Add ingest for Bioportal prefixes #28
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caufieldjh
commented
Oct 26, 2022
•
caufieldjh
commented
- Ingest (including non-canonical prefixes)
- Curated yaml (including non-canonical prefixes)
- Tests
| @@ -24,7 +24,16 @@ | |||
| location: http://prefix.cc/context.jsonld | |||
| comments: | |||
| - prefix.cc is quite a messy source, it has many outdated expansions for OBO ontologies, lots of strange duplicates etc | |||
| - we recommend this is not used in isolatiom but is instead combined, lower in the priority order | |||
| - we recommend this is not used in isolation but is instead combined, lower in the priority order | |||
| semantic: true | |||
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what makes a context semantic or not?
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I've been taking this to mean that the named resources already contains semantic maps without requiring further processing, but perhaps that isn't @cmungall 's intent
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I mean, these are all semantic prefix maps, aren't they?
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if it generates a namespace used as a resource in an RDF triple
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I think that makes sense, but how does this annotation apply at a context level?
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hmm, everything in this repo should be geared towards semantic namespaces.. also this doesn't conform to https://github.com/linkml/prefixmaps/blob/main/src/prefixmaps/datamodel/context.py
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I'm puzzled as to how the semantic slot got there to begin with if it isn't in the data model. Going to remove it.
| @@ -0,0 +1,509 @@ | |||
| name: bioportal | |||
| prefixes: | |||
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would be cool if we could converge on the "extended prefix map" schema
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Would be nice, yes - but for now, this is still parsed to canonical/prefix_alias/namespace_alias so I'll save adopting the extended schema for a near-future PR
Co-authored-by: Charles Tapley Hoyt <cthoyt@gmail.com>
