Schema

Pydantic models for the Bioregistry.

class Attributable(**data)[source]

An upper-level metadata for a person.

Create a new model by parsing and validating input data from keyword arguments.

Raises ValidationError if the input data cannot be parsed to form a valid model.

name: str: The full name of the author

orcid: Optional[str]: The open researcher and contributor identifier (ORCiD) of the author

email: Optional[str]: The email for the author

github: Optional[str]: The GitHub handle for the author

add_triples(graph)[source]

Add triples to an RDF graph for this author.

Parameters: graph (rdflib.Graph) – An RDF graph
Return type: rdflib.term.Node
Returns: The RDF node representing this author using an ORCiD URI.

class Author(**data)[source]

Metadata for an author.

Create a new model by parsing and validating input data from keyword arguments.

Raises ValidationError if the input data cannot be parsed to form a valid model.

orcid: str: The open researcher and contributor identifier (ORCiD) of the author. This is overwritten in the child class to enforce it is not none.

class Provider(**data)[source]

A provider.

Create a new model by parsing and validating input data from keyword arguments.

Raises ValidationError if the input data cannot be parsed to form a valid model.

resolve(identifier)[source]

Resolve the identifier into a URI.

Return type: str

class Resource(**data)[source]

Metadata about an ontology, database, or other resource.

Create a new model by parsing and validating input data from keyword arguments.

Raises ValidationError if the input data cannot be parsed to form a valid model.

name: Optional[str]: The resource’s name

description: Optional[str]: A description of the resource

pattern: Optional[str]: The regular expression pattern for identifiers in the resource

uri_format: Optional[str]: The URI format string, which must have at least one $1 in it

providers: Optional[List[bioregistry.schema.struct.Provider]]: Additional non-default providers for the given resource

homepage: Optional[str]: The URL for the homepage of the resource

contact: Optional[bioregistry.schema.struct.Attributable]: The contact email address for the individual responsible for the resource

example: Optional[str]: An example local identifier for the resource, explicitly excluding any redundant usage of the prefix in the identifier. For example, a GO identifier should only look like 1234567 and not like GO:1234567

example_extras: Optional[List[str]]: Extra example identifiers

license: Optional[str]: The license for the resource

version: Optional[str]: The version for the resource

part_of: Optional[str]: An annotation between this prefix and a super-prefix. For example, chembl.compound is a part of chembl.

provides: Optional[str]: An annotation between this prefix and a prefix for which it is redundant. For example, ctd.gene has been given a prefix by Identifiers.org, but it actually just reuses identifies from ncbigene, so ctd.gene provides ncbigene.

download_owl: Optional[str]: The OWL download URL, preferably an unversioned variant

download_obo: Optional[str]: The OBO download URL, preferably an unversioned variant

banana: Optional[str]: The banana is a generalization of the concept of the “namespace embedded in local unique identifier”. Many OBO foundry ontologies use the redundant uppercased name of the ontology in the local identifier, such as the Gene Ontology, which makes the prefixes have a redundant usage as in GO:GO:1234567. The banana tag explicitly annotates the part in the local identifier that should be stripped, if found. While the Bioregistry automatically knows how to handle all OBO Foundry ontologies’ bananas because the OBO Foundry provides the “preferredPrefix” field, the banana can be annotated on non-OBO ontologies to more explicitly write the beginning part of the identifier that should be stripped. This allowed for solving one of the long-standing issues with the Identifiers.org resolver (e.g., for oma.hog; see https://github.com/identifiers-org/identifiers-org.github.io/issues/155) as well as better annotate new entries, such as SwissMap Lipids, which have the prefix swisslipid but have the redundant information SLM: in the beginning of identifiers. Therefore, SLM: is the banana.

deprecated: Optional[bool]: A flag denoting if this resource is deprecated. Currently, this is a blanket term that covers cases when the prefix is no longer maintained, when it has been rolled into another resource, when the website related to the resource goes down, or any other reason that it’s difficult or impossible to find full metadata on the resource. If this is set to true, please add a comment explaining why. This flag will override annotations from the OLS, OBO Foundry, and Prefix Commons on the deprecation status, since they often disagree and are very conservative in calling dead resources.

mappings: Optional[Dict[str, str]]: A dictionary of metaprefixes (i.e., prefixes for registries) to prefixes in external registries. These also correspond to the registry-specific JSON fields in this model like miriam field.

