Schema
Pydantic models for the Bioregistry.
- pydantic model Attributable[source]
An upper-level metadata for a researcher.
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.
Show JSON schema
{ "title": "Attributable", "description": "An upper-level metadata for a researcher.", "type": "object", "properties": { "name": { "title": "Name", "description": "The full name of the researcher", "type": "string" }, "orcid": { "title": "Open Researcher and Contributor Identifier", "description": "The Open Researcher and Contributor Identifier (ORCiD) provides researchers with an open, unambiguous identifier for connecting various digital assets (e.g., publications, reviews) across the semantic web. An account can be made in seconds at https://orcid.org.", "type": "string" }, "email": { "title": "Email address", "description": "The email address specific to the researcher.", "type": "string" }, "github": { "title": "GitHub handle", "description": "The GitHub handle enables contacting the researcher on GitHub: the *de facto* version control in the computer sciences and life sciences.", "type": "string" } }, "required": [ "name" ] }
- field github: Optional[str] = PydanticUndefined
The GitHub handle for the author
The GitHub handle enables contacting the researcher on GitHub: the de facto version control in the computer sciences and life sciences.
- field orcid: Optional[str] = PydanticUndefined
The Open Researcher and Contributor Identifier (ORCiD) provides researchers with an open, unambiguous identifier for connecting various digital assets (e.g., publications, reviews) across the semantic web. An account can be made in seconds at https://orcid.org.
- add_triples(graph)[source]
Add triples to an RDF graph for this author.
- Parameters
graph (rdflib.Graph) – An RDF graph
- Return type
- Returns
The RDF node representing this author using an ORCiD URI.
- pydantic model Author[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.
Show JSON schema
{ "title": "Author", "description": "Metadata for an author.", "type": "object", "properties": { "name": { "title": "Name", "description": "The full name of the researcher", "type": "string" }, "orcid": { "title": "Open Researcher and Contributor Identifier", "description": "The Open Researcher and Contributor Identifier (ORCiD) provides researchers with an open, unambiguous identifier for connecting various digital assets (e.g., publications, reviews) across the semantic web. An account can be made in seconds at https://orcid.org.", "type": "string" }, "email": { "title": "Email address", "description": "The email address specific to the researcher.", "type": "string" }, "github": { "title": "GitHub handle", "description": "The GitHub handle enables contacting the researcher on GitHub: the *de facto* version control in the computer sciences and life sciences.", "type": "string" } }, "required": [ "name", "orcid" ] }
- Fields
- field orcid: str [Required]
This field is redefined on top of
Attributableto make it required. Otherwise, it has the same semantics.The Open Researcher and Contributor Identifier (ORCiD) provides researchers with an open, unambiguous identifier for connecting various digital assets (e.g., publications, reviews) across the semantic web. An account can be made in seconds at https://orcid.org.
- pydantic model Provider[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.
Show JSON schema
{ "title": "Provider", "description": "A provider.", "type": "object", "properties": { "code": { "title": "Code", "description": "A locally unique code within the prefix for the provider", "type": "string" }, "name": { "title": "Name", "description": "Name of the provider", "type": "string" }, "description": { "title": "Description", "description": "Description of the provider", "type": "string" }, "homepage": { "title": "Homepage", "description": "Homepage of the provider", "type": "string" }, "uri_format": { "title": "URI Format", "description": "The URI format string, which must have at least one ``$1`` in it", "type": "string" } }, "required": [ "code", "name", "description", "homepage", "uri_format" ] }
- pydantic model Resource[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.
