WBConfCall 2019.08.01-Agenda and Minutes

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Variation Backlog Summary

I have prepared this document to identify the processes and potential backlog.



As said before we are currently running Variation curation (molecular details) in a maintenence mode where only the users/large scale submitted data is integrated or where things are specifically requested.

There is a large backlog as there has always been, we have assessed the backlog that we know about that has been generated over the last 13 years.

Moving forward


21 Confirmed micropublications not curated

471 Created in the nameserver by Caltech curators since Mary Ann left.

Michael (HMM) has run the old pipeline and generated 114 new tickets (already in the numbers above)


2913 papers to triage to try and automatically identify the false +ves

~1800 papers to work through but will try and work on better ways to identify high confidence targets.

Possibly re-running them through the new pipeline

NAR Manuscript



Variants (and see Paul's notes above)

-Backlog: was always there.

Improvements going forward

-Micropublication authors are now forced to submit molecular details through variant forms.

-Can we make an easy to use curation tool/submission form? Mary Ann made one. It's available and easy to extract data from that form into the database. Can we strip the form down to get minimal useful information and improve uptake? Remove requirement for flanking sequence? Yes, just need to know the version of the genome. Hinxton to sketch out the genome coordinate approach.

-Can alleles be linked to genes a bit more automatically? For CGC imported strains we already get that automatically (Paul D to double check). Could also ask CGC to request sequence information on our behalf?

Variants and other groups

-Karen is talking to other groups about allele curation (ZFIN, RGD).

-WB is currently the only group capturing genome location information for variants at point of curation. The Alliance working on generalising that.

-How difficult would it be to make it in to a web form? More genome browser appropriate. Hinxton currently using Fmap. Maybe a use case for Apollo?

-Kevin to raise it with the variants group, but might be low on the large priorities list. Need direction from the top. Might be a more appopriate task for a curation tool group, rather than variants group.

-It is our priority, can we just tell the Alliance we're doing it and invite input? No evidence of this approach being tried yet.

NAR Manuscript

-Todd invites submissions