Feature #499

Merge rsids and AA-variant pages

Added by Madeleine Ball over 9 years ago. Updated over 8 years ago.

Status:
New
Priority:
Normal
Assigned To:
Target version:
-
Start date:
Due date:
% Done:

0%

Estimated time:
Billable:
Estimatedhours:
Hours:
Totalhours:
Resolution:
Story points:
-

Description

Take care to merge the rsid pages with the amino acid change pages so that they do not overwrite each other.

Cases:

1. AA page exists with rs# association, rs# page does not exist, robot knows rs# but not AA -- should automatically edit the AA page instead (done(*))
2. Robot knows rs# but not AA, not AA/rs# association available -- robot should add/edit rs# page
3. Robot imports a new variant with AA and rs# (genome importer is currently the only way AA/rs# association is made), rs# page exists, AA page does not exist -- robot should rename rs# page to AA
4. Genome importing robot imports a new variant with AA and rs#, rs# and AA pages already exist (e.g. AA page created by user) -- try automatic merge, or warn editors that a manual merge is needed (incl. a warning on the pages themselves?)

The merge/rename stuff should be done by a separate process, rather than building that logic into the genome importer. (Perhaps tie in with the trait-o-matic data processing side -- e.g. dbsnp->aa change can be a quick db lookup instead of the full gff_nonsynonymous_filter process.)

(*) Need to fix handling of "one rsid -> multiple nsSNPs" case.

History

#1 Updated by Tom Clegg over 9 years ago

Some cases have been corrected, like this one...

...by preventing the PharmGKB robot (and other robots) from adding an rs# variant when an AA variant is already associated with the dbSNP id.

Also, rs# url's now redirect to AA pages where applicable.

#2 Updated by Madeleine Ball about 9 years ago

sufficient for submission...

#3 Updated by Madeleine Ball about 9 years ago

Here's an example I think is somewhat related to this issue:
http://evidence.personalgenomes.org/HFE-C102Y
http://evidence.personalgenomes.org/HFE-C282Y

In this case Trait-o-matic is actually producing the output for all these positions: HFE C102Y/HFE C176Y/HFE C180Y/HFE C190Y/HFE C194Y/HFE C259Y/HFE C268Y/HFE C282Y

The GWAS and PharmGKB hits are showing up on the first one, while PharmGKB (a smaller set of matches, it seems) and OMIM show up on the second.

We need to figure out how to merge AA-variant pages associated with a single genetic variant.

#4 Updated by Ward Vandewege over 8 years ago

  • Project changed from External to GET-Evidence
  • Category deleted (GET-Evidence)

#5 Updated by Madeleine Ball over 8 years ago

  • Priority changed from High to Normal

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