Agenda

Allele / variation curation

Hinxton has made it a priority to get the Micropub alleles curated
Karen puts in alleles in the name server with paperID, these will be prioritized as well
AGR wide focus on allele curation, so give this high priority
Kevin is on the AGR Variation working group, WB are ahead in terms of sequence curation and have doing it for years
Use case is groups such as the UDN who come in with a human variant, we need to begin work on this. Need displays to map human variant to MOD variant
With data with co ordiantes, we have flanking sequences, we have the chromosome sequnce, WB has both
What is the backlog? Hinxton can allocate resources to this--Gary Williams can switch from gene to allele curation
Caltech system has papers flagged with variation, Hinxton has this as 'pending curation'
Karen enters allele data from papers that come through the GSA markup pipeline before publication, maybe display the notes from these on the website
Sometimes things get named on an unnamed assembly and detective work is required, authors don't give complete information
Have the allele author submission form, enough for Paul D., to convert to a variation with molecular change information
Action Item: Paul will report the priority backlog; Textpresso already flags alleles, runs once a month;not high volume, rungs on new papers, maybe run on whole corpus to address old papers

Should it be private? Reasons to make it private
- Can discuss more freely
- Prevents inadvertant leaking of unpublished data
- We don't tell people that it goes on a public website
- People don't really use the issue tracker
We have received a few complaints about this, need full disclosure or need to be made private
What is the workflow-might be made simpler if private, maybe simplify the process even more to avoid writing multiple e-mails
GitHub acts like a FAQ for mostly curators, not for Users
Does Google index GitHub repos?
The group agrees to make it private
Todd will drop a summary of the requested

Current Slack policy- admin can request exports
Direct messages-now can change the retention time, can set in settings, default is to save everything; will keep this so people will need to set this
Note that if you want a retention time after which you want your messages deleted, you have to PROACTIVELY do this in settings

Should we keep this?
Comments have been made on annotations when there are errors in between releases when errors cannot be corrected
Comments are made public, that's the intent of the comment
Advertise it better, more than 4000 User accounts
For now we will keep the comment

The "protein_domains" file, for example here only has Interpro domains
Can we add all domains from all sources (e.g. PFAM, SUPERFAM, SMART etc.)?
Action Item: Chris will file a ticket for this and start the conversation with Hinxton