WBConfCall 2013.11.07-Agenda and Minutes

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Agenda

Models for WS241

(Paul D)

WS241 model details

Summary:

  • ?Person class - Database tag added for ORCID
  • ?Interaction and ?Feature models - linking tags changed
  • ?Movie linking - Added Reference ?Paper XREF Movie and DB_INFO tags
  • ?Expr_pattern - Microarray and Tiling_array now linking to ?Microarray_experiment and ?Analysis. Also added DB_INFO tag
  • ?Gene_cluster - Karen would like to use this underused class for phylogenetic gene clusters
  • ?Construct Class - A new class for storing Construct reagents used for generating Variation data
  • ?Protein Class - Remove the UNIQUE tag on the Database Text field.

SAB 2014

  • planning
  • so far we have not followed through on this because Paul Sternberg has not been in the last two meetings.
  • There are two options:
    • New Year (January or February) at CalTech
    • Later in the Spring at Hinxton

Incorporating Annotations from External Groups

  • New GO annotation pipeline will bring in manual GO annotations made by other groups such as UniProt, IntAct, GO's RefGenome (PAINT) curators, UCL-BHF, etc.
  • These annotations need to be properly credited, so for the new GO annotation model we would like to create WBPerson objects for these groups and use Curator_confirmed evidence (the same evidence we use for WB manual curation)
  • This may also apply when we start sharing interaction data with BioGrid.
  • Any objections? If so, other ideas?

Themed Curation

WS241

WS242

  • is the scheduling still ok for CalTech to go with a ncRNA themed release?

Minutes

Models

  • most models are simple changes with no problems
  • ?Gene_cluster - this is not required for WS241
  • ?Construct Class - Paul D has not spent much time on this. Karen agreed it is not required for WS241.
  • Wen wants a change to the ?Expression_cluster class.
  • Ranjana also wants a model change.

SAB 2014

  • Paul Sternberg was not present.
  • It is probably best to conclude any planning for the SAB via email.

Incorporating Annotations from External Groups

  • Kimberly: Is there any objection to the use of WBPerson objects in curator_confirmed tags?
  • Michael: better to have person not group? Rather than fake persons for institutions.
  • Raymond: what about large publications like NAR papers?
  • Michael: these should use the WBPaper evidence.
  • Kimberly: we use WBPerson in all of our annotation so far
  • PaulD: we import uniprot evidence in other places in the database - linking to an Analysis object is more versatile than a WBPerson object
  • Kevin: do we need to track individual contributions? Would acknowledging the organisation be sufficient?
  • Mary Ann: is it important to differentiate between manual and automatic annotation?
  • Kimberly: that is covered by the GO annotation code. My main concern was proper attribution.
  • Raymond: We could use use WBPerson or Analysis objects as appropriate.
  • Kevin: do you mean to use a new tag 'extenal_curator' that captures this attribution?
  • Michael: we use #Evidence which already has Analysis etc. links. This works very nicely.
  • Kimberly: I feel an external_curator tag is closer to what I need.
  • Michael: so why not use WBPerson for one person and Analysis for a group of people?
  • Kevin: it is simple to make an Analysis object for each group. It comes down to whether you want explicit associations and the new tag would make it clearer to us in WormBase.
  • PaulD: the web display could be tailored to the evidence available but the #Evidence gives you everything you need.
  • Kimberly: OK, I'll look at #Evidence
  • Kevin: individual linking to wormbase curators is fine.

URL Constructors

  • Raymond: Is it OK for these to stay as they are?
  • Kevin: the ones we manage have been removed. If you wish to keep the citace URL constructors, you can keep these. These are no model changes being done.

Themed Curation

WS241

  • Chris: yes, we want to do a blog post when it goes live. Caltech are finishing papers and wiki pathways.
  • Raymond: is there anything scientifically interesting that came out of this? If so could we do a Worm Breeders Gazette article?
  • Michael: no - nothing.
  • Chris: core members of the pathways missing in the other species could be interesting.
  • Kevin: how was the topic chosen?
  • Chris: disease genes are interesting.
  • Ranjana: put it in the release notes?
  • Kevin: yes - the release letter is available at the end of the Build. 2 months later the web site is available. We need content for the release notes at the end of the Build.

WS242 Theme

  • Raymond: we need to narrow this topic of ncRNA genes down.
  • Chris: ncRNAs as a whole is straightforward but for literature curation it is too wide.
  • Kevin: thought this would fill in gaps in other species ncRNA curation by using RFAM.
  • PaulK: RFAM will be providing access to their own analysis pipelines in about a year.
  • Kevin: we should check the proper concise descriptions for all understood ncRNAs. Many are speculative but there are some well-studied ones and we should check the elegans ones are done well.
  • PaulD: yes, we have had criticism of the modENCODE '7K' set and other big ncRNA gene sets as these are not well understood. We have been doing this a little bit for the rRNA genes.
  • Kimberley: yes, that's fine. We could have concise descriptions for the well-studied ones in general.
  • Raymond: are these human-readable descriptions?
  • PaulD: we can quickly add stub descriptions that are human-readable.
  • Raymond: this has been tried but update procedures made it not tameable. Kimberly, do you think we can automate these?
  • Kimberly: updating and maintaining them will be challenging.
  • PaulK: could we get the users to do this?
  • Kimberly: we talked about this in the past. We could talk about getting the community involved.

Non-peer review articles

  • Mary Ann: It is not standard current WormBase policy to incorporate data from non-peer review articles. However, this policy has been in place for some time and a helpdesk query (#1920) from a user has prompted a review. I want to talk to Paul Sternberg about this. The Worm Breeders Gazette does not count as a publication. It is a personal communication.
  • Raymond: there are two different forms of personal communication: one where we are informed directly and where the Worm Breeders Gazette is cited then the author has to give their permission to quote them in an email.
  • Juancarlos: we could generate a WBPaper object.
  • Mary Ann: then I could add them? There are thousands with links to Worm Breeders Gazette articles.
  • Kimberly: Worm Breeders Gazette articles are personal communications.
  • Raymond: if we use email as a type of personal communication then we need a way of archiving them.
  • Kimberly: we can do this if we have the authors' permission.
  • Raymond: it doesn't have to be immediately accessible.
  • Kevin: could we get the author to fill in a personal communication permission form agreeing to allow Worm Breeders Gazette articles etc. to be used?
  • Raymod: yes, good idea.
  • Mary Ann: OK, I'll have a think about this and talk to the appropriate people.

Sanger accounts

  • Karen: any update on these?
  • Michael: yes - I mailed them out yesterday
  • Karen: I didn't get them
  • discussion of email accounts
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