Taxonomy

PAMPA offers the possibility to add taxonomic information to the species identification. In this case, it uses a taxonomy file. PAMPA source code comes with several pre-computed taxonmy files. Alternatively, users can define their own taxonomy file.

Available taxonomy files

PAMPA's taxonomy files are available in the Taxonomy folder of the source code. Please avoid modifying these files, as it may damage the behaviour of the program.

Construction of a taxonomy file

The taxonomy must be in the form of a Tab-Separated Values (TSV) file comprising five columns: Taxid, Common name, Scientific name, Parent (taxid), and Rank (species, genus, etc.).

You can obtain this type of file directly from UniProt (https://www.uniprot.org/taxonomy) by following these steps:

1. Use the search bar to find your desired clade, entering its common name, scientific name, or taxid.
2. Select the clade of interest and click on 'Browse all descendants.'
3. Locate the 'download' link.
4. Choose the TSV format and customize the columns in the following order: Common name, Scientific name, Parent, and Rank.
5. Proceed to download the taxonomy file.

See an example (taxonomy of caprinae).

Utilization of a taxonomy file

Taxonomy files are utilized in various contexts within PAMPA:

• To enrich species predictions generated by PAMPA CLASSIFY, providing information on the taxonomic rank and resolution of the results.
• To specify a taxon in a simple and compact format within limit files.
• To automatically augment a peptide table by adding new columns that specify the common name, genus, family, and other ranks using PAMPA CRAFT with the fillin module.