Class AnnotationsWebService.ExternalIdentificationValueObject

java.lang.Object

ubic.gemma.rest.AnnotationsWebService.ExternalIdentificationValueObject

Enclosing class:

AnnotationsWebService

public static class AnnotationsWebService.ExternalIdentificationValueObject
extends Object

What an external naming authority says a query string is, when nothing Gemma has loaded names it — plus enough provenance to check the claim.

🛑 getIdentifier() is not an annotation. The only URI here a curator may commit is getGroundedTermUri(), and it is present precisely when the identification could be bridged back to a term Gemma already has: ChEMBL says WY-14643 is pirinixic acid, Gemma's own search says pirinixic acid is CHEBI_32509 with 17 corpus uses, and that CHEBI URI is the answer. When the bridge does not land the identification still tells a curator what they are looking at, and there is nothing to annotate with — which is the honest outcome, not a gap to paper over.

The provenance fields are the point of the object as much as the name is. An identification a curator cannot trace back to a source, a release and a matched string is an unsourced assertion, and those are what the curation pipeline is trying to stop emitting.

Author:

tesarst

Constructor Summary

Constructors

Constructor	Description
ExternalIdentificationValueObject(String source, String identifier, String name, String matchedSynonym, String sourceRelease, String sourceUrl, String groundedTermUri, String groundedTermLabel)

Method Summary

Modifier and Type	Method	Description
String	getGroundedTermLabel()	Label of getGroundedTermUri().
String	getGroundedTermUri()	A term Gemma already has whose name equals getName() — the one URI here that is safe to commit.
String	getIdentifier()	The authority's accession, e.g.
String	getMatchedSynonym()	The synonym string that matched — the evidence for the identification, not decoration.
String	getName()	The authority's preferred name, e.g.
String	getSource()	Which authority answered, e.g.
String	getSourceRelease()	Release the identification was read from, e.g.
String	getSourceUrl()	Link to the authority's record, for a curator who wants to check it.

Methods inherited from class Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Details

ExternalIdentificationValueObject

public ExternalIdentificationValueObject(String source,
 @Nullable
 String identifier,
 @Nullable
 String name,
 @Nullable
 String matchedSynonym,
 @Nullable
 String sourceRelease,
 @Nullable
 String sourceUrl,
 @Nullable
 String groundedTermUri,
 @Nullable
 String groundedTermLabel)

Method Details

getSource

public String getSource()

Which authority answered, e.g. ChEMBL.

getIdentifier

@Nullable
public String getIdentifier()

The authority's accession, e.g. CHEMBL295416. NOT a term URI — do not annotate with it.

getName

@Nullable
public String getName()

The authority's preferred name, e.g. PIRINIXIC ACID.

getMatchedSynonym

@Nullable
public String getMatchedSynonym()

The synonym string that matched — the evidence for the identification, not decoration.

getSourceRelease

@Nullable
public String getSourceRelease()

Release the identification was read from, e.g. ChEMBL_37.

getSourceUrl

@Nullable
public String getSourceUrl()

Link to the authority's record, for a curator who wants to check it.

getGroundedTermUri

@Nullable
public String getGroundedTermUri()

A term Gemma already has whose name equals getName() — the one URI here that is safe to commit. Null when the identification could not be bridged.

getGroundedTermLabel

@Nullable
public String getGroundedTermLabel()

Label of getGroundedTermUri().