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Gene/protein names should be case normalized #2

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johnbachman opened this issue Feb 1, 2015 · 1 comment
Closed

Gene/protein names should be case normalized #2

johnbachman opened this issue Feb 1, 2015 · 1 comment

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@johnbachman
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Gene names are parsed in from BELscript/RDF using whatever case they have, which leads to different rules having, e.g., "Braf" and others "BRAF". When converted into PySB, these lead to different monomers.

Possible solutions:

  • Store all names as ALL CAPS
  • Store all names as first letter Caps
  • Use the first appearance of the gene name as the convention, store it, and then canonicalize all other-case appearances of the gene to that
  • Look up the name in a database somewhere.
@johnbachman johnbachman mentioned this issue Feb 1, 2015
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johnbachman referenced this issue in johnbachman/indra Feb 2, 2015
@johnbachman
Canonicalize all gene names to ALL CAPS
c7628db 
Addresses issue #2. Also identified some duplicate rules, which I
addressed in the specific case of the ActivityModifications by checking
the model for preexisting rules before adding.
@johnbachman
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Closed by c7628db (resolved to ALL CAPS, at least for now)

johnbachman referenced this issue in johnbachman/indra May 18, 2015
@bgyori
Merge pull request #2 from jmuhlich/biopax_demo
44287aa 
add heap size setting; fix data source url in comment
@bgyori bgyori mentioned this issue Oct 12, 2020
Merged
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@johnbachman