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belbio / bel

BEL python package
https://bel.rtfd.io
Apache License 2.0
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Add geneAbundance modifier function #14

Open wshayes opened 6 years ago

wshayes commented 6 years ago

From @wshayes on July 11, 2017 12:12

For next version of BEL:

To support methylation http://varnomen.hgvs.org/bg-material/consultation/svd-wg005/

See also pyBEL: http://pybel.readthedocs.io/en/latest/overview.html#syntax-for-epigenetics

This looks like it's covered by the g(, var()) - inserting the HGVS proposed methylation construct in the var() modifier for the gene will do the same as the mod() function proposed by pyBEL.

_Copied from original issue: belbio/bellang#6

wshayes commented 6 years ago

From @cthoyt on October 16, 2017 13:48

Until we find a really good HGVS parser/validator, it's still not a bad idea to introduce BEL syntax that can be converted directly into HGVS

wshayes commented 6 years ago

@cthoyt I think the payload for the var() modifier function can be anything at this point since we aren't validating it as HGVS. We could point release a change to BEL 2.0.0 to officially support this (which won't be onerous in the VERY near future). Please take a look at https://github.com/belbio/bel_lang/blob/master/bel_lang/versions/bel_v2_0_0.yaml and see if it makes sense to you.