Alignment

bioregistry.align Package

Workflows for aligning external registries.

Classes

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

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])	Get the MIRIAM registry.
get_n2t([force_download])	Get the N2T registry.
get_ncbi([force_download])	Get the NCBI data.
get_obofoundry([force_download])	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.