Alignment

bioregistry.align Package

Workflows for aligning external registries.

Classes

Aligner([force_download])	A class for aligning new registries.
AberOWLAligner([force_download])	Aligner for AberOWL.
BioContextAligner([force_download])	Aligner for BioContext.
BiolinkAligner([force_download])	Aligner for Biolink.
BioPortalAligner([force_download])	Aligner for BioPortal.
CropOCTAligner([force_download])	Aligner for CropOCT.
EcoPortalAligner([force_download])	Aligner for EcoPortal.
AgroPortalAligner([force_download])	Aligner for AgroPortal.
CellosaurusAligner([force_download])	Aligner for the Cellosaurus.
ChemInfAligner([force_download])	Aligner for the Chemical Information Ontology.
FairsharingAligner([force_download])	Aligner for the FAIRsharing.
GoAligner([force_download])	An aligner for the Gene Ontology (GO) registry.
MiriamAligner([force_download])	Aligner for the MIRIAM registry.
N2TAligner([force_download])	Aligner for the N2T.
NcbiAligner([force_download])	Aligner for NCBI xref registry.
OBOFoundryAligner([force_download])	Aligner for the OBO Foundry.
OLSAligner([force_download])	Aligner for the OLS.
OntobeeAligner([force_download])	Aligner for OntoBee xref registry.
PrefixCommonsAligner([force_download])	Aligner for Prefix Commons.
UniProtAligner([force_download])	Aligner for UniProt.
WikidataAligner([force_download])	Aligner for Wikidata properties.
EDAMAligner([force_download])	Aligner for the EDAM ontology.
Re3dataAligner([force_download])	Aligner for the Registry of Research Data Repositoris (r3data).
HL7Aligner([force_download])	Aligner for HL7 External Code Systems.
BartocAligner([force_download])	Aligner for BARTOC.

bioregistry.external Package

Workflows for downloading and aligning various external registries.

Functions

get_biocontext([force_download])	Get the BioContext context map.
get_biolink([force_download])	Get Biolink.
get_bioportal([force_download])	Get the BioPortal registry.
get_cellosaurus([force_download, ...])	Get the Cellosaurus registry.
get_cheminf([force_download])	Get the Chemical Information Ontology registry.
get_fairsharing([force_download, use_tqdm])	Get the FAIRsharing registry.
get_go([force_download])	Get the GO registry.
get_miriam([force_download, force_process])	Get the MIRIAM registry.
get_n2t([force_download])	Get the N2T registry.
get_ncbi([force_download])	Get the NCBI data.
get_obofoundry([force_download, force_process])	Get the OBO Foundry registry.
get_ols([force_download])	Get the OLS registry.
get_ontobee([force_download])	Get the OntoBee registry.
get_prefixcommons([force_download, ...])	Get the Life Science Registry.
get_uniprot([force_download])	Get the UniProt registry.
get_wikidata([force_download])	Get the wikidata registry.
get_edam([force_download])	Get the EDAM registry.
get_re3data([force_download])	Get the re3data registry.
get_hl7([force_download])	Get HL7 OIDs.
get_bartoc([force_download])	Get the BARTOC registry.