synonyms: Optional[List[str]]: A list of synonyms for the prefix of this resource. These are used in normalization of prefixes and are a useful reference tool for prefixes that are written many ways. For example, snomedct has many synonyms including typos like SNOWMEDCT, lexical variants like SNOMED_CT, version-variants like SNOMEDCT_2010_1_31, and tons of other nonsense like SNOMEDCTCT.

references: Optional[List[str]]: A list of URLs to also see, such as publications describing the resource

appears_in: Optional[List[str]]: A list of prefixes whose corresponding resources use this resource for xrefs, provenance, etc.

depends_on: Optional[List[str]]: A list of prefixes that use this resource depends on, e.g., ontologies that import each other.

namespace_in_lui: Optional[bool]: A flag denoting if the namespace is embedded in the LUI (if this is true and it is not accompanied by a banana, assume that the banana is the prefix in all caps plus a colon, as is standard in OBO). Currently this flag is only used to override identifiers.org in the case of gramene.growthstage, oma.hog, and vario.

no_own_terms: Optional[bool]: A flag to denote if the resource mints its own identifiers. Omission or explicit marking as false means that the resource does have its own terms. This is most applicable to ontologies, specifically application ontologies, which only reuse terms from others. One example is ChIRO.

comment: Optional[str]: A field for a free text comment.

contributor: Optional[bioregistry.schema.struct.Author]: Contributor information, including the name, ORCiD, and optionally the email of the contributor. All entries curated through the Bioregistry GitHub Workflow must contain this field.

reviewer: Optional[bioregistry.schema.struct.Author]: Reviewer information, including the name, ORCiD, and optionally the email of the reviewer. All entries curated through the Bioregistry GitHub Workflow must contain this field pointing to the person who reviewed it on GitHub.

proprietary: Optional[bool]: A flag to denote if this database is proprietary and therefore can not be included in normal quality control checks nor can it be resolved. Omission or explicit marking as false means that the resource is not proprietary.

has_canonical: Optional[str]: An annotation between this prefix and another prefix if they share the same provider IRI to denote that the other prefix should be considered as the canonical prefix to which IRIs should be contracted as CURIEs.

See also

This field was added and described in detail in https://github.com/biopragmatics/bioregistry/pull/164

preferred_prefix: Optional[str]: An annotation of stylization of the prefix. This appears in OBO ontologies like FBbt as well as databases like NCBIGene. If it’s not given, then assume that the normalized prefix used in the Bioregistry is canonical.

miriam: Optional[Mapping[str, Any]]: External data from Identifiers.org’s MIRIAM Database

n2t: Optional[Mapping[str, Any]]: External data from the Name-to-Thing service

prefixcommons: Optional[Mapping[str, Any]]: External data from Prefix Commons

wikidata: Optional[Mapping[str, Any]]: External data from Wikidata Properties

go: Optional[Mapping[str, Any]]: External data from the Gene Ontology’s custom registry

obofoundry: Optional[Mapping[str, Any]]: External data from the Open Biomedical Ontologies (OBO) Foundry catalog

bioportal: Optional[Mapping[str, Any]]: External data from the BioPortal ontology repository

ols: Optional[Mapping[str, Any]]: External data from the Ontology Lookup Service

ncbi: Optional[Mapping[str, Any]]: External data from the NCBI Genbank’s custom registry

uniprot: Optional[Mapping[str, Any]]: External data from UniProt’s custom registry

biolink: Optional[Mapping[str, Any]]: External data from the BioLink Model’s custom registry

cellosaurus: Optional[Mapping[str, Any]]: External data from the Cellosaurus custom registry

ontobee: Optional[Mapping[str, Any]]: External data from the OntoBee

cheminf: Optional[Mapping[str, Any]]: External data from ChemInf

fairsharing: Optional[Mapping[str, Any]]: External data from FAIRsharing

get_external(metaprefix)[source]

Get an external registry.

Return type: Mapping[str, Any]

get_mapped_prefix(metaprefix)[source]

Get the prefix for the given external.

Parameters: metaprefix (str) – The metaprefix for the external resource
Return type: Optional[str]
Returns: The prefix in the external registry, if it could be mapped

>>> from bioregistry import get_resource
>>> get_resource("chebi").get_mapped_prefix("wikidata")
'P683'

get_prefix_key(key, metaprefixes)[source]: Get a key enriched by the given external resources’ data.

get_default_uri(identifier)[source]

Return the default URI for the identifier.