Show JSON schema
{ "title": "Resource", "description": "Metadata about an ontology, database, or other resource.", "type": "object", "properties": { "prefix": { "title": "Prefix", "description": "The prefix for this resource", "integration_status": "required", "type": "string" }, "name": { "title": "Name", "description": "The name of the resource", "integration_status": "required", "type": "string" }, "description": { "title": "Description", "description": "A description of the resource", "integration_status": "required", "type": "string" }, "pattern": { "title": "Pattern", "description": "The regular expression pattern for local unique identifiers in the resource", "integration_status": "required_for_new", "type": "string" }, "uri_format": { "title": "URI format string", "description": "The URI format string, which must have at least one ``$1`` in it", "integration_status": "required_for_new", "type": "string" }, "providers": { "title": "Providers", "description": "Additional, non-default providers for the resource", "type": "array", "items": { "$ref": "#/definitions/Provider" } }, "homepage": { "title": "Homepage", "description": "The URL for the homepage of the resource, preferably using HTTPS", "integration_status": "required", "type": "string" }, "repository": { "title": "Repository", "description": "The URL for the repository of the resource", "type": "string" }, "contact": { "title": "Contact", "description": "The contact email address for the resource. This must correspond to a specific person and not be a listserve nor a shared email account.", "integration_status": "suggested", "allOf": [ { "$ref": "#/definitions/Attributable" } ] }, "example": { "title": "Example", "description": "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``", "integration_status": "required", "type": "string" }, "example_extras": { "title": "Example Extras", "description": "Extra example identifiers", "type": "array", "items": { "type": "string" } }, "example_decoys": { "title": "Example Decoys", "description": "Extra example identifiers that explicitly fail regex tests", "type": "array", "items": { "type": "string" } }, "license": { "title": "License", "description": "The license for the resource", "type": "string" }, "version": { "title": "Version", "description": "The version for the resource", "type": "string" }, "part_of": { "title": "Part Of", "description": "An annotation between this prefix and a super-prefix. For example, ``chembl.compound`` is a part of ``chembl``.", "type": "string" }, "provides": { "title": "Provides", "description": "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``.", "type": "string" }, "download_owl": { "title": "OWL Download URL", "description": "The URL to download the resource as an ontology encoded in the OWL format. More information about this format can be found at https://www.w3.org/TR/owl2-syntax/.", "type": "string" }, "download_obo": { "title": "OBO Download URL", "description": "The URL to download the resource as an ontology encoded in the OBO format. More information about this format can be found at https://owlcollab.github.io/oboformat/doc/obo-syntax.html.", "type": "string" }, "download_json": { "title": "OBO Graph JSON Download URL", "description": "The URL to download the resource as an ontology encoded in the OBO Graph JSON format. More information about this format can be found at https://github.com/geneontology/obographs.", "type": "string" }, "banana": { "title": "Banana", "description": "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.", "type": "string" }, "deprecated": { "title": "Deprecated", "description": "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.", "type": "boolean" }, "mappings": { "title": "Mappings", "description": "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.", "type": "object", "additionalProperties": { "type": "string" } }, "synonyms": { "title": "Synonyms", "description": "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``.", "type": "array", "items": { "type": "string" } }, "references": { "title": "References", "description": "A list of URLs to also see, such as publications describing the resource", "type": "array", "items": { "type": "string" } }, "appears_in": { "title": "Appears In", "description": "A list of prefixes that use this resource for xrefs, provenance, etc.", "type": "array", "items": { "type": "string" } }, "depends_on": { "title": "Depends On", "description": "A list of prefixes that use this resource depends on, e.g., ontologies that import each other.", "type": "array", "items": { "type": "string" } }, "namespace_in_lui": { "title": "Namespace Embedded in Local Unique Identifier", "description": "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``.", "type": "boolean" }, "no_own_terms": { "title": "No Own Terms", "description": "A flag denoting 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.", "type": "boolean" }, "comment": { "title": "Comment", "description": "A field for a free text comment", "type": "string" }, "contributor": { "title": "Contributor", "description": "The contributor of the prefix to the Bioregistry, including at a minimum their name and ORCiD and optionall their email address and GitHub handle. All entries