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Feature #473

closed

Implement auto-scoring mechanism

Added by Tom Clegg about 12 years ago. Updated over 11 years ago.

Status:
Closed
Priority:
High
Assigned To:
Target version:
-
Start date:
Due date:
% Done:

0%

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

Description

Remaining to do:

  • "within 1 base of a splice site" test
  • "indel in a coding region" and "...with frame shift" tests
Actions #1

Updated by Madeleine Ball about 12 years ago

Autoscoring is split into three sections: computational,
variant-specific, and gene-specific, each 2 points for a max of 6
points.

Computational (max of 2 points):
If an non-synonymous substitution:
+1 for NBLOSUM >= 3,
another +1 (+2 total) if NBLOSUM = 10 (a nonsense mutation)
For all variants:
+1 if within 1 base of a splice site
(Trait-o-matic has splicing data, presumably it could spot these?)
Indels:
+1 for indel in coding region
another +1 (+2 total) if causes a frameshift (not a multiple of 3 in
coding region)

Variant-specific lists (max of 2 points):
+2 if in OMIM
+1 if in PharmGKB
+1 if in HuGENet
another +1 (+2 total) if HuGENet's OR >= 1.5

Gene-specific lists (max of 2 points):
+1 if in GeneTests
another +1 (+2 total) if in a GeneReviews gene

See discussion:
Actions #2

Updated by Madeleine Ball about 12 years ago

Two more requirements:
  • Let's put the autoscore into the "Other in silico analyses" section.
  • The GET-Evidence dump should also have an autoscore column.
    Both of these are urgent for completion of the ticket.
Actions #3

Updated by Madeleine Ball about 12 years ago

N.B. this is not so much a "robot" since it is not editing the page.

Actions #4

Updated by Tom Clegg about 12 years ago

Autoscoring code:

http://github.com/tomclegg/get-evidence/blob/d188d93fd7321cdd952443c338a6f14382e29a7c/public_html/lib/evidence.php#L776

The score shows up in an "autoscore" column in latest-flat.tsv, and in the "in silico" section.

The "within 1 base of a splice site" and "indel in a coding region" tests are not implemented yet.

Actions #5

Updated by Ward Vandewege over 11 years ago

  • Project changed from 19 to GET-Evidence
  • Category deleted (GET-Evidence)
Actions #6

Updated by Madeleine Ball over 11 years ago

  • Status changed from New to Closed

One way or another, autoscoring is done now. Ideally it'd be done by the php and python wouldn't have redundant and potentially disagreeing versions, but I consider this bug/request to be "done".

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