The BioGRID PTMTAB and PTMREL formats are custom BioGRID formats that are designed to provide the entirety of our post translational modification curation efforts in a format that is simple to read in Microsoft Excel or to script into Bioinformatics applications. All Columns are separated by tabulations.

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BioGRID PTMTAB files are denoted by the extension .ptmtab.txt or .ptmtab.zip

The first line of a BioGRID PTMTAB file is the heading line and starts with a hash (#). This line is purely for informational purposes and gives a brief description of the content contained in each column. If you are scripting the use of this file, you can simply ignore it.

The column contents of BioGRID PTMTAB files should be as follows:

1. PTM ID. A unique identifier for each post translational modification within the file. These IDs are non-persistant and only relevant to this specific file download.
2. Entrez Gene ID. The identifier from the Entrez-Gene database that corresponds to this PTM Site.
3. BioGRID ID. The identifier in the BioGRID database that corresponds to this PTM Site. These identifiers are best used for creating links to the BioGRID from your own websites or applications. To link to a page within our site, simply append the URL: http://www.thebiogrid.org/ID/ to each ID. For example, http://www.thebiogrid.org/31623/.
4. Systematic name. A plain text systematic name if known. Will be a “-” if no name is available.
5. Official symbol. A common gene name/official symbol. Will be a “-” if no name is available.
6. Synonyms/Aliases. A “|” separated list of alternate identifiers. Will be “-” if no aliases are available.
7. Sequence. A protein sequence referenced for this PTM Site.
8. Refseq ID. The Refseq ID of the Sequence.
9. Position. Residue position within the sequence for this PTM Site.
10. PTM Type. A descriptive name for the type of PTM Site referenced (examples: Phosphorylation, Ubiquitination)
11. Residue. The residue that is in location in Position within the Sequence.
12. First author surname of the publication in which the interaction has been shown, optionally followed by additional indicators, e.g. Stephenson A (2005)
13. Pubmed ID of the publication in which the interaction has been shown.
14. Organism ID. This is the NCBI Taxonomy ID for this Sequence.
15. Has Relationships. Will be TRUE or FALSE. When TRUE, this PTM Site will have accompanying relationships within the PTMREL data file.
16. Qualifications. If additional plain text information was recorded for an interaction, it will be listed with unique qualifiers separated by “|”. If no qualification is available, this field will contain “-”.
17. Source Database. This field will contain the name of the database in which this interaction was provided.

All columns are mandatory so columns with no values are filled with “-“

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