Parameters: identifier (str) – The local identifier in the nomenclature represented by this resource
Return type: Optional[str]
Returns: The first-party provider URI for the local identifier, if one can be constructed

>>> from bioregistry import get_resource
>>> get_resource("chebi").get_default_uri("24867")
'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:24867'

get_banana()[source]

Get the optional redundant prefix to go before an identifier.

A “banana” is an embedded prefix that isn’t actually part of the identifier. Usually this corresponds to the prefix itself, with some specific stylization such as in the case of FBbt. The banana does NOT include a colon “:” at the end

Return type: Optional[str]
Returns: The banana, if the prefix is valid and has an associated banana.

Explicitly annotated banana

>>> from bioregistry import get_resource
>>> get_resource("go.ref").get_banana()
'GO_REF'

Banana imported through OBO Foundry

>>> get_resource("fbbt").get_banana()
'FBbt'

Banana inferred for OBO Foundry ontology

>>> get_resource("chebi").get_banana()
'CHEBI'

No banana, no namespace in LUI

>>> get_resource("pdb").get_banana()
None

Banana is not inferred for OBO Foundry ontologies that were imported: >>> get_resource(“ncit”).get_banana() None >>> get_resource(“ncbitaxon”).get_banana() None

get_default_format()[source]

Get the default, first-party URI prefix.

Return type: Optional[str]
Returns: The first-party URI prefix string, if available.

>>> from bioregistry import get_resource
>>> get_resource("ncbitaxon").get_default_format()
'https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=$1'
>>> get_resource("go").get_default_format()
'http://amigo.geneontology.org/amigo/term/GO:$1'

get_synonyms()[source]

Get synonyms.

Return type: Set[str]

get_preferred_prefix()[source]

Get the preferred prefix (e.g., with stylization) if it exists.

Return type: Optional[str]
Returns: The preferred prefix, if annotated in the Bioregistry or OBO Foundry.

No preferred prefix annotation, defaults to normalized prefix >>> from bioregistry import get_resource >>> get_resource(“rhea”).get_preferred_prefix() None

Preferred prefix defined in the Bioregistry >>> get_resource(“wb”).get_preferred_prefix() ‘WormBase’

Preferred prefix defined in the OBO Foundry >>> get_resource(“fbbt”).get_preferred_prefix() ‘FBbt’

Preferred prefix from the OBO Foundry overridden by the Bioregistry (see also https://github.com/OBOFoundry/OBOFoundry.github.io/issues/1559) >>> get_resource(“dpo”).get_preferred_prefix() ‘DPO’

get_obo_preferred_prefix()[source]

Get the OBO preferred prefix, if this resource is mapped to the OBO Foundry.

Return type: Optional[str]

get_mappings()[source]

Get the mappings to external registries, if available.

Return type: Optional[Mapping[str, str]]

get_name()[source]

Get the name for the given prefix, it it’s available.

Return type: Optional[str]

get_description()[source]

Get the description for the given prefix, if available.

Return type: Optional[str]

get_pattern()[source]

Get the pattern for the given prefix, if it’s available.

Return type: Optional[str]
Returns: The pattern for the prefix, if it is available, using the following order of preference: 1. Custom 2. MIRIAM 3. Wikidata

get_pattern_re()[source]: Get the compiled pattern for the given prefix, if it’s available.

get_namespace_in_lui()[source]

Check if the namespace should appear in the LUI.

Return type: Optional[bool]

get_homepage()[source]

Return the homepage, if available.

Return type: Optional[str]

get_repository()[source]

Return the repository, if available.

Return type: Optional[str]

get_contact()[source]

Get the contact, if available.

Return type: Optional[Attributable]

get_contact_email()[source]

Return the contact email, if available.

Return type: Optional[str]
Returns: The resource’s contact email address, if it is available.

>>> from bioregistry import get_resource
>>> get_resource("bioregistry").get_contact_email()  # from bioregistry curation
'cthoyt@gmail.com'
>>> get_resource("chebi").get_contact_email()
'amalik@ebi.ac.uk'

get_contact_name()[source]

Return the contact name, if available.

Return type: Optional[str]
Returns: The resource’s contact name, if it is available.

>>> from bioregistry import get_resource
>>> get_resource("bioregistry").get_contact_name()  # from bioregistry curation
'Charles Tapley Hoyt'
>>> get_resource("chebi").get_contact_name()
'Adnan Malik'

get_contact_github()[source]

Return the contact GitHub handle, if available.

