Uploaded Gene File Format
Here is the file format:
line1: taxonomyID=<taxonomy id>
line2: moleculeType=<molecule type>
line3: dataSource=<data source>
line4: interactionLevel=<interaction level>
line5: searchPathBetweenGenes=<yes/no>
line6: <gene 1 >
line7: <gene 2 >
...
linen: <gene n >
line1 must start with "taxonomyID=" followed by a taxonomy id. If user does not want to specify a taxonomy id, "all" will be used to follow "taxonomyID=".
line2 must start with "moleculeType=" followed by a molecule type. The molecule type must be one of "DNA, gene, nucleic_acid, protein, RNA, small_molecule" . If user does not want to specify a molecule type, "all" will be used to follow "moleculeType=".
line3 must start with "dataSource=" fllowed by a data source. The data source must be one of below data set. If user does not want to specify a data source, "all" will be used to follow "dataSource=".
Data Sources used in MiMI:
Data Sources
BIND Samuel Lunenfeld Research Institute (UPDATED 11/06/2006) CCSB-HI1 Center for Cancer Systems Biology, Harvard (UPDATED 09/28/2005) DIP UCLA (UPDATED 11/02/2006) BioGRID Mount Sinai Hospital (UPDATED 10/31/2006) HPRD Johns Hopkins University and Institute of Bioinformatics (UPDATED 11/07/2006) IntAct EMBL-EBI (UPDATED 10/31/2006) InterPro EMBL-EBI (UPDATED 10/31/2006) IPI_Sequence EMBL-EBI (UPDATED 11/02/2006) MDC PPI Max-Delbrueck Center for Molecular Medicine (UPDATED 11/02/2005) ProtoNet Hebrew University SwissProt_ORF Swiss Institute of Bioinformatics (UPDATED 11/17/2006) RefSeq_ORF NCBI (UPDATED 11/06/2006) Line4 must start with " interactionLevel=" followed by an integer from 1 to 3.
Line5 must start with "searchPathBetweenGenes=" followed by "yes" or "no" . "yes" means finding only connecting nodes between genes in starting list, in this situation, interactionLevel in Line4 means up to how many connecting nodes in the path between genes. "no" means finding all neighbour genes for genes in starting list, in this situation, interactionLevel in Line4 means how many steps of expansion to find neighobor genes. .
Line 6 to Linen, each line includes a gene name
Here is an example :
taxonomyID=10090
moleculeType=all
dataSource =all
interactionLevel=1
searchPathBetweenGenes=yes
pwp1
cbl
csf1r