IGB User's Guide
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The IGB file species.txt Every version of IGB contains a copy of a file named species.txt that maps scientific names for species onto common names and an IGB-friendly genome version prefix.

This is a tab-delimited file that listswith the following data:

  • Column 1: scientific (Latin) name for an organism
  • Column 2: common name for the organism
  • Column 3: IGB-friendly  genome version name prefix (e.g., H_sapiens, O_sativa_japonica, or C_sativa_CBDRx)
  • Column 4, 5, etc. (optional): Genome version name prefixes used by Galaxy, UCSC Genome Bioinformatics, or other data providers

IGB uses these data to populate the Species menu in the Current Genome tab. It also uses these data to associate species with genome assemblies. This is why the species.txt file also lists the IGB-friendly genome version prefix in the file in column 3. Because many data providers also use common prefixes to indicate genome versions for a species, we also include those whenever possible.

When IGB accesses a QuickLoad site, it tries to retrieve a an optional, supplemental species.txt file from the QuickLoad root directory. If the file is available, IGB reads the file and adds any new species to the Species menu.

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