Return type: Optional[str]
Returns: The resource’s contact GitHub handle, if it is available.

>>> from bioregistry import get_resource
>>> get_resource("bioregistry").get_contact_github()  # from bioregistry curation
'cthoyt'
>>> get_resource("agro").get_contact_github()  # from OBO Foundry
'marieALaporte'

get_contact_orcid()[source]

Return the contact ORCiD, if available.

Return type: Optional[str]
Returns: The resource’s contact ORCiD, if it is available.

>>> from bioregistry import get_resource
>>> get_resource("bioregistry").get_contact_orcid()  # from bioregistry curation
'0000-0003-4423-4370'

get_example()[source]

Get an example identifier, if it’s available.

Return type: Optional[str]

is_deprecated()[source]

Return if the given prefix corresponds to a deprecated resource.

Return type: bool
Returns: If the prefix has been explicitly marked as deprecated either by the Bioregistry, OBO Foundry, OLS, or MIRIAM. If no marks are present, assumed not to be deprecated.

>>> from bioregistry import get_resource
>>> assert get_resource("imr").is_deprecated()  # marked by OBO
>>> assert get_resource("iro").is_deprecated() # marked by Bioregistry
>>> assert get_resource("miriam.collection").is_deprecated() # marked by MIRIAM

get_obofoundry_prefix()[source]

Get the OBO Foundry prefix if available.

Return type: Optional[str]
Returns: The OBO prefix, if available.

>>> from bioregistry import get_resource
>>> get_resource("go").get_obofoundry_prefix()  # standard
'GO'
>>> get_resource("ncbitaxon").get_obofoundry_prefix()  # mixed case
'NCBITaxon'
>>> assert get_resource("sty").get_obofoundry_prefix() is None

get_obofoundry_uri_prefix()[source]

Get the OBO Foundry URI prefix for this entry, if possible.

Return type: Optional[str]
Returns: The OBO PURL URI prefix corresponding to the prefix, if mappable.

>>> from bioregistry import get_resource
>>> get_resource("go").get_obofoundry_uri_prefix()  # standard
'http://purl.obolibrary.org/obo/GO_'
>>> get_resource("ncbitaxon").get_obofoundry_uri_prefix()  # mixed case
'http://purl.obolibrary.org/obo/NCBITaxon_'
>>> assert get_resource("sty").get_obofoundry_uri_prefix() is None

get_obofoundry_uri_format()[source]

Get the OBO Foundry URI format string for this entry, if possible.

Return type: Optional[str]
Returns: The OBO PURL format string, if available.

>>> from bioregistry import get_resource
>>> get_resource("go").get_obofoundry_uri_format()  # standard
'http://purl.obolibrary.org/obo/GO_$1'
>>> get_resource("ncbitaxon").get_obofoundry_uri_format()  # mixed case
'http://purl.obolibrary.org/obo/NCBITaxon_$1'
>>> assert get_resource("sty").get_obofoundry_uri_format() is None

get_prefixcommons_uri_format()[source]

Get the Prefix Commons URI format string for this entry, if available.

Return type: Optional[str]
Returns: The Prefix Commons URI format string, if available.

>>> from bioregistry import get_resource
>>> get_resource("hgmd").get_prefixcommons_uri_format()
'http://www.hgmd.cf.ac.uk/ac/gene.php?gene=$1'

get_identifiers_org_prefix()[source]

Get the identifiers.org prefix if available.

Return type: Optional[str]
Returns: The Identifiers.org/MIRIAM prefix corresponding to the prefix, if mappable.

>>> from bioregistry import get_resource
>>> get_resource('chebi').get_identifiers_org_prefix()
'chebi'
>>> get_resource('ncbitaxon').get_identifiers_org_prefix()
'taxonomy'
>>> assert get_resource('MONDO').get_identifiers_org_prefix() is None

get_miriam_uri_prefix()[source]

Get the Identifiers.org URI prefix for this entry, if possible.

Return type: Optional[str]
Returns: The Identifiers.org/MIRIAM URI prefix, if available.

>>> from bioregistry import get_resource
>>> get_resource('ncbitaxon').get_miriam_uri_prefix()
'https://identifiers.org/taxonomy:'
>>> get_resource('go').get_miriam_uri_prefix()
'https://identifiers.org/GO:'
>>> assert get_resource('sty').get_miriam_uri_prefix() is None

get_miriam_uri_format()[source]

Get the Identifiers.org URI format string for this entry, if possible.

