Interface AnnotationRelationService

All Known Implementing Classes:

AnnotationRelationServiceImpl

public interface AnnotationRelationService

Read access to the relations Gemma knows between annotation terms.

Three consumers, and they want three different shapes of the same rows:

• Display — an experiment page captioning what its own annotations imply. findRelationsForExperiment(ExpressionExperiment, AnnotationRelationDao.Direction, Set, int) seeds from the experiment's annotations and answers "what does this dataset's genotype stand for?"
• Browse and search — a disease selector that must still return a dataset annotated only as Chd8 mutant. findRelatedTermsForSearch(Collection, Collection, AnnotationRelationDao.Direction, Set, Long, Collection, int, int) is the expansion primitive.
• Suppression — a producer asking whether the tag it is about to write is already implied. Also findRelatedTermsForSearch(Collection, Collection, AnnotationRelationDao.Direction, Set, Long, Collection, int, int), read as set membership.

🛑 The suppression consumer must exclude the experiment under test. The curation pipeline is gold-blind: it never sees the current experiment's own curation, and a gate that read the experiment's own statements would be reading the very thing being evaluated. Peer precedent from the rest of the corpus is the honest source, which is what excludedExperimentIds is for. It is also what makes "this tag is inferable, so it can be dropped" a claim rather than a circle: hold the dataset out and ask whether the rest of the corpus still recovers the disease.

Method Summary

Modifier and Type	Method	Description
List<String[]>	findRelatedTermsForSearch(Collection<String> seedValueUris, Collection<String> seedValues, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, Long taxonId, Collection<Long> excludedExperimentIds, int maximumObjectBreadth, int maxResults)	Terms related to the seeds, for widening a query or testing membership.
List<AnnotationRelationDao.RelationSummary>	findRelations(AnnotationRelationDao.RelationQuery query)	The ranked, evidenced read.
List<AnnotationRelationDao.RelationSummary>	findRelationsForExperiment(ExpressionExperiment ee, AnnotationRelationDao.Direction direction, Set<AnnotationRelationBasis> bases, int maxResults)	What this experiment's own annotations imply, for display beside them.

Method Details

findRelations

List<AnnotationRelationDao.RelationSummary> findRelations(AnnotationRelationDao.RelationQuery query)

The ranked, evidenced read. See AnnotationRelationDao.findRelations(AnnotationRelationDao.RelationQuery).

findRelationsForExperiment

List<AnnotationRelationDao.RelationSummary> findRelationsForExperiment(ExpressionExperiment ee,
 AnnotationRelationDao.Direction direction,
 Set<AnnotationRelationBasis> bases,
 int maxResults)

What this experiment's own annotations imply, for display beside them.

Seeds from every annotation the experiment carries and reports what each stands in relation to, with the experiment itself held out of the evidence — a dataset shown its own annotation as support for itself is showing a tautology.

Only forward walks, and no conclusion the experiment already carries: both follow from AnnotationRelationDao.RelationQuery.seedFromExperimentId(Long), which is what makes this an inference rather than a symmetric browse.

Parameters:

direction - which way to read: what the experiment's terms stand for, or what stands for them

findRelatedTermsForSearch

List<String[]> findRelatedTermsForSearch(Collection<String> seedValueUris,
 Collection<String> seedValues,
 AnnotationRelationDao.Direction direction,
 Set<AnnotationRelationBasis> bases,
 @Nullable
 Long taxonId,
 Collection<Long> excludedExperimentIds,
 int maximumObjectBreadth,
 int maxResults)

Terms related to the seeds, for widening a query or testing membership.

No ranking and no ambiguity resolution, on purpose: SURF1's three diseases all belong in the set, and a caller testing membership gets the right answer whichever one is meant. A caller that needs to choose one wants findRelations(AnnotationRelationDao.RelationQuery) and its evidence instead.