How IGB recognizes species and genome versions
IGB is distributed with a two tab-delimited file files called "species.txt" and "synonyms.txt" that allow it to match genome names between QuickLoad sites, Galaxy, and other sites. Whenever IGB accesses a QuickLoad site, it also request these two files from the top-level, root directory.
If you are setting up your own QuickLoad site, you can create and distribute these same files as part of your site to ensure the species names are displayed correctly and that you can use IGB in conjunction with Galaxy sites that contain the same genomes.
Species.txt
The species.txt file is a tab-delimited file that lists
- binomial (Latin) names for species
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- common name for the species
- IGB-friendly genome version name prefix (e.g., H_sapiens or A_gambiae)
- Zero or more 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 their 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 will also attempt to retrieve a species.txt file from the QuickLoad root directory. If available, it will use those data to add new species to the Species menu.
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If you are building a QuickLoad site for a newly sequenced genome, create a species.txt file containing your newly added species to ensure that the IGB Species menu will display the genus, species, and common names properly.
Species.txt
The species.txt file that is distributed with IGB is version-controlled and . It resides in the igb/resource directory in the project repository. To see the latest version of this file, go to https://bitbucket.Here org/lorainelab/integrated-genome-browser, select the source button, and navigate to the resources folder as shown below:
Also, here is a version that was current as of December, 2014.
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