API External References

Shariant parses all submitted values and note fields looking for external reference patterns (such as PMID). e.g.

“See the paper PMID:123456 about this”

Would parse out a reference to PubMed

{
"value": "See the paper PMID:123456 about this",
"db_refs": [{
    "db": "PubMed",
    "id": "PubMed: 123456",
    "idx": "123456",
    "url": "https://www.ncbi.nlm.nih.gov/pubmed/?term=123456",
    "internal_id": 50165
}]
}

These values will be formatted into a specific structure on download, but for upload they just need to be in the format of REF_TYPE:REF_NUMBER.

There is some leeway on the formatting, e.g. for PMID the following are allowed:

  • PMID:123456

  • PMID123456

  • PMID 123456

  • PMID#123456

  • PMID 123456,6543321

  • pmid 123456

Typically it’s the case insensitive key term followed by any number of spaces, hashes or colons and then the referenced ID.

Some terms do allow a comma separated list of values, but this is not preferred.

As of October 2019 the following are supported:

ref type term example reference resulting URL
ClinGen CA CA123456 http://reg.clinicalgenome.org/redmine/projects/registry/genboree_registry/by_caid?caid=CA123456
Clinvar VariationID VariationID:12345 https://www.ncbi.nlm.nih.gov/clinvar/variation/12345/
COSMIC COSM COSM112085121 https://cancer.sanger.ac.uk/cosmic/mutation/overview?id=112085121
GTR GTR GTR:516181 https://www.ncbi.nlm.nih.gov/gtr/tests/516181/
HPO HP or HPO HPO:0001631 https://hpo.jax.org/app/browse/term/HP:0001631
MedGen MedGen MEDGEN:12345 https://www.ncbi.nlm.nih.gov/medgen/?term=12345
NCBIBookShelf NCBIBookShelf NCBIBookShelf:NBK11530 https://www.ncbi.nlm.nih.gov/books/NBK11530/
NIHMS NIHMS NIHMS:123456 https://www.ncbi.nlm.nih.gov/pubmed/?term=NIHMS123456
OMIM OMIM OMIM:115500 https://www.omim.org/entry/115500
PMC PMCID PMCID:1234567 https://www.ncbi.nlm.nih.gov/pubmed/?term=PMC1234567
PUBMED PUBMED or PMID or PubMedCentral PMID:123456 https://www.ncbi.nlm.nih.gov/pubmed/?term=123456
SNP rs rs123456 https://www.ncbi.nlm.nih.gov/snp/rs123456
UNIPROTKB UNIPROTKB UNIPROTKB:P30440 https://www.uniprot.org/uniprot/P30440