curated through the Bioregistry GitHub Workflow must contain this field.", "integration_status": "required_for_new", "allOf": [ { "$ref": "#/definitions/Author" } ] }, "contributor_extras": { "title": "Contributor Extras", "description": "Additional contributors besides the original submitter.", "type": "array", "items": { "$ref": "#/definitions/Author" } }, "reviewer": { "title": "Reviewer", "description": "The reviewer of the prefix to the Bioregistry, including at a minimum their name and ORCiD and optionall their email address and GitHub handle. All entries curated through the Bioregistry GitHub Workflow should contain this field pointing to the person who reviewed it on GitHub.", "integration_status": "required_for_new", "allOf": [ { "$ref": "#/definitions/Author" } ] }, "proprietary": { "title": "Proprietary", "description": "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.", "type": "boolean" }, "has_canonical": { "title": "Has Canonical", "description": "If this shares an IRI with another entry, maps to which should be be considered as canonical", "type": "string" }, "preferred_prefix": { "title": "Preferred Prefix", "description": "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.", "type": "string" }, "twitter": { "title": "Twitter", "description": "The twitter handle for the project", "type": "string" }, "miriam": { "title": "Miriam", "type": "object" }, "n2t": { "title": "N2T", "type": "object" }, "prefixcommons": { "title": "Prefixcommons", "type": "object" }, "wikidata": { "title": "Wikidata", "type": "object" }, "go": { "title": "Go", "type": "object" }, "obofoundry": { "title": "Obofoundry", "type": "object" }, "bioportal": { "title": "Bioportal", "type": "object" }, "ols": { "title": "Ols", "type": "object" }, "ncbi": { "title": "Ncbi", "type": "object" }, "uniprot": { "title": "Uniprot", "type": "object" }, "biolink": { "title": "Biolink", "type": "object" }, "cellosaurus": { "title": "Cellosaurus", "type": "object" }, "ontobee": { "title": "Ontobee", "type": "object" }, "cheminf": { "title": "Cheminf", "type": "object" }, "fairsharing": { "title": "Fairsharing", "type": "object" } }, "required": [ "prefix" ], "definitions": { "Provider": { "title": "Provider", "description": "A provider.", "type": "object", "properties": { "code": { "title": "Code", "description": "A locally unique code within the prefix for the provider", "type": "string" }, "name": { "title": "Name", "description": "Name of the provider", "type": "string" }, "description": { "title": "Description", "description": "Description of the provider", "type": "string" }, "homepage": { "title": "Homepage", "description": "Homepage of the provider", "type": "string" }, "uri_format": { "title": "URI Format", "description": "The URI format string, which must have at least one ``$1`` in it", "type": "string" } }, "required": [ "code", "name", "description", "homepage", "uri_format" ] }, "Attributable": { "title": "Attributable", "description": "An upper-level metadata for a researcher.", "type": "object", "properties": { "name": { "title": "Name", "description": "The full name of the researcher", "type": "string" }, "orcid": { "title": "Open Researcher and Contributor Identifier", "description": "The Open Researcher and Contributor Identifier (ORCiD) provides researchers with an open, unambiguous identifier for connecting various digital assets (e.g., publications, reviews) across the semantic web. An account can be made in seconds at https://orcid.org.", "type": "string" }, "email": { "title": "Email address", "description": "The email address specific to the researcher.", "type": "string" }, "github": { "title": "GitHub handle", "description": "The GitHub handle enables contacting the researcher on GitHub: the *de facto* version control in the computer sciences and life sciences.", "type": "string" } }, "required": [ "name" ] }, "Author": { "title": "Author", "description": "Metadata for an author.", "type": "object", "properties": { "name": { "title": "Name", "description": "The full name of the researcher", "type": "string" }, "orcid": { "title": "Open Researcher and Contributor Identifier", "description": "The Open Researcher and Contributor Identifier (ORCiD) provides researchers with an open, unambiguous identifier for connecting various digital assets (e.g., publications, reviews) across the semantic web. An account can be made in seconds at https://orcid.org.", "type": "string" }, "email": { "title": "Email address", "description": "The email address specific to the researcher.", "type": "string" }, "github": { "title": "GitHub handle", "description": "The GitHub handle enables contacting the researcher on GitHub: the *de facto* version control in the computer sciences and life sciences.", "type": "string" } }, "required": [ "name", "orcid" ] } } }
- Fields
- field appears_in: Optional[List[str]] = PydanticUndefined
A list of prefixes that use this resource for xrefs, provenance, etc.
- field banana: Optional[str] = PydanticUndefined
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., foroma.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 prefixswisslipidbut have the redundant informationSLM:in the beginning of identifiers. Therefore,SLM:is the banana.
