TreeFam

InterMine comes with a data converter for TreeFam. Follow the instructions below to include TreeFam data in your InterMine.

1. Get the data from TreeFam
   •  ftp://ftp.sanger.ac.uk/pub/treefam/release-7.0/MySQL/
     • download two tables:
       • genes.txt.table
       • ortholog.txt.table
2. Add TreeFam to your project.xml file

   <source name="treefam" type="treefam">
     <property name="src.data.dir" location="/DATA/treefam"/>
     <property name="src.data.dir.includes" value="ortholog.txt.table"/>
     <property name="geneFile" value="/DATA/treefam/genes.txt.table"/>
     <property name="treefam.organisms" value="7227 6239 7165 4932"/> 
     <property name="treefam.homologues" value="9606 10090 10116 7955"/> 
   </source>
   

   • treefam.organisms - all genes from the listed organisms will be processed
   • treefam.homologues - genes will *only* be loaded into the database if they are a homologue of an organism of interest
3. Run a build

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See: BioSources