Difference between revisions of "WBConfCall 2019.01.03-Agenda and Minutes"

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=== Apologies for absence ===
=== Apologies for absence ===
Michael P.
Michael P.
Paulo Nuin
=== HelpDesk===
=== HelpDesk===

Revision as of 17:23, 3 January 2019


Apologies for absence

Michael P. Paulo Nuin


New types of Gene Ids

  • Gene Ids of type 'PRJEB28388_chrIII_pilon.g6753' are causing problems for the WS270 run of the gene descriptions pipeline
  • How do we handle these, or can they be ignored?

Meeting Abstracts

  • International meeting abstracts are always included in WB (reliable file format, i.e. easily parsed)
  • Regional and topical meeting abstracts are no longer included as the file formats (and sometimes permissions) are inconsistent and not easily parsed
  • Sometimes users want search access to the regional and topical meeting abstracts and/or want to include them on their Person report pages
  • Possible solutions:
    • Provide a form for upload
      • Would need to check for potential dups
      • Assume that abstracts weren't modified post-submission
      • Possible issues with permissions?
      • Could input more than just regional/topical meetings (e.g. ASCB meeting)
    • Advertise acceptable file format (i.e. international meeting format) and be more proactive about trying to get regional/topical meeting organizers to generate files in this format
    • Other options?
  • What should be included in Textpresso Central?

WB workshops at IWM 2019

  • WormBase workshop:
    • Gene page
    • WB tools-SimpleMine, RNA seq related tools, SoBA, WoBR, Gene set enrichment, etc
    • Community curation-new author first pass form, phenotype submission
    • Parasite talk
    • Alliance update
  • WormMine and JBrowse workshop
  • Micropublication (maybe separate or folded into the WB workshop)


  • Gene IDs issue seems to be resolved
- Hinxton to make code change to remove the problem IDs from the production files.
  • Meeting Abstracts
- Worm board could set a requirement for worm meeting organisers to allow WormBase to use them.

- Work closer with organising groups to get the data in a format that we need.
  As soon as we get a meeting announcement we should contact to try and make things easier.
  Abstract platform provided by WormBase? - Raymond/JC
     Different meetings have different systems that are rolled into the reg and payment process.

- Here is a the GSA file format please supply data in this format

- Some meeting might not care....but the community will buy into this

- Kimberly will work on a proposal for WormBoard and send it round.

- Ask other Mods.

Do we want them in TextPresso

In the old system they were flagged as cannot be cited (Personal Communication Only).
If they are included should be flagged.
Abstract should be easy, poss have them as a separate pipeline. HMM
There will be lots of options for input into the pipeline so should be pretty easy.
So YES and TP central need to  work on pipeline.
Useful for AGR?
TP Central will be integrated into AGR for literature.

IWM Workshop

Registration Deadline extended to Jan 15th
We aren't meeting as a group before then so need to get things sorted

   WormBase workshop: Ranjana organising
   WormMine and JBrowse workshop - Chris
   Micropublication - Karen & Daniela

Any more simple tools we want to talk about?

Adam will be doing Alliance data retrieval in the Jbroswe workshop
Ranjana will start adding names to talks and co-ordinating with people.

Ok to have some redundancy between workshops as not all will be attended by everyone.

Should we co-ordinate times between workshops so introduction could be made in one for a topic in the other workshops.
Talk with organisers once we have them registered.