- field biolink: Optional[Mapping[str, Any]] = PydanticUndefined
External data from the BioLink Model’s custom registry
- field bioportal: Optional[Mapping[str, Any]] = PydanticUndefined
External data from the BioPortal ontology repository
- field cellosaurus: Optional[Mapping[str, Any]] = PydanticUndefined
External data from the Cellosaurus custom registry
- field comment: Optional[str] = PydanticUndefined
A field for a free text comment.
A field for a free text comment
- field contact: Optional[bioregistry.schema.struct.Attributable] = PydanticUndefined
The contact email address for the resource. This must correspond to a specific person and not be a listserve nor a shared email account.
- field contributor: Optional[bioregistry.schema.struct.Author] = PydanticUndefined
The contributor of the prefix to the Bioregistry, including at a minimum their name and ORCiD and optionall their email address and GitHub handle. All entries curated through the Bioregistry GitHub Workflow must contain this field.
- field contributor_extras: Optional[List[bioregistry.schema.struct.Author]] = PydanticUndefined
Additional contributors besides the original submitter.
- field depends_on: Optional[List[str]] = PydanticUndefined
A list of prefixes that use this resource depends on, e.g., ontologies that import each other.
- field deprecated: Optional[bool] = PydanticUndefined
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.
- field download_json: Optional[str] = PydanticUndefined
The URL to download the resource as an ontology encoded in the OBO Graph JSON format. More information about this format can be found at https://github.com/geneontology/obographs.
- field download_obo: Optional[str] = PydanticUndefined
The URL to download the resource as an ontology encoded in the OBO format. More information about this format can be found at https://owlcollab.github.io/oboformat/doc/obo-syntax.html.
- field download_owl: Optional[str] = PydanticUndefined
The URL to download the resource as an ontology encoded in the OWL format. More information about this format can be found at https://www.w3.org/TR/owl2-syntax/.
- field example: Optional[str] = PydanticUndefined
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
1234567and not likeGO:1234567
- field example_decoys: Optional[List[str]] = PydanticUndefined
Extra example identifiers that explicitly fail regex tests
- field go: Optional[Mapping[str, Any]] = PydanticUndefined
External data from the Gene Ontology’s custom registry
- field has_canonical: Optional[str] = PydanticUndefined
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
If this shares an IRI with another entry, maps to which should be be considered as canonical
- field homepage: Optional[str] = PydanticUndefined
The URL for the homepage of the resource, preferably using HTTPS
- field mappings: Optional[Dict[str, str]] = PydanticUndefined
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
miriamfield.
- field miriam: Optional[Mapping[str, Any]] = PydanticUndefined
External data from Identifiers.org’s MIRIAM Database
- field n2t: Optional[Mapping[str, Any]] = PydanticUndefined
External data from the Name-to-Thing service
- field namespace_in_lui: Optional[bool] = PydanticUndefined
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, andvario.
- field ncbi: Optional[Mapping[str, Any]] = PydanticUndefined
External data from the NCBI Genbank’s custom registry
- field no_own_terms: Optional[bool] = PydanticUndefined
A flag denoting 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.
- field obofoundry: Optional[Mapping[str, Any]] = PydanticUndefined
External data from the Open Biomedical Ontologies (OBO) Foundry catalog
- field ols: Optional[Mapping[str, Any]] = PydanticUndefined
External data from the Ontology Lookup Service
- field part_of: Optional[str] = PydanticUndefined
An annotation between this prefix and a super-prefix. For example,
chembl.compoundis a part ofchembl.
- field pattern: Optional[str] = PydanticUndefined
The regular expression pattern for local unique identifiers in the resource
- field preferred_prefix: Optional[str] = PydanticUndefined
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.
- field prefixcommons: Optional[Mapping[str, Any]] = PydanticUndefined
External data from Prefix Commons
- field proprietary: Optional[bool] = PydanticUndefined
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.
- field providers: Optional[List[bioregistry.schema.struct.Provider]] = PydanticUndefined
Additional, non-default providers for the resource
- field provides: Optional[str] = PydanticUndefined
An annotation between this prefix and a prefix for which it is redundant. For example,
ctd.genehas been given a prefix by Identifiers.org, but it actually just reuses identifies fromncbigene, soctd.geneprovidesncbigene.
