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Published 20 hours ago • verified publisher icon sorgerlab

New modification statements

Open kkaris opened this issue 3 years ago • 2 comments

This PR adds new Modification statement types:

  • Carboxylation/Decarboxylation
  • Amidation/Deamidation
  • Sulfation/Desulfation
  • Neddylation/Deneddylation
  • Alkylation/Dealkylation
  • Prenylation/Deprenylation

kkaris avatar Aug 19 '20 21:08 kkaris

I found some places that potentially need to be updated if the new types are integrated:

  • https://github.com/sorgerlab/indra/blob/master/indra/assemblers/pysb/sites.py
  • https://github.com/sorgerlab/indra/blob/master/indra/tests/test_english_assembler.py
  • https://github.com/sorgerlab/indra/blob/master/indra/sources/ctd/processor.py

kkaris avatar Aug 20 '20 13:08 kkaris

Maybe it makes sense to add a bit of metadata along with each statement type to align them with related entries in other controlled vocabularies. For example, neddylation corresponds to the GO biological process "protein neddylation" (GO:0045116).

I did this for PyBEL and you could copy relevant parts if you think this is a good idea. No single controlled vocabulary is covering all types of modifications, though. See: https://github.com/pybel/pybel/blob/57b24a9ddf6d5d73d82c92294ed2186ddf4443c5/src/pybel/language.py#L320-L524

cthoyt avatar Sep 15 '20 12:09 cthoyt