What's in a gene name? Automated refinement of gene name dictionaries

"What's in a name? That which we call a rose by any other name would smell as sweet." By William Shakespeare

Supplementary information

Publication: Jörg Hakenberg, Proceedings of the BioNLP 2007 workshop at ACL 2007, p.153-160, June 29 2007, Prague.
[Abstract]

Enriched dictionary

• Original dictionary: "masterlist" as provided by BioCreative II (GN task); derived from Entrez Gene (32,980 human genes)
• Enriched dictionary

Variation patterns

   -1   L         -1   " ligand"     => 'L' at the last position can be replaced by " ligand" at the same position
   -1   R          1   "receptor of" => 'R' at the last position can be replaced by "receptor of" at the first position
   -1   antigen   -1   ""            => 'antigen' at end of name can be missing

• 1: first position, 2: second position, ..
• 0: any position
• -1: last position, -2: pre-last, ..

• Set of rules -- regrettably, I have not yet found a convenient way to export&express all transformation rules; however, all rules were somehow inferred from examples, so I should come up with a proper grammar at some point

More literature

What's in a Gene Name? Why mapping the language of the human genome may be more of a headache than sequencing it.

Carol Reeves, The Scientist 2005, 19(4):56. [Article]

The molecule role ontology: an ontology for annotation of signal transduction pathway molecules in the scientific literature.

Satoko Yamamoto, Takao Asanuma, Toshihisa Takagi, Ken Ichiro Fukuda, Comparative and Functional Genomics, 5(6-7):528-536.
[Abstract] - [PDF] - [Web page at OBO Foundry]
---A structured controlled vocabulary of concrete protein names and generic (abstract) protein names.