- field references: Optional[List[str]] = PydanticUndefined
A list of URLs to also see, such as publications describing the resource
- field reviewer: Optional[bioregistry.schema.struct.Author] = PydanticUndefined
The reviewer of the prefix to the Bioregistry, including at a minimum their name and ORCiD and optionall their email address and GitHub handle. All entries curated through the Bioregistry GitHub Workflow should contain this field pointing to the person who reviewed it on GitHub.
- field synonyms: Optional[List[str]] = PydanticUndefined
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,
snomedcthas many synonyms including typos likeSNOWMEDCT, lexical variants likeSNOMED_CT, version-variants likeSNOMEDCT_2010_1_31, and tons of other nonsense likeSNOMEDCTCT.
- field uniprot: Optional[Mapping[str, Any]] = PydanticUndefined
External data from UniProt’s custom registry
- field uri_format: Optional[str] = PydanticUndefined
The URI format string, which must have at least one
$1in it
- field wikidata: Optional[Mapping[str, Any]] = PydanticUndefined
External data from Wikidata Properties
- 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
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_contact_email()[source]
Return the contact email, if 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_github()[source]
Return the contact GitHub handle, if 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_name()[source]
Return the contact name, if 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_orcid()[source]
Return the contact ORCiD, if available.
>>> from bioregistry import get_resource >>> get_resource("bioregistry").get_contact_orcid() # from bioregistry curation '0000-0003-4423-4370' >>> get_resource("aero").get_contact_orcid() '0000-0002-9551-6370'
- get_default_format()[source]
Get the default, first-party URI prefix.
>>> 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_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
- 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_description(use_markdown=False)[source]
Get the description for the given prefix, if available.
- get_identifiers_org_prefix()[source]
Get the identifiers.org prefix if available.
- Return type
- 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_mapped_prefix(metaprefix)[source]
Get the prefix for the given external.
- Parameters
metaprefix (
str) – The metaprefix for the external resource- Return type
- 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_miriam_uri_format()[source]
Get the Identifiers.org URI format string for this entry, if possible.
>>> 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_miriam_uri_prefix()[source]
Get the Identifiers.org URI prefix for this entry, if possible.
>>> 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_obo_preferred_prefix()[source]
Get the OBO preferred prefix, if this resource is mapped to the OBO Foundry.
- get_obofoundry_prefix()[source]
Get the OBO Foundry 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_format()[source]
Get the OBO Foundry URI format string for this entry, if possible.
>>> 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_obofoundry_uri_prefix()[source]
Get the OBO Foundry URI prefix for this entry, if possible.
>>> 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_ols_uri_format()[source]
Get the OLS URI format string for this entry, if possible.
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
- get_ols_uri_prefix()[source]
Get the OLS URI prefix for this entry, if possible.
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_preferred_prefix()[source]
Get the preferred prefix (e.g., with stylization) if it exists.
- Return type
- 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_prefix_key(key, metaprefixes)[source]
Get a key enriched by the given external resources’ data.
- get_prefixcommons_uri_format()[source]
Get the Prefix Commons URI format string for this entry, 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_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
- Returns
The best URI format string, where the
$1should be replaced by a local unique identifier.$1could 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
prioritykeyword. This is of particular interest to ontologists and semantic web people who might want to usepurl.obolibrary.orgURL 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 forget_format().- Return type
- Returns
The URI prefix. Similar to what’s returned by
get_uri_format(), but it MUST have only one$1and end with$1to use thie function.
>>> import bioregistry >>> bioregistry.get_uri_prefix('chebi') 'https://www.ebi.ac.uk/chebi/searchId.do?chebiId=CHEBI:'
- is_canonical_identifier(identifier)[source]
Check that a local unique identifier is canonical, meaning no bananas.
- is_deprecated()[source]
Return if the given prefix corresponds to a deprecated resource.
- Return type
- 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
- is_known_identifier(identifier)[source]
Check that a local unique identifier can be normalized and also matches a prefix’s pattern.
