Gene symbol disambiguation using knowledge-based profiles

Hua Xu , Jung-Wei Fan , George Hripcsak , Eneida A. Mendonça , Marianthi Markatou , and Carol Friedman

Bioinformatics, doi:10.1093/bioinformatics/btm056

Available Data Sets:

• Total document set: from gene2pubmed file, removed abstracts that are associated more than 25 genes - 3 columns: Taxonomy ID, GeneID, PMID

  • mouse
  • fly
  • yeast


• Testing sets:
  • mouse
  • fly
  • yeast
  
  ** Format: PMID\tGene Mention (Upper Case)\tSpecies\tGeneID\t#of PMIDs for profile, the "+" before species indicates it is the correct GeneID as identified by BioMedLEE and gene2pubmed file as described in the paper.
  

Available Programs:

Perl Scripts and Folder Structure

Please Note: all the disambiguation programs are written in Perl, and they are highly dependent on the pre-defined folder stucture. Please read the README file before using the scripts.

Contact:

Email: hua.xu@dbmi.columbia.edu

Phone: 1-212-342-1639