This document is part of the BioCompute Object User Guide

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3.2 Appendix-II: External reference database list

This list contains the databases that are currently being used in our BCOs. We use the CURIEs that map to URIs maintained by http://identifiers.org/

Identifiers.org is an established resolving system the enables the referencing of data for the scientific community, with a current focus on the Life Sciences domain. Identifiers.org provides direct access to the identified data using one selected physical location (or resource). Where multiple physical locations are recorded in the registry the most stable one is selected for resolution. This allows the location independent referencing (and resolution if required) of data records."

In the entries below the namespace and identifier combine to become the CURIEs.

Recommended name: Taxonomy
Namespace: taxonomy
Identifier pattern: ^\d+$
Registry identifier: MIR:00000006
URI: http://identifiers.org/taxonomy/


Recommended name: Sequence Ontology
Namespace: so
Identifier pattern: ^SO:\d{7}$
Registry identifier: MIR:00000081
URI: http://identifiers.org/so/

Recommended name: PubMed
Namespace: pubmed
Identifier pattern: ^\d+$
Registry identifier: MIR:00000015
URI: http://identifiers.org/pubmed/

Recommended name: PubChem-compound
Namespace: pubchem.compound
Identifier pattern: ^\d+$
Registry identifier: MIR:00000034
URI: http://identifiers.org/pubchem.compound/

For instance, the inline CURIE [taxonomy:31646] expands to http://identifiers.org/taxonomy/31646 as the namespace taxonomy corresponds to the prefix http://identifiers.org/taxonomy/ to be augmented with the identifier 31646. Resolving the resulting URI will redirect (currently to https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=31646) showing that term [taxonomy:31646] means Hepatitis C virus subtype 1a in the NCBI Taxonomy browser.

Note that some identifier patterns result in a repetition when combined with the prefix, e.g. [so:SO:0000667] expands to http://identifiers.org/so/SO:0000667 where so: is the prefix and SO: is part of the Sequence Ontology identifier.

References

McMurry JA et al: Identifiers for the 21st century: How to design, provision, and reuse persistent identifiers to maximize utility and impact of life science data. PLoS Biology 15(6): e2001414. https://doi.org/10.1371/journal.pbio.2001414