd session, send feedback to Ensembl, etc.
  • Action item: remind community of search capabilities, provide examples (curators)
  • Action item: look into home page changes (time frame approx 2 months) - Mark talk to Bren; curators think of possible content

PomBase Website

Also see user testing above

Post-preview and GeneDB-decommissioning Criteria and Progress

  • "Preview" tag removal
    • The big outstanding BioMart problem: database population fine; problem is linking db to interface correctl
      • there's a bug in the XML for BioMart; Mark talking to Rhoda to find & fix; turn on all conceivable logging
      • once fixed, should stay fixed ("touch wood" - Dan)
  • GeneDB decommissioning: raise priority of items needed for the post-geneDB world (but not required for immediate post-preview); also see below

Other website issues & Jira items

  • Mark requests: use "blocker" status only for severe problems that MUST BE FIXED NOW. (Recent curator usage meaning "blocks coming out of preview" is ok.)
  • Can use the "Fix Version" selector to have "critical for x" and separately indicate what it's critical for (e.g. out-of-preview, GeneDB-decommissioning, etc.).
    • Action item: Mark to add some fix-version options
  • Page aesthetics: Looked at gene page to point out specific improvement possibilities
    • Not trivial to customize what shows up on image from genome browser
    • Some other points suitable for Jira (of which some are in)
    • Action item: Mark to do any changes that are in Jira and easy to do
    • Action item: Val to add Jira items to: add vertical space under protein graphic; horizontal seq download option arrangement; space above literature section
    • Action item: Val to check capitalization of species distribution vocabulary terms

Annotation Extensions

  • still OK to wait until post-preview, make it high priority thereafter
  • storage in Ensembl works for display, but is clunky and needs improvement
  • also want to do some final fixes and aesthetic tweaks before going live
  • annotations from curation tool include lots of extensions, so want to show them (otherwise, will look like lots and lots of redundant un-extended annotations)

Download options

Some things can be done by adding advanced query filter options; others are best done as canned result sets; decide on case-by-case basis

Meetings

Discussed length & format of demo and workshop possibilities and which would be suitable for various meetings. Mark can give Val some material for the EMBO course. Later, work on more comprehensive workshop content.

AOB

  • No rush on variation data - will be a few months before it's published
  • will wait for updated S. octosporus & S. japonicus sequences
  • Action item: Val find out if annotation included, or just sequence, in nucleotide databases

New Action Items

  • Action item: Paul et al. at EBI to pare down Ensembl help (http://genomebrowser.pombase.org/info/index.html) to items relevant to PomBase
    • Related task: also consider what's relevant to PomBase on Ensembl Tools and Ensembl Downloads pages
  • Action item: Mark to mock up link to PomBase gene page in popup
  • Action item: Val to send RNAseq data screenshots
  • Action-ish: Have goal to map datasets from ENA onto PomBase genome periodically - every n releases (Dan lead)
  • Action item: Find ENA accessions for initial datasets; load them by standard EG procedure, which will put RNAseq into one track. Can also consider specific datasets to go on specific tracks. (Mark, Dan)

DONE (retrieved accession numbers for these datasets)

  • Action item: Chat about datasets inclusion & display with Jurg's group at next meeting (at UCL) (all)

DONE, asked for feedback from Jurg and Sam...

  • Action item: Dan to forward relevant portions of the Friday-afternoon summary of "what we did and what we plan for next week", esp. for Mark, to curators
  • Action item: Ensembl request for new feature - option to propagate over 'regulates' (curators to open item)

DONE, logged a very wooly jira item, need some thought

  • Action item: Adjust GO slim to take reg handling into account (curators)

DONE (logged in jira)

  • Action item: Mark to type up notes from 2nd session, send feedback to Ensembl, etc.
  • Action item: remind community of search capabilities, provide examples (curators)
  • Action item: look into home page changes (time frame approx 2 months) - Mark talk to Bren; curators think of possible content
  • Action item: Mark to add some fix-version options to PomBase Jira
  • Action item: Just after fixing BioMart bug, Mark to do any website changes that are in Jira and easy to do
  • Action item: Val to add Jira items to: add vertical space under protein graphic; horizontal seq download option arrangement; space above literature section

DONE

  • Action item: Val to check capitalization of species distribution vocabulary terms
  • Action item: Val find out if annotation included, or just sequence, in nucleotide databases

DONE I think it is probably just sequence in the archive (not sure), but I have annotation of processed data (EMBL format) for all 3 data-sets

Last modified 8 years ago Last modified on May 3, 2012, 4:12:47 PM