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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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Plan for integration with BEL #22

Open goodb opened 6 years ago

goodb commented 6 years ago

See e.g. https://github.com/OpenBEL http://openbel.org http://openbel.org/language/version_2.0/bel_specification_version_2.0.html#_terms https://www.biorxiv.org/content/early/2018/09/03/353235

goodb commented 6 years ago

See also mapping document https://docs.google.com/document/d/10xi10oyISribbssR9CYgz6YVgC_rAVR3W2RvSt7Vdqg/edit?ts=5ba932a0 python converter code https://github.com/cthoyt/pybel-obo/blob/master/tests/test_convert.py

cthoyt commented 4 years ago

@goodb is there any forwards movement on this? I could help when it comes to PyBEL stuff (if there's a certain format you want to come from BEL, it's not so hard to implement)

goodb commented 4 years ago

Hi @cthoyt the general project of converting from BioPAX to GO-CAM has come along and is in what we might call a 1.0 version.. We haven't done anything with BEL yet but @dustine32 and @thomaspd have apparently been working with Causal Tab https://pubmed.ncbi.nlm.nih.gov/30793173/ . They might have more input there.

Given the python focus for pyBEL, you may want to touch base with @dustine32 . He has written python code that generates GO-CAMs. It would be cool to see his library integrate with yours to allow GO-CAMs to be drawn from BEL sources and perhaps vice versa.