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mapping-commons / sssom-api

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sssom api should use prefixes from mapping sets first, and obocontext second #85

Open matentzn opened 9 months ago

matentzn commented 9 months ago

SSSOM will have a wild variety of all prefixes, some of which are in the obo context, others of which are not.

What is ok is to try and standardise the prefixes mapping sets pre-ingest using curies.standardize() command, but we always have to prefer the built-in curie maps over the obo_context when interpreting the mappings.

@anitacaron I know we talked about this dependency at some point, which may have been ok for a first prototype, but not for the full fledged API; the point of sssom mapping sets is that they spring their own mapping sets.

Can you share the part of the code that would need to be changed to get rid of the obo context dependency?

anitacaron commented 9 months ago

mapping sets first, and obocontext second

This is exactly what I'm doing. The problem is when they have different definitions for the same prefix.

matentzn commented 9 months ago

Maybe we need to think a bit more in this direction: https://curies.readthedocs.io/en/latest/reconciliation.html

I think you should be able to chain conflicting maps and curies somehow pics them in some order.