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BRL-BCM / Allele-Registry

This repository contains the source code for the ClinGen Allele Registry. The Allele Registry provides unique identifiers for alleles. It can be accessed at https://reg.genome.network/.
GNU Affero General Public License v3.0
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surface "MANE Preferred" tag through API #3

Open obigriffith opened 4 years ago

obigriffith commented 4 years ago

There are now Transcript Alleles for some AR records with the "MANE Preferred" tag. Very cool. Could this information also be made available through the API?

ronakypatel commented 4 years ago

This information is not directly available for a given variant from /allele GET path. However, you can use our /gene GET path to access it.

For example:

Consider a variant with HGVS expression: NM_001610.4:c.342T>G

Now look at one of the many transcript variants:

{ "coordinates": [ { "allele": "G", "end": 400, "referenceAllele": "T", "start": 399 } ], "gene": "http://reg.genome.network/gene/GN000123", "geneNCBI_id": 53, "geneSymbol": "ACP2", "hgvs": [ "NM_001302491.1:c.342T>G" ], "proteinEffect": { "hgvs": "NP_001289420.1:p.Ala114=" }, "referenceSequence": "http://reg.genome.network/refseq/RS025291" }

Note: "gene": "http://reg.genome.network/gene/GN000123"

When you dereference this gene URI, you will find MANE preferred transcript:

{ "@context": "http://reg.genome.network/schema/gene.jsonld", "@id": "http://reg.genome.network/gene/GN000123", "externalRecords": { "HGNC": { "@id": "http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=HGNC:123", "id": "HGNC:123", "name": "acid phosphatase 2, lysosomal", "symbol": "ACP2" }, "NCBI": { "@id": "http://www.ncbi.nlm.nih.gov/gene/53", "id": 53 }, "MANEPrefRefSeq": { "@id": "https://www.ncbi.nlm.nih.gov/nuccore/NM_001610.4", "id": "NM_001610.4" } } }

You can directly query the /gene path if you know the Gene Symbol to get MANE preferred transcript.

http://reg.genome.network/genes?name=APC