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geneontology / pathways2GO

Code for converting between BioPAX pathways and Gene Ontology Causal Activity Models (GO-CAM)
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rewrite the conversion process to Python and implement using straightforward conversion rules #3

Open goodb opened 6 years ago

goodb commented 6 years ago

The mapping process follows a set of rules that could probably be expressed in a logic programming framework such as prolog or SWRL rules. This would be beneficial as it would be easier to collaboratively develop the rules if they were first class entities in github rather than chunks of code buried in the converter app. Would also make it feasible to apply them in other contexts.

Investigate formalizations is the ticket here.

Notes from @balhoff on how to get started: SWRLtab (in Protege) comes with its onw reasoner; you don’t really need it just edit in the Rules tab it’s built in look at some of the rules that are in RO already. then you need to run them - you an use the Arachne Protege plugin, which is kind of hacky or just save your rules in an OWL file and use like the other OWL files in your program

cmungall commented 2 years ago

I think the priority is to rewrite the conversion process to Python and implement using straightforward conversion rules

goodb commented 2 years ago

@cmungall I humbly suggest the conversion rules aren't all that straightforward all the time :). And that the best way to rewrite the conversion framework in python would be to use sparql on the biopax. A rewrite of the same approach I took in Java in python would not be beneficial - IMHO - Just two cents!

ukemi commented 2 years ago

Hi @goodb. @cmungall can you ponder the possibilities and change the ticket if you feel it is appropriate?

kltm commented 1 year ago

@dustine32 Has picked this up.

deustp01 commented 1 year ago

@dustine32 can you bring @ukemi up to speed on this, maybe at the "weeds" call on Monday 8/28?

dustine32 commented 1 year ago

@deustp01 Can do! Do you know what time the call is at?

deustp01 commented 1 year ago

11 AM EDT / 8 AM PDT (sorry about that). @ukemi do you need to send invites to Dustin and Huaiyu?