Triple
T19992626
| Position | Surface form | Disambiguated ID | Type / Status |
|---|---|---|---|
| Subject | APOE gene |
E494100
|
entity |
| Predicate | protectiveAlleleForDisease |
P138240
|
FINISHED |
| Object | APOE ε2 |
—
|
NE NERFINISHED |
How this triple was built (3 steps)
Every LLM step that produced this triple, in pipeline order — named-entity classification, the disambiguation choices (the exact options shown, with the pick highlighted), and the generated description. The batch + timestamp of each is in the Provenance table below.
NER
Named-entity recognition
gpt-5-mini
Instruction
Given a phrase, classify it is english named entity (e.g., persons, organizations, works of art) in Latin script, or not (e.g., literals, dates, URLs, verbose phrases). For disambiguation, the statement where the phrase occurs as object is also given. Please return a JSON object with `phrase` (string, the phrase being analyzed) and `is_ne` (boolean, indicating whether the phrase is a Named Entity).
Input
Phrase: APOE ε2 | Statement: [APOE gene, protectiveAlleleForDisease, APOE ε2]
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: APOE ε2 Context triple: [APOE gene, protectiveAlleleForDisease, APOE ε2]
-
A.
APOE ε2
chosen
APOE ε2 is a common apolipoprotein E gene variant associated with a reduced risk of late-onset Alzheimer’s disease but an increased risk of type III hyperlipoproteinemia.
-
B.
APOE ε3 allele
The APOE ε3 allele is the most common and generally considered the “neutral” variant of the apolipoprotein E gene, associated with average risk for Alzheimer’s disease and typical lipid metabolism compared to other APOE alleles.
-
C.
APOE ε4 allele
The APOE ε4 allele is a genetic variant of the apolipoprotein E gene that significantly increases an individual's susceptibility to late-onset Alzheimer's disease.
-
D.
APOE gene
The APOE gene encodes apolipoprotein E, a key protein in lipid metabolism whose variants, especially ε4, strongly influence risk for Alzheimer’s disease and cardiovascular disorders.
-
E.
APO-E
APO-E is a protein encoded by the APOE gene that plays a key role in lipid transport and is strongly associated with risk for Alzheimer’s disease and cardiovascular disorders.
- F. None of above.
- G. Unsure - the case is ambiguous/there is not enough information to decide.
PD
Predicate disambiguation
gpt-5-mini-2025-08-07
Target predicate: protectiveAlleleForDisease Context triple: [APOE gene, protectiveAlleleForDisease, APOE ε2]
-
A.
geneticallyLinkedTo
Indicates a relationship where two entities share a genetic connection, such as common ancestry, shared genes, or hereditary association.
-
B.
associatedWithPhenotype
Indicates that an entity has a documented connection or correlation with a particular phenotype or observable trait.
-
C.
hasGeneticLocus
Indicates that a genetic feature or trait is located at, or associated with, a specific position (locus) on a genome or chromosome.
-
D.
geneticAffinity
Indicates a relationship where entities share a notable degree of genetic similarity or relatedness.
-
E.
geneticStatus
Indicates the genetic condition or variant state an entity has in relation to a specific gene or set of genes.
- F. None of above. chosen
Provenance (4 batches)
The batch behind each pipeline step, in order, with when it ran. Timestamps are batch-level — stages were processed in waves, so the object chain (NER → NED1 → NEDg → NED2) reads in order, but predicate / elicitation batches can sit in a different wave.
| Step | Stage | Batch ID | Status | When |
|---|---|---|---|---|
| creating | Elicitation | batch_69da626a67648190af9653832a3aeced |
completed | April 11, 2026, 3:02 p.m. |
| NER | Named-entity recognition | batch_69e65fe10ffc81908c94168b0a8ea9c9 |
completed | April 20, 2026, 5:18 p.m. |
| PD | Predicate disambiguation | batch_69e537fd311881908448f2aea8b4812e |
completed | April 19, 2026, 8:15 p.m. |
| PDg | Predicate description generation | batch_69e543c42c688190a22f4d31ec692377 |
completed | April 19, 2026, 9:06 p.m. |
Created at: April 11, 2026, 3:31 p.m.