Contexts Open Biomedical Ontologies Context
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The OBO Context exists for the following reasons:

  • Reconciling "database cross-references" used by OBO ontologies and centralising their validation.
  • Standardising and validating SSSOM mappings provided in the context of OBO ontologies.
  • Providing an incentive for the documentation of non-standard prefixes for OBO ontologies.
Identifier
obo
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Maintainers
Properties
Synonyms
Prefix Priority

This ordering of metaprefixes (i.e., prefixes for registries) is used to determine the priority of which registry's prefixes are used. By default, the canonical Bioregistry prefixes are highest priority. Add in "preferred" for explicitly using preferred prefixes or "default" for explicitly using Bioregistry canonical prefixes.

  1. obofoundry.preferred
  2. preferred
  3. obofoundry
  4. default
URI Prefix Priority

This ordering of metaprefixes (i.e., prefixes for registries) is used to determine the priority of which registry's URI prefixes are used. By default, the canonical Bioregistry URI prefixes are highest priority.

  1. obofoundry
  2. rdf
  3. default
  4. biocontext
  5. miriam
  6. ols
Prefix Remapping

This is a mapping from canonical Bioregistry prefixes to custom prefixes used in this context.

ensembl
ENSEMBL
icd10
ICD10WHO
mesh
MESH
omim.ps
OMIMPS
orphanet.ordo
Orphanet
pubmed
PMID
snomedct
SCTID
umls
UMLS
Custom Prefix Map

This is a custom prefix map (which contains custom URL/URI expansions) that is added after all other logic is applied. Keys must either be canonical Bioregistry prefixes, prefixes used based on the given prefix priority, or values in the given prefix remapping.

PMID
https://www.ncbi.nlm.nih.gov/pubmed/
Prefix Blacklist

This is a list of canonical Bioregistry prefixes that should not be included in the context.