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bioportal client should implement mapping between OBO prefixes and bioportal prefixes #588

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cmungall opened this issue Jun 1, 2023 · 1 comment
Open

bioportal client should implement mapping between OBO prefixes and bioportal prefixes #588

cmungall opened this issue Jun 1, 2023 · 1 comment

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@cmungall
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cmungall commented Jun 1, 2023

Currently using the bioportal client with some ontologies like FBbt, WBbt results in failure, because bioportal uses different names eg FB-BT

We should implement the mapping - using bioregistry? in this lib or in https://github.com/cthoyt/ontoportal-client?
@cmungall cmungall mentioned this issue Jun 13, 2023
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@cthoyt
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cthoyt commented Jul 2, 2023 •
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You can use one of the two endpoints in the Bioregistry:

I realize that the route implements the logic in https://github.com/biopragmatics/bioregistry/blob/db0ef92f1f52fd871d62ee71fd876fb6c93003a1/src/bioregistry/app/api.py#L273-L315, so it's not reusable at the moment from the Python API. Update: you can use the following code in Bioregistry v0.9.64:

>>> from bioregistry import manager
>>> diff = manager.get_external_mappings("obofoundry", "bioportal")
>>> diff.mappings["gaz"]
'GAZ'

cthoyt added a commit to biopragmatics/bioregistry that referenced this issue Jul 3, 2023
@cthoyt
Get mappings between external registries
c32a137 
Related to INCATools/ontology-access-kit#588
@cthoyt cthoyt mentioned this issue Jul 3, 2023
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cthoyt added a commit to biopragmatics/bioregistry that referenced this issue Jul 3, 2023
@cthoyt
Get mappings between external registries (#902)
e82a658 
There's an API endpoint that lets you get all if the mappings from one
external registry to another. For example, getting all mappings from OBO
Foundry to Bioportal can be done with
https://bioregistry.io/api/metaregistry/obofoundry/mapping/bioportal.

However, the implementation of this functionality is built in to the API
route itself. This PR externalizes that implementation into the
Bioregistry's manager class so it can be reused.

Related to INCATools/ontology-access-kit#588
@caufieldjh caufieldjh mentioned this issue Jul 5, 2023
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@cmungall @cthoyt