WBConfCall 2013.11.07-Agenda and Minutes
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- 1 Agenda
- 2 Minutes
Models for WS241
- ?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.
- 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?
- All of the genes for the protein unfolding pathways (including the orthologs in the core WormBase species) have been curated to improve their structures.
- There is a Google Docs page summarising the changes made (412 genes looked at. 72 structures modified. 118 new isoforms):
- Is any more curation required for the "protein unfolding pathways" themed curation?
- is the scheduling still ok for CalTech to go with a ncRNA themed release?
- 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.
- 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.
- 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.
- 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.
- 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.
- Karen: any update on these?
- Michael: yes - I mailed them out yesterday
- Karen: I didn't get them
- discussion of email accounts