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Add case variant synonyms to Orphanet and ORDO #1003

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Add case variant synonyms to Orphanet and ORDO #1003

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a1285ab
Update ORDO
cthoyt Nov 28, 2023
7da3427
Merge branch 'main' into update-orphanet
cthoyt Nov 28, 2023
9339784
Merge branch 'main' into update-orphanet
cthoyt Nov 28, 2023
59ced11
Add orphanet synonym
cthoyt Nov 29, 2023
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10 changes: 5 additions & 5 deletions src/bioregistry/data/bioregistry.json
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Original file line number Diff line number Diff line change
Expand Up @@ -73384,7 +73384,8 @@
}
],
"synonyms": [
"ORPHA"
"ORPHA",
"Orphanet"
],
"uniprot": {
"abbreviation": "Orphanet",
Expand Down Expand Up @@ -73447,9 +73448,6 @@
},
"download_owl": "http://www.orphadata.org/data/ORDO/ordo_orphanet.owl",
"example": "C023",
"example_extras": [
"478"
],
"fairsharing": {
"abbreviation": "ORDO",
"contact": {
Expand Down Expand Up @@ -73514,7 +73512,7 @@
"version": "4.3",
"version.iri": "https://www.orphadata.com/data/ontologies/ordo/last_version/ORDO_en_4.3.owl"
},
"pattern": "^C?\\d+$",
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With this change, you wont validate any "normal" orpha codes, they don't have that "C"

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This was on purpose. The goal of the bioregistry is to give a summary of all of the semantic spaces. Just because it turns out that Orphanet smashed two semantic spaces into the same URI format string, it doesn't mean we can't describe them as accurately as possible.

Like David said, Orphanet's ORDO vocabulary is for the properties. The rest is regular Orphanet

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@matentzn matentzn Nov 29, 2023 •
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Yes but like I noted, it make more practical sense to push them together instead of having two, else how will you be able to say that both have the same uri_prefix?

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So far I have not heard a clear argument why the separation is necessary. I have good reasons why it is not necessary. I can only think of a single reason, which is being able to redirect xrefs from browsers to separate destinations depending on whether they are properties or diseases. Can you point me to the issue that clearly explains that this is what you are trying to solve?

"pattern": "^C\\d+$",
"publications": [
{
"pubmed": "22874158",
Expand All @@ -73523,6 +73521,8 @@
}
],
"synonyms": [
"ORDO",
"ORPHANET.ORDO",
"ordo"
],
"uri_format": "http://www.orpha.net/ORDO/Orphanet_$1"
Expand Down
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