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bio2bel / ctd

A Bio2BEL package for converting the Comparative Toxicogenomics Database (CTD) to BEL

MIT License

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Open cthoyt opened 7 years ago

cthoyt commented 7 years ago

start with a given gene
use query.get_chem_gene_interaction_actions with the filter for the gene you want and also interaction_action='inhibitor' (I think 'inhibitor' is the right one, you can also check that)
print a BEL statement

cthoyt commented 7 years ago

I'd also suggest doing this in a jupyter notebook before writing a huge library full of it

aramgrigoryan commented 7 years ago

the library has issues... simple examples from the documentation aren't working

aramgrigoryan commented 7 years ago

to save genes names app, akt1

cthoyt commented 7 years ago

What did you do? Can't help without seeing the code :p

aramgrigoryan commented 7 years ago

is the same problems as Christian had...

cthoyt commented 7 years ago

share your code with me

aramgrigoryan commented 7 years ago

what about this now?

cthoyt commented 7 years ago

Need to explore a couple more things:

How many entities can be matched to either ChEBI names or synonyms from ChEBI?
How many remaining entities can be matched by using ChemSpider and only find one search result?
how many have multiple search results (looks like we'll be doing some manual chemistry curation!)?
for how many are we really screwed?

aramgrigoryan commented 7 years ago

this kinda feels left out

cthoyt commented 7 years ago

yeah this is sidelined for a bit