- 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
- 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
namespaceEmbeddedInLuiastrueExamples 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’
- standardize_identifier(identifier, prefix=None)[source]
Normalize the identifier to not have a redundant prefix or banana.
- Parameters
- Return type
- 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’
- DEFAULT_URI_FORMATTER_PRIORITY: ClassVar[Sequence[str]] = ('default', 'obofoundry', 'prefixcommons', 'miriam', 'n2t', 'ols')
- URI_FORMATTERS: ClassVar[Mapping[str, Callable[[bioregistry.schema.struct.Resource], Optional[str]]]] = {'default': <function Resource.get_default_format>, 'miriam': <function Resource.get_miriam_uri_format>, 'n2t': <function Resource.get_n2t_uri_format>, 'obofoundry': <function Resource.get_obofoundry_uri_format>, 'ols': <function Resource.get_ols_uri_format>, 'prefixcommons': <function Resource.get_prefixcommons_uri_format>}
- pydantic model Collection[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.
Show JSON schema
{ "title": "Collection", "description": "A collection of resources.", "type": "object", "properties": { "identifier": { "title": "Identifier", "description": "The collection's identifier", "pattern": "^\\d{7}$", "type": "string" }, "name": { "title": "Name", "description": "The name of the collection", "type": "string" }, "description": { "title": "Description", "description": "A description of the collection", "type": "string" }, "resources": { "title": "Resources", "description": "A list of prefixes of resources appearing in the collection", "type": "array", "items": { "type": "string" } }, "authors": { "title": "Authors", "description": "A list of authors/contributors to the collection", "type": "array", "items": { "$ref": "#/definitions/Author" } }, "context": { "title": "Context", "type": "string" } }, "required": [ "identifier", "name", "description", "resources", "authors" ], "definitions": { "Author": { "title": "Author", "description": "Metadata for an author.", "type": "object", "properties": { "name": { "title": "Name", "description": "The full name of the researcher", "type": "string" }, "orcid": { "title": "Open Researcher and Contributor Identifier", "description": "The Open Researcher and Contributor Identifier (ORCiD) provides researchers with an open, unambiguous identifier for connecting various digital assets (e.g., publications, reviews) across the semantic web. An account can be made in seconds at https://orcid.org.", "type": "string" }, "email": { "title": "Email address", "description": "The email address specific to the researcher.", "type": "string" }, "github": { "title": "GitHub handle", "description": "The GitHub handle enables contacting the researcher on GitHub: the *de facto* version control in the computer sciences and life sciences.", "type": "string" } }, "required": [ "name", "orcid" ] } } }
- Fields
- field authors: List[bioregistry.schema.struct.Author] [Required]
A list of authors/contributors to the collection
- add_triples(graph)[source]
Add triples to an RDF graph for this collection.
- Parameters
graph (rdflib.Graph) – An RDF graph
- Return type
- Returns
The RDF node representing this collection using a Bioregistry IRI.
- pydantic model Registry[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.
