core.annotation

core.annotation

Annotation.

Core data structure to store annotations.

Classes

Name	Description
ProviderType	Provider type.
RDFAnnotation	RDFAnnotation class.
RDFAnnotationData	Annotation with resolved information.

ProviderType

core.annotation.ProviderType()

Provider type.

RDFAnnotation

core.annotation.RDFAnnotation(qualifier, resource, validate=True)

RDFAnnotation class.

Basic storage of annotation information. This consists of the relation and the resource. The annotations can be attached to other objects thereby forming triples which can be converted to RDF.

Resource can be either

• http(s)://identifiers.org/collection/term, i.e., a identifiers.org URI
• collection/term, i.e., the combination of collection and term
• http(s)://arbitrary.url, an arbitrary URL
• urn:miriam:uniprot:P03023
• https://bioregistry.io/chebi:15996 urls via the bioregistry provider

Attributes

Name	Description
resource_normalized	Normalize resource for given annotation.

Methods

Name	Description
check_miriam_term	Check that term follows id pattern for collection.
check_qualifier	Check that the qualifier is an allowed qualifier.
from_tuple	Construct from tuple.
shorten_compact_term	Shorten the compact terms and return term.
to_dict	Convert to dict.
validate	Validate annotation.

check_miriam_term

core.annotation.RDFAnnotation.check_miriam_term()

Check that term follows id pattern for collection.

Uses the Identifiers collection information.

check_qualifier

core.annotation.RDFAnnotation.check_qualifier(qualifier)

Check that the qualifier is an allowed qualifier.

:param qualifier: :return:

from_tuple

core.annotation.RDFAnnotation.from_tuple(t)

Construct from tuple.

shorten_compact_term

core.annotation.RDFAnnotation.shorten_compact_term(term, collection)

Shorten the compact terms and return term.

If the namespace is not embedded in the term return the shortened term.

to_dict

core.annotation.RDFAnnotation.to_dict()

Convert to dict.

validate

core.annotation.RDFAnnotation.validate()

Validate annotation.

RDFAnnotationData

core.annotation.RDFAnnotationData(annotation)

Annotation with resolved information.

queries for the resource should happen here; this resolves additional information.

Methods

Name	Description
query_ols	Query ontology lookup service.
to_dict	Convert to dict.

query_ols

core.annotation.RDFAnnotationData.query_ols()

Query ontology lookup service.

to_dict

core.annotation.RDFAnnotationData.to_dict()

Convert to dict.