Return type: Optional[str]
Returns: The Identifiers.org/MIRIAM URL format string, if available.

>>> from bioregistry import get_resource
>>> get_resource('ncbitaxon').get_miriam_uri_format()
'https://identifiers.org/taxonomy:$1'
>>> get_resource('go').get_miriam_uri_format()
'https://identifiers.org/GO:$1'
>>> assert get_resource('sty').get_miriam_uri_format() is None

get_nt2_uri_prefix()[source]

Get the Name-to-Thing URI prefix for this entry, if possible.

Return type: Optional[str]

get_n2t_uri_format()[source]: Get the Name-to-Thing URI format string, if available.

get_scholia_prefix()[source]: Get the Scholia prefix, if available.

get_ols_prefix()[source]

Get the OLS prefix if available.

Return type: Optional[str]

get_ols_uri_prefix()[source]

Get the OLS URI prefix for this entry, if possible.

Return type: Optional[str]
Returns: The OLS URI prefix, if available.

Warning

This doesn’t have a normal form, so it only works for OBO Foundry at the moment.

>>> from bioregistry import get_resource
>>> get_resource("go").get_ols_uri_prefix()  # standard
'https://www.ebi.ac.uk/ols/ontologies/go/terms?iri=http://purl.obolibrary.org/obo/GO_'
>>> get_resource("ncbitaxon").get_ols_uri_prefix()  # mixed case
'https://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?iri=http://purl.obolibrary.org/obo/NCBITaxon_'
>>> assert get_resource("sty").get_ols_uri_prefix() is None

get_ols_uri_format()[source]

Get the OLS URI format string for this entry, if possible.

Return type: Optional[str]
Returns: The OLS format string, if available.

Warning

This doesn’t have a normal form, so it only works for OBO Foundry at the moment.

>>> from bioregistry import get_resource
>>> get_resource("go").get_ols_uri_format()  # standard
'https://www.ebi.ac.uk/ols/ontologies/go/terms?iri=http://purl.obolibrary.org/obo/GO_$1'
>>> get_resource("ncbitaxon").get_ols_uri_format()  # mixed case
'https://www.ebi.ac.uk/ols/ontologies/ncbitaxon/terms?iri=http://purl.obolibrary.org/obo/NCBITaxon_$1'
>>> assert get_resource("sty").get_ols_uri_format() is None

DEFAULT_URI_FORMATTER_PRIORITY: ClassVar[Sequence[str]] = ('default', 'obofoundry', 'prefixcommons', 'miriam', 'n2t', 'ols'): The default priority for generating URIs

get_uri_format(priority=None)[source]

Get the URI format string for the given prefix, if it’s available.

Parameters

priority (Optional[Sequence[str]]) –

The priority order of metaresources to use for format URI lookup. The default is:

Default first party (from bioregistry, prefix commons, or miriam)
OBO Foundry
Prefix Commons
Identifiers.org
N2T
OLS
BioPortal

Return type

Optional[str]

Returns

The best URI format string, where the $1 should be replaced by a local unique identifier. $1 could potentially appear multiple times.

>>> from bioregistry import get_resource
>>> get_resource("chebi").get_uri_format()
'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:$1'

If you want to specify a different priority order, you can do so with the priority keyword. This is of particular interest to ontologists and semantic web people who might want to use purl.obolibrary.org URL prefixes over the URL prefixes corresponding to the first-party providers for each resource (e.g., the ChEBI example above). Do so like:

>>> from bioregistry import get_resource
>>> priority = ['obofoundry', 'bioregistry', 'prefixcommons', 'miriam', 'ols']
>>> get_resource("chebi").get_uri_format(priority=priority)
'http://purl.obolibrary.org/obo/CHEBI_$1'

get_uri_prefix(priority=None)[source]

Get a well-formed URI prefix, if available.

Parameters: priority (Optional[Sequence[str]]) – The prioirty order for get_format().
Return type: Optional[str]
Returns: The URI prefix. Similar to what’s returned by get_uri_format(), but it MUST have only one $1 and end with $1 to use thie function.

>>> import bioregistry
>>> bioregistry.get_uri_prefix('chebi')
'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:'

get_extra_providers()[source]

Get a list of all extra providers.

