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sorgerlab / indra

INDRA (Integrated Network and Dynamical Reasoning Assembler) is an automated model assembly system interfacing with NLP systems and databases to collect knowledge, and through a process of assembly, produce causal graphs and dynamical models.
http://indra.bio
BSD 2-Clause "Simplified" License
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Activity type for micro-RNAs #254

Open bgyori opened 7 years ago

bgyori commented 7 years ago

Currently micro-RNAs are extracted with transcriptional activity from databases (as subjects of RegulateAmount Statements). We should introduce a special activity type for the regulatory activity of micro-RNAs and extract them accordingly. There is no applicable activity type in BEL that we could adopt.

cthoyt commented 7 years ago

Do you think it would be worth adding something to the BEL language to better represent the types statements that are generally made about miRNA's?

johnbachman commented 7 years ago

Interesting question. How do you go about extending BEL for things like this? Is there a process for formalizing updates? I know @dexterpratt has some ideas about BEL extensions as well.

cthoyt commented 7 years ago

Technically, it's not hard to extend PyBEL, but Dexter proposed the idea of having modules that can be "imported" to the parser. That would require quite a bit of development to get right.

When it comes to these types of interactions, maybe it would make sense to make BEL statements like act(m(X), ma(regulatoryActivity)) =| p(Y). The appropriate term for regulatoryActivity could probably be matched to something in GO.

cthoyt commented 7 years ago

Just ran into this article: http://www.geneontology.org/page/microrna-go-annotation-manual. Might be relevant