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belbio / bep

BEL Enhancement Proposals
http://bep.bel.bio
Apache License 2.0
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Adding new terms to BEL default namespace #25

Open ncatlett opened 5 years ago

ncatlett commented 5 years ago

  1. We have a specific need to add the modification type Acylation/Acyl to the default namespace. (this general term seems like a good fit to describe acylated Ghrelin, as this is how it is frequently referred to in the literature. (The specific modification appears to be o-octanoylation (MOD_00295) or o-decanoylation (MOD_00390), but many/most papers do not refer to the modification in this way)

  2. We need a mechanism to make additions and other changes to the BEL default namespace. This could be a BEP, but the level of discussion/review and the review and update cycle timing needs may be different.

See also related issue https://github.com/belbio/bel_resources/issues/98

wshayes commented 5 years ago

For now until the BEP to extract these from the BEL Specs is written and approved and implemented, I'd recommend that these BEP default namespaces are patch releases and can be expedited - e.g. this Acylation addition would be a 2.1.1 release target.

cthoyt commented 5 years ago

Also requested: protein oxidation (GO:0018158)

Might we make a repository that has the namespace as a TSV that we can just make PRs and releases from, independently of BEL version?

wshayes commented 5 years ago

I need to find time to write a BEP to remove these 'default' namespaces from the BEL Specs and indicate that the BELNS or DEF prefix stands for default terms. We also can't just change default namespace terms without giving people the option of managing this 'default' namespace on their own.

I definitely agree putting these default namespaces in the BEL Spec was a mistake. We also don't have all of the other options from the other terminologies (equivalences, hierarchy, synonyms, etc).