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 |