On BioGRID Database, PTMREL is a file that describes relationships of the PTMs (Post Translation Modification) tabulated in a PTMTAB file.
I have several issues with this file.
- Foremost, I am not sure how to interpret the 'relationships'.
There are two columns 'Relationship' and 'Identity' that supposedly describe the relationships of PTMs.
Relationship. A plain text descriptor of the type of relation represented. (Unique values: ['-', 'kinase', 'phosphatase']) Identity. A plain text descriptor of additional identity details if available. (Unique values: ['catalytic', 'regulatory', 'PTM'])
Lets say, a gene has a relationship (in in PTMTAB file, column 'Has relationship' is True) and in PTMREL file it is 'kinase' (in PTMREL file column 'Relationship'), does that mean that the gene is kinase or it is phoshorylated by a kinase? Also what does it mean if the gene is additionally 'catalytic', 'regulatory' or a 'PTM' (in PTMREL file column 'Identity')?
Here's BioGRID's wiki page describing (but not detailing) the file format of PTMREL file. https://wiki.thebiogrid.org/doku.php/biogrid_ptmtab_ptmrel.
If PTMREL contains data associated with PTMTAB file, why not simply combine it with PTMTAB file? Without knowing how to interpret the relationships of the PTMS, the users too, can not combine the two files.
Additionally, there are PTMs included in 'BioGRID TAB 2.0' too, and the number of PTMs (for a species) in that file are not the same as in PTMTAB file(!).
I understand that BioGRID provide this data 'WITHOUT ANY WARRANTY'. But still, since BioGRID is the most unified and constantly updated resource of gene interaction networks, users should know about basic usage of the data.
After some data explorations, I could guess the meanings of the data. If Relationship is '-' -> Identity is always 'PTM'. So, these are the PTMs that do not have known relationships. If Relationship is 'kinase' or 'phosphatase' -> Identity is 'catalytic' or 'regulatory'. Now, here, I am not sure what do 'catalytic' or 'regulatory' mean.