Gene/protein names should be case normalized

sorgerlab / indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.

http://indra.bio

BSD 2-Clause "Simplified" License

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Gene/protein names should be case normalized #2

Closed johnbachman closed 9 years ago

johnbachman commented 9 years ago

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 commented 9 years ago

Closed by c7628db6db4698ff8df960c3fb217d66b157bfe1 (resolved to ALL CAPS, at least for now)