bridgedb / bridgedb/BridgeDb

hgnc identifiers - support with and without HGNC:

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#15 6 comments 0 reactions 1 assignee Claimed by @stain View on GitHub
enhancement in progress
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Description

In http://identifiers.org/hgnc/ we see Identifier pattern `^((HGNC|hgnc):)?\d{1,5}$` which is (somewhat) reflected in the HGNC Accession number entry https://github.com/bridgedb/BridgeDb/blob/master/org.bridgedb.rdf/resources/IdentifiersOrgDataSource.ttl#L2762

``` turtle
bridgeDB:hasRegexPattern "^(HGNC:)?\\d{1,5}$" ;
```

This means that identifiers http://identifiers.org/hgnc/47710 and http://identifiers.org/hgnc/HGNC:47710 and http://identifiers.org/hgnc/hgnc:47710 are all valid - and indeed all resolve to RNU6-747P.

The IdentityMappingService is however unable to know these are the same thing, unless we move `HGNC:` out of the regular expression and add alternative URI prefixes. Currently this will be tracked as three identifier `47710`, `HGNC:47710` and `hgnc:47710` in the same dataset.

HGNC itself consistently identifies a "HGNC ID" with the prefix, e.g. `HGNC:47710` - which is in accordance with the [10 Simple rules for design, provision, and reuse of persistent identifiers for life science data](http://dx.doi.org/10.5281/zenodo.18003) rule 2 to use CURIEs.

In Open PHACTS, earlier linksets used the style http://identifiers.org/hgnc/47710 - however @JonathanMELIUS's latest [Ensembl-to-HGNC linkset])(http://bridgedb.org/data/linksets/HomoSapiens/Ensembl_Hs_hgnc.direct.LS.ttl) uses the style http://identifiers.org/hgnc/HGNC:47710 which adds the CURIE to the alternative base - perhaps this is not ideal (and can probably by changed upstream) - anyway as both patterns are accepted the org.bridgedb.rdf entry should be updated to support both.

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