How IGB recognizes species and genome versions

IGB is distributed with a two tab-delimited file files called "species.txt" and " that lists binomial (Latin) names for species with sequence genomes along with their common names and the IGB-friendly prefixes used to designate genome versions for that species.

IGB uses these data to populate the Species menu in the Current Genome tab. It also uses these data to associate species with their genome assemblies.

When synonyms.txt" that allow it to match genome version names across QuickLoad sites, Galaxy, and the UCSC Genome Bioinformatics system. Also, whenever IGB accesses a QuickLoad site, it will also attempt to retrieve a speciestries to download species.txt and synonyms.txt file from the QuickLoad top-level, root directory of the site. If available, it will use those data the files are not present, no harm is done, but if they are, IGB can use them to add new species and genome versions to the Species menu.

Species.txt

The species.txt file that is distributed with IGB is version-controlled and resides in the igb/resource directory in the project repository.

Here is a version that was current as of December, 2014.

To create a species.txt file for a QuickLoad site:

• Open an editor (Microsoft Word is fine, but you'll need to save the file as a plain text (.txt) file.)
• Type the Latin name for the species, including a subspecies (e.g., Zea mays B73)
• Type TAB
• Type the common name for the species (e.g., maize)
• Type TAB
• Type the IGB genome version prefix you'll use for every genome assembly from this species (e.g., Z_mays_B73)
• Type TAB
• Type the Galaxy/UCSC genome version prefix, if available. You only need to do this if the genome versions is supported by Galaxy and UCSC and you would like to use open files and data from Galaxy in IGB.
• Repeat the previous steps for all new species you'd like to include in your QuickLoad site.
• Save the file as plain text.
• Place the file in the root directory of your QuickLoad site.

  and Genome Version menus in the Current Genome tab.  IGB does this so that if you have set up your own custom IGB QuickLoad site with new genome, IGB will display your data in the same way as other genomes.

See:

• Use species.txt to link species names to IGB genome names
• Use synonyms.txt to link genome versions names to each other