= Enrichment Map Genesets = 
<<TableOfContents(3)>>

== Summary ==
  * Enrichment Map Genesets are a set of Gene Set files in GMT format (compatible with [[http://www.broadinstitute.org/gsea/index.jsp| GSEA]]) updated '''monthly''' from original source locations available with:
    1. Entrez gene ids
    1. !UniProt accessions
    1. Gene symbols

== Sources ==
|| '''Source''' || '''File Origin''' || '''File Type''' || ''ID extracted'' ||
|| KEGG || static (July 2011) || gmt || symbol ||
|| IOB || static (July 2011) || biopax || Entrez gene ||
|| Msigdb - c2|| static (needs to be updated manually) || gmt || Entrez gene ||
|| !NetPath || website (scripted grab of file numbered 1-25) || biopax || Entrez gene ||
|| !HumanCyc || scripted grab of zipped release from password protected website. || biopax || Uniprot ||
|| NCI || scripted grab from pathwaycommons || gmt || Entrez gene ||
|| Biocarta || msigDB -c2 || gmt || Entrez gene ||
|| Reactome || scripted grab of zipped release from website || biopax || Uniprot ||
|| GO || scripted grab from ftp site || GAF || Uniprot ||
|| Specialty GMTs <<BR>> mirs, transcription factors || grab from Msigdb || gmt || Entrez gene ||

== File Structure ==
'''< > denotes directory'''
  * <Release> - directory is named according to date sets were updated.
    * <Species> 
      * <Identifier> - (either Entrez gene, !UniProt, Gene symbol)
        * <GO>
          * BP = biological process
          * MF = molecular function
          * CC = Cellular component
          * All = BP + MF + CC
          * no_GO_IEA - indicates that the file '''excludes''' GO annotations with evidence codes - 'IEA' (inferred from electronic annotation), 'ND' (No biological data available), 'RCA' (inferred from reviewed computational analysis)
          * with_GO_IEA - indicates that the file '''includes''' GO annotations with evidence codes - 'IEA' (inferred from electronic annotation), 'ND' (No biological data available), 'RCA' (inferred from reviewed computational analysis)
        * <Pathways>
        * <miRs>
        * <TF>
        * <Disease phenotypes>
        
  * In each <identifier> directory There are amalgamated gene set files:
    * AllPathways - contains all pathway sources in the Pathways directory
    * GOPathways - contains all GO (mf, bp, cc) and all Pathway sources in the Pathways directory.

== Creating customized Genesets ==