Show JSON schema
{ "title": "Registry", "description": "Metadata about a registry.", "type": "object", "properties": { "prefix": { "title": "Prefix", "description": "The metaprefix for the registry itself. For example, the metaprefix for Identifiers.org is `miriam`.", "type": "string" }, "name": { "title": "Name", "description": "The human-readable label for the registry", "type": "string" }, "description": { "title": "Description", "description": "A full description of the registry.", "type": "string" }, "homepage": { "title": "Homepage", "description": "The URL for the homepage of the registry.", "type": "string" }, "example": { "title": "Example", "description": "An example prefix inside the registry.", "type": "string" }, "availability": { "title": "Availability", "description": "A structured description of the metadata that the registry collects", "allOf": [ { "$ref": "#/definitions/RegistrySchema" } ] }, "download": { "title": "Download", "description": "A download link for the data contained in the registry", "type": "string" }, "provider_uri_format": { "title": "Provider Uri Format", "description": "A URL with a $1 for a prefix to resolve in the registry", "type": "string" }, "resolver_uri_format": { "title": "Resolver Uri Format", "description": "A URL with a $1 for a prefix and $2 for an identifier to resolve in the registry", "type": "string" }, "resolver_type": { "title": "Resolver Type", "description": "An optional type annotation for what kind of resolver it is (i.e., redirect or lookup)", "type": "string" }, "contact": { "title": "Contact", "description": "The contact for the registry.", "allOf": [ { "$ref": "#/definitions/Attributable" } ] }, "bioregistry_prefix": { "title": "Bioregistry Prefix", "description": "The prefix for this registry in the Bioregistry", "type": "string" }, "logo_url": { "title": "Logo Url", "description": "The URL for the logo of the resource", "type": "string" }, "license": { "title": "License", "description": "The license under which the resource is redistributed", "type": "string" }, "short_name": { "title": "Short Name", "description": "A short name for the resource, e.g., for use in charts", "type": "string" } }, "required": [ "prefix", "name", "description", "homepage", "example", "availability", "contact" ], "definitions": { "RegistrySchema": { "title": "RegistrySchema", "description": "Metadata about a registry's schema.", "type": "object", "properties": { "name": { "title": "Name", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "homepage": { "title": "Homepage", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "description": { "title": "Description", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "example": { "title": "Example", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "pattern": { "title": "Pattern", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "provider": { "title": "Provider", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "alternate_providers": { "title": "Alternate Providers", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "synonyms": { "title": "Synonyms", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "license": { "title": "License", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "version": { "title": "Version", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "contact": { "title": "Contact", "enum": [ "required", "required*", "present", "present*", "missing", "irrelevant", "irrelevant*" ], "type": "string" }, "search": { "title": "Search", "description": "Does this resource have a search functionality for prefixes", "type": "boolean" }, "fair": { "title": "Fair", "description": "Does this resource provide a structured dump of the data is easily findable, accessible, and in a structured format in bulk", "type": "boolean" }, "fair_note": { "title": "Fair Note", "description": "Explanation for why data isn't FAIR", "type": "string" } }, "required": [ "name", "homepage", "description", "example", "pattern", "provider", "alternate_providers", "synonyms", "license", "version", "contact", "search", "fair" ] }, "Attributable": { "title": "Attributable", "description": "An upper-level metadata for a researcher.", "type": "object", "properties": { "name": { "title": "Name", "description": "The full name of the researcher", "type": "string" }, "orcid": { "title": "Open Researcher and Contributor Identifier", "description": "The Open Researcher and Contributor Identifier (ORCiD) provides researchers with an open, unambiguous identifier for connecting various digital assets (e.g., publications, reviews) across the semantic web. An account can be made in seconds at https://orcid.org.", "type": "string" }, "email": { "title": "Email address", "description": "The email address specific to the researcher.", "type": "string" }, "github": { "title": "GitHub handle", "description": "The GitHub handle enables contacting the researcher on GitHub: the *de facto* version control in the computer sciences and life sciences.", "type": "string" } }, "required": [ "name" ] } } }
- Fields
- field availability: bioregistry.schema.struct.RegistrySchema [Required]
A structured description of the metadata that the registry collects
- field bioregistry_prefix: Optional[str] = PydanticUndefined
The prefix for this registry in the Bioregistry
- field contact: bioregistry.schema.struct.Attributable [Required]
The contact for the registry.
- field download: Optional[str] = PydanticUndefined
A download link for the data contained in the registry
- field license: Optional[str] = PydanticUndefined
The license under which the resource is redistributed
- field prefix: str [Required]
The metaprefix for the registry itself. For example, the metaprefix for Identifiers.org is miriam.
- field provider_uri_format: Optional[str] = PydanticUndefined
A URL with a $1 for a prefix to resolve in the registry
- field resolver_type: Optional[str] = PydanticUndefined
An optional type annotation for what kind of resolver it is (i.e., redirect or lookup)
- field resolver_uri_format: Optional[str] = PydanticUndefined
A URL with a $1 for a prefix and $2 for an identifier to resolve in the registry
- field short_name: Optional[str] = PydanticUndefined
A short name for the resource, e.g., for use in charts
- add_triples(graph)[source]
Add triples to an RDF graph for this registry.
- Parameters
graph (rdflib.Graph) – An RDF graph
- Return type
- Returns
The RDF node representing this registry using a Bioregistry IRI.
