Unrecognised HGNC URI pattern

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Repository with the BridgeDb data source.

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Unrecognised HGNC URI pattern #6

Closed ianwdunlop closed 4 months ago

ianwdunlop commented 7 years ago

The pattern http://identifiers.org/hgnc/HGNC%253A29350 was found in a linkset but was not recognized by BridgeDB. However it does redirect to the correct place which suggests that identifiers.org does recognize it. So, either the pattern needs added to BridgeDB or the linkset file changed. The URI looks like it has been escaped wrong in some way.

egonw commented 7 years ago

@ianwdunlop it comes from the http://bridgedb.org/data/linksets/release87/MusMusculus/Ensembl_Mm_dataset.void.ttl file, right?

@JonathanMELIUS, can you please check that file for HGNC%253Axxxx identifiers, and see if your code introduces that double escaped ':' and how we can solve that?

ianwdunlop commented 7 years ago

I found the pattern in http://bridgedb.org/data/linksets/release87/MusMusculus/Ensembl_Mm_hgnc.projection.LS.ttl It may be in other files, I haven't looked

egonw commented 1 year ago

Bioregistry/Identifiers.org (via Bioregistry):

hgnc.symbol: https://bioregistry.io/registry/hgnc.symbol
hgnc: https://bioregistry.io/registry/hgnc

BridgeDb has both.

egonw commented 4 months ago

Closing this for now. So much has changed, and the IMS currently needs a lot of attention anyway, but still no funding for this.