Update 2022-10-25

The functionality of the biocontext repo is being subsumed into https://github.com/linkml/prefixmaps/

BioContext: JSON-LD Contexts for Bioinformatics Data

The goal is to provide a modular set of JSON-LD contexts for mapping abbreviated names of biological objects onto URIs for use in semantic web tool chains. Here, "abbreviated name" usually means a CURIE but optionally human-friendly symbolic names (e.g. gene) can also be used as abbrevations for complete URIs (although this is more dangerous).

A CURIE is a bipartite identifier of the form Prefix:LocalID, in which the prefix is a convenient abbreviation of a URI prefix. CURIEs in JSON-LD documents are expanded to URIs, if that prefix is defined in a @context object.

Note that you don't need to be using JSON-LD to find this useful. Bipartite unique IDs are common in bioinformatics, and mandated in formats such as OBO (the most common way of consuming ontologies in bioinformatics toolchains).

There are many situations where it's necessary to translate a bioinformatics ID to URI for use in the semantic web stack. This includes the SciGraph Neo4j application as well as triplestores, OWL tooling (ROBOT), standard prefixes for SPARQL queries, etc.

Here are some examples of expansions from abbreviated names to URIs using these contexts:

• Ontology class CURIEs
  • GO:0006915 ==> http://purl.obolibrary.org/obo/GO_0006915
  • CHEBI:26619 ==> http://purl.obolibrary.org/obo/CHEBI_26619
  • UBERON:0001685 ==> http://purl.obolibrary.org/obo/UBERON_0001685
  • NCBITaxon:9606 ==> http://purl.obolibrary.org/obo/NCBITaxon_9606
• Databases CURIEs
  • ENSEMBL:ENSG00000123374 ==> http://identifiers.org/ensembl/ENSG00000123374
  • FlyBase:FBgn0011293 ==> http://identifiers.org/flybase/FBgn0011293
• Literature CURIEs
  • PMID:16516152 ==> http://www.ncbi.nlm.nih.gov/pubmed/16516152
  • PMCID:PMC3178059 ==> http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3178059
  • DOI:10.1371/journal.pone.0015506 ==> http://dx.doi.org/10.1371/journal.pone.0015506
• Metadata CURIEs
  • dc:title ==> http://purl.org/dc/terms/title
  • xsd:Int ==> http://www.w3.org/2001/XMLSchema#Int
  • owl:Class ==> http://www.w3.org/2002/07/owl#Class
  • foaf:is_about ==> http://xmlns.com/foaf/0.1/is_about
• Abbreviated non-CURIE names
  • is_about ==> http://xmlns.com/foaf/0.1/is_about
  • part_of ==> http://purl.obolibrary.org/obo/BFO_0000050
  • assay ==> http://purl.obolibrary.org/obo/OBI_0000070
  • Association ==> http://semanticscience.org/resource/SIO_000897

The contexts are modular and remixable; for example, if you want to use the OBO Library purls for ontology class CURIEs you can reference obo_context.json, but you are free to ignore the commitment to map ENSMEBL etc to identifiers.org URIs.

Organization

The project is organized as a set of JSON-LD context files in the registry/ directory. The current set is preliminary and unstable.

Different contexts can be concatenated together. Warning: there is a possibility that combinations can confict. See the scripts in bin for concatenating and subtracting.

The current list is:

• obo : derived from the OBO registry
• idot : derived from identifiers-org/MIRIAM registry
• idot_nr : idot minus OBO
• goxrefs : derived from http://amigo.geneontology.org/xrefs
• semweb : Standard semantic web prefixes
• commons : The commons set: OBO + idot_nr + monarch

Clash Reporting

• reports/clashes.txt

Use in JSON-LD documents

You can simply copy the portions of the contexts files here to use in your own JSON-LD documents.

When this project is more stable, you can reference any of the contexts over the web.

For testing purposes you can do this for now:

 {
   "@context", "https://raw.githubusercontent.com/cmungall/biocontext/master/registry/obo_context.jsonld"
   ...

but this is not stable

Examples

TODO

Remixing your own contexts

TODO - provide links to JSON-LD scripts

Philosophy

When mapping an OBO-style ID there is no ambiguity as to what to map to. The ID "CHEBI:26619" corresponds to the OWL class with IRI "http://purl.obolibrary.org/obo/CHEBI_26619".

However, when presented with something like "OMIM:224050" or "ENSEMBL:ENSG00000123374", what should the interpretation of these be when we refer to them from within the semantic web? Are these information artefacts about a biological entity, or are they biological entities themselves? If they are biological entities, is a gene an individual or a class?

This registry provides a pluralistic approach. The default is to map a database ID to an identifiers.org URI, which makes no ontological commitments to the nature of the entity. This does not preclude the possibility of including separate mappings to ontologically committed OWL objects. For example, one group may use to use CURIEs of the form "OMIM:224050" as an abbreviation for an OWL Class URI. There is no mandate in the semantic web that all groups must use the same CURIEs. However, to avoid confusion groups should in general coordinate for example through obo-discuss regarding different ontological interpretations of database objects.

Note this is already built in to some extent with some databases such as the NCBITaxonomy. The OBO Library uses the NCBITaxon prefix for a class-based mirror of the ncbi taxonomy database. For example "NCBITaxon:9606" is a shorthand for http://purl.obolibrary.org/obo/NCBITaxon_9606

What this does not do

The scope of biocontext is limited to mapping of prefixes and short names to URIs. It is not a general purpose registry. It stores no metadata about the prefixes used. It reuses mappings from other registries such as identifiers.org and the OBO library when possible.

PrefixCommons separately harmonizes additional identifier metadata (beyond the mappings alone); this metadata harmonization is instead done in the data ingest repository. The sources for prefix metadata are primarily Identifiers.org, Bio2RDF registry, the OBO foundry, and BioPortal.

Contributing

• new issue
• Fork, branch, make a pull request
• Edit any file directly via github web interface and make a pull request