Table of Contents

How IGB recognizes species and genome versions

IGB is distributed with two tab-delimited files called "species.txt" and "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, tries to download species.txt and synonyms.txt from the top-level, root directory of the site. If 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 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

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• maps species names to IGB

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The IGB file species.txt is a tab-delimited file that lists

• Column 1: binomial (Latin) names for species
• Column 2: common name for the species
• Column 3: IGB-friendly  genome version name prefix (e.g., H_sapiens or A_gambiae)
• 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 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.

The species.txt file that is distributed with IGB is version-controlled as part of the IGB source code repository. To see the latest version of this file, go to https://bitbucket.org/lorainelab/integrated-genome-browser, select the source button, and navigate to the resources folder as shown below.

For developers: This is the "master branch" which we use to create the released versions of IGB you download at BioViz. See also Developing IGB from the IGB Developers Guide.

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

How to make a species.txt file for a QuickLoad site

First check to see if your species and genome version prefixes are alread present in the species.txt file. If they are, then you do not need to distribute a species.txt file with your QuickLoad site. If not, then to make 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.

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• genome names
• Use synonyms.txt to map

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• genome versions

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The IGB file synonyms.txt is a tab-delimited file that lists alternative names for the same genome version. Each line contains one or more synonyms.

Before making your own synonyms.txt file, first find out if there is entry for it in the synonyms.txt file that is packaged with the latest IGB release. To see the latest version of this file, go to https://bitbucket.org/lorainelab/integrated-genome-browser, select the source button, and navigate to the resources folder as shown below.

For developers: This is the "master branch" which we use to create the released versions of IGB you download at BioViz. See also Developing IGB from the IGB Developers Guide.

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How to make a species.txt file for a QuickLoad site or for your personal use

First check to see if your species and genome version prefixes are already present in the species.txt file. If they are, then you don't need to create a synonyms.txt file. If not, and if you want to merge data from multiple sites that use different names for the same genome version, then make a synonyms.txt file. Here's how:

• Open an editor (Microsoft Word is fine, but you'll need to save the file as a plain text (.txt) file.)
• Type the IGB name for the genome
• Type TAB
• Type a synonym
• Repeat the previous two steps for every synonym

If making the file for a QuickLoad site, save the file in the root directory, same level as the "contents.txt" and "species.txt" files.

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• names to each other