Encoding a phosphorylation residue in biopax

[Eric]

Dear BioPAXers,

As far as I understood, post-translational modifications in biopax are encoded using a ModificationFeature object, itself having a SequenceModificationVocabulary term attached (plus a FeatureLocation object eventually).

Now if I want to specify that a phosphorylation is taking place on the threonine or serine residue, this is encoded directly in the vocabulary term, e.g. "Thr_15_pho" or "o-phospho-serine".

is that correct or is there an alternative way of encoding this info?

Thanks for your help,

Eric

[Emek]

Hi Eric,

1) We highly recommend using MOD controlled vocabulary (http://
www.ebi.ac.uk/ontology-lookup/browse.do?ontName=MOD) for the term.
Specifically we expect data providers to use "protein modification
categorized by amino acid modified" branch.
2) It is not a good practice in general to encode location info on the
term. This should go to the feature location.
3) Unless it is a "generic" feature the amino acid is already
specified since you know the location AND the sequence( via the
associated ProteinReference). So this info is already encoded.

Does that answer your question? Are there special cases where this
would not be sufficient? If you can provide some examples I am happy
to discuss further.

Best,
ED