Return type: List[Provider]

standardize_identifier(identifier, prefix=None)[source]

Normalize the identifier to not have a redundant prefix or banana.

Parameters

identifier (str) – The identifier in the CURIE
prefix (Optional[str]) – If an optional prefix is passed, checks that this isn’t also used as a caseolded banana like in go:go:1234567, which shouldn’t techinncally be right becauase the banana for gene ontology is GO.

Return type

str

Returns

A normalized identifier, possibly with banana/redundant prefix removed

Examples with explicitly annotated bananas: >>> from bioregistry import get_resource >>> get_resource(“vario”).standardize_identifier(‘0376’) ‘0376’ >>> get_resource(“vario”).standardize_identifier(‘VariO:0376’) ‘0376’ >>> get_resource(“swisslipid”).standardize_identifier(‘000000001’) ‘000000001’ >>> get_resource(“swisslipid”).standardize_identifier(‘SLM:000000001’) ‘000000001’

Examples with bananas from OBO: >>> get_resource(“fbbt”).standardize_identifier(‘00007294’) ‘00007294’ >>> get_resource(“fbbt”).standardize_identifier(‘FBbt:00007294’) ‘00007294’ >>> get_resource(“chebi”).standardize_identifier(‘1234’) ‘1234’ >>> get_resource(“chebi”).standardize_identifier(‘CHEBI:1234’) ‘1234’

Examples from OBO Foundry that should not have a redundant prefix added: >>> get_resource(“ncit”).standardize_identifier(“C73192”) ‘C73192’ >>> get_resource(“ncbitaxon”).standardize_identifier(“9606”) ‘9606’

Standard: >>> get_resource(“pdb”).standardize_identifier(‘00000020’) ‘00000020’

miriam_standardize_identifier(identifier)[source]

Normalize the identifier for legacy usage with MIRIAM using the appropriate banana.

Parameters: identifier (str) – The identifier in the CURIE
Return type: str
Returns: A normalize identifier, possibly with banana/redundant prefix added

Because identifiers.org used to have URIs in the form of https://identifiers.org/<prefix>/<prefix>:<identifier> for entries annotated with namespaceEmbeddedInLui as true

Examples with explicitly annotated bananas: >>> from bioregistry import get_resource >>> get_resource(“vario”).miriam_standardize_identifier(‘0376’) ‘VariO:0376’ >>> get_resource(“vario”).miriam_standardize_identifier(‘VariO:0376’) ‘VariO:0376’

Examples with bananas from OBO: >>> get_resource(“fbbt”).miriam_standardize_identifier(‘00007294’) ‘FBbt:00007294’ >>> get_resource(“fbbt”).miriam_standardize_identifier(‘FBbt:00007294’) ‘FBbt:00007294’

Examples from OBO Foundry: >>> get_resource(“chebi”).miriam_standardize_identifier(‘1234’) ‘CHEBI:1234’ >>> get_resource(“chebi”).miriam_standardize_identifier(‘CHEBI:1234’) ‘CHEBI:1234’

Examples from OBO Foundry that should not have a redundant prefix added: >>> get_resource(“ncit”).miriam_standardize_identifier(“C73192”) ‘C73192’ >>> get_resource(“ncbitaxon”).miriam_standardize_identifier(“9606”) ‘9606’

Standard: >>> get_resource(“pdb”).miriam_standardize_identifier(‘00000020’) ‘00000020’

is_canonical_identifier(identifier)[source]

Check that a local unique identifier is canonical, meaning no bananas.

Return type: Optional[bool]

is_known_identifier(identifier)[source]

Check that a local unique identifier can be normalized and also matches a prefix’s pattern.

Return type: Optional[bool]

get_download_obo()[source]

Get the download link for the latest OBO file.

Return type: Optional[str]

get_download_obograph()[source]

Get the download link for the latest OBOGraph JSON file.

Return type: Optional[str]

get_download_owl()[source]

Get the download link for the latest OWL file.

Return type: Optional[str]

get_license()[source]

Get the license for the resource.

Return type: Optional[str]

get_version()[source]

Get the version for the resource.

Return type: Optional[str]

class Collection(**data)[source]

A collection of resources.

Create a new model by parsing and validating input data from keyword arguments.

