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BEP-0008 - Update Namespace and Identifier Handling #28

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merged 8 commits into from Sep 24, 2019

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cthoyt commented Jul 25, 2019

After discussion with @sgebel, I've written this BEP to suggest an improvement to the <namespace>:<name> used in BEL terms. See the full proposal at https://github.com/belbio/bep/blob/add-bep-0008-obo-identifiers/docs/drafts/bep-0008.md

I propose that we (optionally) adopt the OBO syntax for references (<namespace>:<identifier>!<name>) anywhere that the old references were valid.

For example, p(HGNC:MAPT), could be optionally written using the OBO syntax of p(HGNC:6893!MAPT), which includes both the identifier (6893) and the label (MAPT) of the human Tau protein. See the BEP for more examples and rationale.

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wshayes commented Jul 25, 2019

I like this - great idea Charlie and @sgebel the name is an optional element so it is backwards compatible. In presentation mode, we can hide the id and just show the name - with a rollover to show the full official name. This solves some of the terminology evolution issues I have with name identifiers vs database id's.

I'm not a fan of the GO:GO:1234 - let's try to come up with a better way of handling identifiers.org ids and namespaces.

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cthoyt commented Jul 29, 2019

I think it's reasonable to bake in logic that if an identifier starts with the prefix and a semicolon, then one can be omitted. It would take only trivial logic (str.startswith()) when looking up information from MIRIAM on each one. But if we agree on that, let's make it explicit in this BEP

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wshayes commented Jul 29, 2019

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cthoyt commented Jul 30, 2019

Before this BEP is reviewed, I will submit another BEP for yet another way to define namespaces using MIRIAM, which will support this

@cthoyt cthoyt changed the title Add BEP-0008 for OBO identifiers BEP-0008 - OBO identifiers Aug 1, 2019
@cthoyt cthoyt added this to the BEL v2.2 milestone Aug 1, 2019
@cthoyt cthoyt changed the title BEP-0008 - OBO identifiers BEP-0008 - Update Namespace and Identifier Handling Sep 20, 2019
cthoyt and others added 2 commits Sep 20, 2019
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wshayes commented Sep 23, 2019

@cthoyt Please review the character/regex definitions. I'd like to make sure we can build a functional parser without too much difficulty before releasing this to production (e.g. the Reference Implementation). I'm planning on redoing my parser, but it is behind 3 higher priority tasks so it will be a month or so before I can do the reference implementation).

cthoyt and others added 5 commits Sep 23, 2019
Approved by william natalie and john
@cthoyt cthoyt merged commit 8d0acb1 into master Sep 24, 2019
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@cthoyt cthoyt deleted the add-bep-0008-obo-identifiers branch Sep 24, 2019
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