- get_provider_uri_format(prefix)[source]
Get the provider string.
- Parameters
prefix (
str) – The prefix used in the metaregistry- Return type
- 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_provider_uri_prefix()[source]
Get provider URI prefix.
- Return type
- 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_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
- 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:$1'
- resolve(prefix, identifier)[source]
Resolve the registry-specific prefix and identifier.
- Parameters
- Return type
- Returns
The URI format string for the given CURIE.
>>> from bioregistry import get_registry >>> get_registry("miriam").resolve("go", "0032571") 'https://identifiers.org/go:0032571' >>> get_registry("cellosaurus").resolve("go", "0032571") 'https://bioregistry.io/metaregistry/cellosaurus/go:0032571'
- pydantic model Context[source]
A prescriptive context contains configuration for generating fit-for-purpose prefix maps to serve various communities based on the standard Bioregistry prefix map, custom prefix remapping rules, custom URI prefix remapping rules, custom prefix maps, and other community-specific logic.
Create a new model by parsing and validating input data from keyword arguments.
Raises ValidationError if the input data cannot be parsed to form a valid model.
Show JSON schema
{ "title": "Context", "description": "A prescriptive context contains configuration for generating fit-for-purpose\nprefix maps to serve various communities based on the standard Bioregistry\nprefix map, custom prefix remapping rules, custom URI prefix remapping rules,\ncustom prefix maps, and other community-specific logic.", "type": "object", "properties": { "name": { "title": "Name", "description": "The name of the context", "type": "string" }, "description": { "title": "Description", "description": "A description of the context, can include Markdown", "type": "string" }, "maintainers": { "title": "Maintainers", "description": "A list of maintainers for the context", "type": "array", "items": { "$ref": "#/definitions/Author" } }, "prefix_priority": { "title": "Prefix Priority", "description": "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.", "type": "array", "items": { "type": "string" } }, "include_synonyms": { "title": "Include Synonyms", "description": "Should synonyms be included in the prefix map?", "default": false, "type": "boolean" }, "use_preferred": { "title": "Use Preferred", "description": "Should preferred prefixes (i.e., stylized prefixes) be preferred over canonicalized ones?", "default": false, "type": "boolean" }, "uri_prefix_priority": { "title": "Uri Prefix Priority", "description": "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.", "type": "array", "items": { "type": "string" } }, "prefix_remapping": { "title": "Prefix Remapping", "description": "This is a mapping from canonical Bioregistry prefixes to custom prefixes used in this context.", "type": "object", "additionalProperties": { "type": "string" } }, "custom_prefix_map": { "title": "Custom Prefix Map", "description": "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.", "type": "object", "additionalProperties": { "type": "string" } } }, "required": [ "name", "description", "maintainers", "prefix_priority", "uri_prefix_priority", "prefix_remapping", "custom_prefix_map" ], "definitions": { "Author": { "title": "Author", "description": "Metadata for an author.", "type": "object", "properties": { "name": { "title": "Name", "description": "The full name of the researcher", "type": "string" }, "orcid": { "title": "Open Researcher and Contributor Identifier", "description": "The Open Researcher and Contributor Identifier (ORCiD) provides researchers with an open, unambiguous identifier for connecting various digital assets (e.g., publications, reviews) across the semantic web. An account can be made in seconds at https://orcid.org.", "type": "string" }, "email": { "title": "Email address", "description": "The email address specific to the researcher.", "type": "string" }, "github": { "title": "GitHub handle", "description": "The GitHub handle enables contacting the researcher on GitHub: the *de facto* version control in the computer sciences and life sciences.", "type": "string" } }, "required": [ "name", "orcid" ] } } }
- Fields
- field custom_prefix_map: Optional[Dict[str, str]] [Required]
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.
- field maintainers: List[bioregistry.schema.struct.Author] [Required]
A list of maintainers for the context
- field prefix_priority: Optional[List[str]] [Required]
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.
- field prefix_remapping: Optional[Dict[str, str]] [Required]
This is a mapping from canonical Bioregistry prefixes to custom prefixes used in this context.