Raises ValidationError if the input data cannot be parsed to form a valid model.

identifier: str: The collection’s identifier

name: str: The name of the collection

description: str: A description of the collection

resources: List[str]: A list of prefixes of resources appearing in the collection

authors: List[bioregistry.schema.struct.Author]: A list of authors/contributors to the collection

context: Optional[str]: JSON-LD context name

add_triples(graph)[source]

Add triples to an RDF graph for this collection.

Parameters: graph (rdflib.Graph) – An RDF graph
Return type: rdflib.term.Node
Returns: The RDF node representing this collection using a Bioregistry IRI.

as_context_jsonld()[source]

Get the JSON-LD context from a given collection.

Return type: Mapping[str, Mapping[str, str]]

as_prefix_map()[source]

Get the prefix map for a given collection.

Return type: Mapping[str, str]

class Registry(**data)[source]

Metadata about a registry.

Create a new model by parsing and validating input data from keyword arguments.

Raises ValidationError if the input data cannot be parsed to form a valid model.

prefix: str: The registry’s metaprefix

name: str: The name of the registry

description: str: A description of the registry

homepage: str: The registry’s homepage

example: str: An example prefix in the registry

availability: bioregistry.schema.struct.RegistrySchema: A structured description of the metadata the registry collects

download: Optional[str]: A URL to download the registry’s contents

provider_uri_format: Optional[str]: A URL with a $1 for a prefix to resolve in the registry

resolver_uri_format: Optional[str]: A URL with a $1 for a prefix and $2 for an identifier to resolve in the registry

resolver_type: Optional[str]: An optional type annotation for what kind of resolver it is (i.e., redirect or lookup)

contact: bioregistry.schema.struct.Attributable: The contact for the registry

score()[source]

Calculate a metadata score/goodness for this registry.

Return type: int

get_provider_uri_prefix()[source]

Get provider URI prefix.

Return type: str
Returns: The URI prefix for the provider for prefixes in this registry.

>>> from bioregistry import get_registry
>>> get_registry("fairsharing").get_provider_uri_prefix()
'https://fairsharing.org/'
>>> get_registry("miriam").get_provider_uri_prefix()
'https://registry.identifiers.org/registry/'
>>> get_registry("n2t").get_provider_uri_prefix()
'https://bioregistry.io/metaregistry/n2t/'

get_provider_uri_format(prefix)[source]

Get the provider string.

Parameters: prefix (str) – The prefix used in the metaregistry
Return type: Optional[str]
Returns: The URL in the registry for the prefix, if it’s able to provide one

>>> from bioregistry import get_registry
>>> get_registry("fairsharing").get_provider_uri_format("FAIRsharing.62qk8w")
'https://fairsharing.org/FAIRsharing.62qk8w'
>>> get_registry("miriam").get_provider_uri_format("go")
'https://registry.identifiers.org/registry/go'
>>> get_registry("n2t").get_provider_uri_format("go")
'https://bioregistry.io/metaregistry/n2t/go'

get_resolver_uri_format(prefix)[source]

Generate a provider URI string based on mapping through this registry’s vocabulary.

Parameters: prefix (str) – The prefix used in the metaregistry
Return type: str
Returns: The URI format string to be used for identifiers in the semantic space based on this resolver or the Bioregistry’s meta-resolver.

>>> from bioregistry import get_registry
>>> get_registry("miriam").get_resolver_uri_format("go")
'https://identifiers.org/go:$1'
>>> get_registry("cellosaurus").get_resolver_uri_format("go")
'https://bioregistry.io/metaregistry/cellosaurus/go:$1'
>>> get_registry("n2t").get_resolver_uri_format("go")
'https://n2t.net/go:$1'

resolve(prefix, identifier)[source]

Resolve the registry-specific prefix and identifier.

Parameters

prefix (str) – The prefix used in the metaregistry
identifier (str) – The identifier in the semantic space

Return type

Optional[str]

Returns

The URI format string for the given CURIE.

>>> from bioregistry import get_registry
>>> get_registry("miriam").resolve("go", "0032571")
'https://identifiers.org/go:0032571'
>>> get_registry("cellosaurus").resolve("go", "0032571")
'https://bioregistry.io/metaregistry/cellosaurus/go:0032571'

add_triples(graph)[source]

Add triples to an RDF graph for this registry.

Parameters: graph (rdflib.Graph) – An RDF graph
Return type: rdflib.term.Node
Returns: The RDF node representing this registry using a Bioregistry IRI.

get_json_schema()[source]: Get the JSON schema for the bioregistry.