wiki:PombasePlanningMeetingMinutes20131009

Version 1 (modified by antonialock, 7 years ago) (diff)

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PomBase Planning Meeting 09 Oct 2013


Agenda for this meeting


Wednesday 09 October, 14:00, EBI

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

New AIs (some very minor) from this meeting

For HTP data hosted:

  • AI: Midori to make track names mandatory
  • AI Antonia to ask Katrina to fill in track names
  • AI Mark, remove tracks from gene pages
  • AI Mark genes and transcripts must be separated out in the genome browser, Paul says this is possible.


For targetis annotations:

  • AI: Mark: We want to group by genes first and then relationship. For future we also want to group by relationship.

Action items commented on

  • Demo of curation tool (postponed)
    • this will stay postponed for now
  • 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?)
    • This is now done
  • AI: Mark needs to know when new SO qualifiers (like TR box) are added (open jira item for Kim to generate a list) (https://www.ebi.ac.uk/panda/jira/browse/PB-1343).. also NOTE: TR box is a gene feature not a transcript feature
    • We want pages for features that are studied in their own right. Some might get annotations attached to them. These are linear features on a sequence eg centromere.
  • AI:? Discussed moving to similar schema for proteins 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)
    • Can be taken off list, we know what needs doing

Action items from

  • AI: send instructions to Val about how to submit data to ftp site? (Mark) (what file format for what data-types. Using accession numbers or uploading data files, genome assembly date, PMID) (Ensembl https://www.ebi.ac.uk/panda/jira/browse/PB-1411) rest is in https://www.ebi.ac.uk/panda/jira/browse/PB-1407)
    • DONE. What should we do with the instructions now? We just need to send it to people when they need to upload a file.
  • AI: Sort out display of reciprocal interactions, this should be done post-chado (as part of loading into ensembl), at the moment they are just mirrored (?) so take care with assymetrical ones (Mark)
    • There is a ticket for this now so can be removed from agenda?

New (and continuing) Agenda items

Hosting high throughput datasets

  • Mark demo htp data sets from Marc Bühler DAM 1 D data (discuss display pulled through to PomBase? page, and details displayed)
  • ditto Juan's poly A data
  • AI: Midori to make track names mandatory
  • AI Antonia to ask Katrina to fill in track names
  • AI Mark, remove tracks from gene pages
  • AI Mark genes and transcripts must be separated out in the genome browser, Paul says this is possible.

Chado

Started tidying code and documenting for GMOD acceptance.

  • We need to release the code that loads Canto data into Chado so it can be mentioned in the Canto paper.
  • Currently the code works for us but we need to split the PomBase specific code from the more general code.

Usage stats

http://tinyurl.com/7qs2zap

  • Corrupted stats EVERY month *All data still there, will be recalculated end of year. If we need stats earlier Mark will have to spend time on it.

Versioning

Website

  • User reported intermittent browser speed issues
    • Chinese spiders very active. These will be banned at some point.
  • Mark demo reciprocal "targetis" annotation
    • AI: Mark: We want to group by genes first and then relationship. For future we also want to group by relationship.

Helpdesk

Mark - 2 open tickets midori - 21 stalled, 5 new, 2 open Antonia - 1 new, 3 open, 2 stalled Val - 7 stalled, 2 open, 8 new

Survey

Survey, look at results so far and address related jira priorities (many moans are ticketed)

  • Proper review postponed until final results

Grant

Deadlines: Dec 2 for pre-ap, April for full-ap
Reviewed old aims. Steve concerned pombe not important enough to keep funding for what we do. Paul think they are giving money to proposals with good applications. Steve wonders how many pombe labs have welcome trust grants. Is it a resource needed by grant holders? Need to be careful to ask for money we have already been given for. We now have metrics so we can show how we are catching up. Acjnowledge there is still a backlog? We do not want this to be a focus. We need good rationalisation for keeping people on the grant. One pos for curator/trainer to reach out to small communities. Other organisms? Japonicus and octosporus. Small number of papers. Huamn pathogenic fungus? Paul thinks we will need letters to support. Is GeneDB going down? No one knows. They might have contacts in those communities. Paul thinks visualization is interesting (pahways etc). Users also asking for graphical representation of mutations etc. Sustain effort, enhance pombase by following requests, third we will do novel things, such as outreach to communities.