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core.annotation

MIRIAM annotations.

An annotation combines a qualifier (BQB, BQM) with a resource pointing at a database entry, forming the statement this element is CHEBI:17234.

RDFAnnotation parses the notations found in the wild, normalizes them to identifiers.org compact identifiers and validates them against the identifiers.org registry. RDFAnnotationData resolves what an identifier refers to via the Ontology Lookup Service.

from pymetadata.core.annotation import RDFAnnotation
from pymetadata.core.miriam import BQB

annotation = RDFAnnotation(qualifier=BQB.IS, resource="chebi/CHEBI:33699")
print(annotation.resource_normalized)  # https://identifiers.org/CHEBI:33699
print(annotation.validate())

ProviderType

Bases: str, Enum

Resolver a resource was written for.

IDENTIFIERS_ORG and BIOREGISTRY_IO resources can be normalized and validated, NONE marks an arbitrary url which is kept as it is.

RDFAnnotation 

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

Parse a resource into collection and term.

Parameters:

Name Type Description Default
qualifier BQB | BQM

MIRIAM qualifier of the annotation

 required
resource str

the annotated resource, as an identifiers.org url (https://identifiers.org/CHEBI:33699), a bioregistry.io url, a compact identifier (CHEBI:33699), a collection and term (chebi/CHEBI:33699), a MIRIAM urn (urn:miriam:chebi:CHEBI%3A33699) or an arbitrary url

 required
validate bool

log warnings and errors for an invalid annotation

 True

Raises:

Type Description
ValueError

if the qualifier or the resource is missing, or if the resource is not a string

resource_normalized property 

resource_normalized

Normalize resource for given annotation.

This is the correct usage. Resources are normalized to identifiers.org compact identifiers of the form https://identifiers.org/<prefix>:<accession>. If the namespace is embedded in the LUI the prefix is already part of the term, otherwise the prefix of the identifiers.org registry is prepended.

shorten_compact_term staticmethod 

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.

from_tuple staticmethod 

from_tuple(t)

Create an annotation from a (qualifier, resource) tuple.

to_dict 

to_dict()

Convert the annotation to a dictionary.

check_miriam_term 

check_miriam_term()

Check that term follows id pattern for collection.

Uses the Identifiers collection information.

check_qualifier staticmethod 

check_qualifier(qualifier)

Check that the qualifier is a MIRIAM qualifier.

Parameters:

Name Type Description Default
qualifier BQB | BQM

qualifier to check

 required

Returns:

Type Description
bool

True if the qualifier is a BQB or BQM term.

validate 

validate()

Validate qualifier and term of the annotation.

Returns:

Type Description
bool

True if the qualifier is a MIRIAM qualifier and the term matches the
bool

pattern of its collection.

RDFAnnotationData 

RDFAnnotationData(annotation)

Bases: RDFAnnotation

An annotation with the information behind the identifier resolved.

Constructing the object resolves the cross references: for every provider the identifiers.org registry lists for the collection, the url pattern is filled in with the term. query_ols then adds label, description and synonyms from the Ontology Lookup Service, and replaces xrefs with the cross references reported by OLS.

Attributes:

Name Type Description
url str | None

url of the first provider of the collection
label str | None

name of the term
description str | None

definition of the term
synonyms list

synonyms of the term
xrefs list

cross references of the term
warnings list

problems which do not invalidate the annotation
errors list

problems which do
Example 
data = RDFAnnotationData(RDFAnnotation(BQB.IS, "chebi/CHEBI:33699"))
data.query_ols()
print(data.label)

Raises:

Type Description
ValueError

if the collection of the annotation is not in the registry

Resolve the cross references of the annotation.

to_dict 

to_dict()

Convert the annotation to a dictionary.

query_ols 

query_ols()

Resolve the term in the Ontology Lookup Service.

Fills in label, description and synonyms, and replaces xrefs with the cross references reported by OLS. Requires network access; errors are collected in errors instead of raising.

Returns:

Type Description
dict

The processed OLS response.

get_ols_query 

get_ols_query()

Get the shared OLS query object, created on first use.

Returns:

Type Description
OLSQuery

The shared OLSQuery for the ontologies in ONTOLOGIES.