Triple
T17521717
| Position | Surface form | Disambiguated ID | Type / Status |
|---|---|---|---|
| Subject | Bioconductor |
E426691
|
entity |
| Predicate | hasComponent |
P35
|
FINISHED |
| Object |
edgeR package
The edgeR package is a Bioconductor software tool for statistical analysis of differential expression in count-based genomics data, particularly RNA-seq.
|
E1274383
|
NE FINISHED |
How this triple was built (4 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: edgeR package | Statement: [Bioconductor, hasComponent, edgeR package]
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: edgeR package Context triple: [Bioconductor, hasComponent, edgeR package]
-
A.
Bioconductor
Bioconductor is an open-source project that provides R packages and tools for the analysis and comprehension of high-throughput genomic and biological data.
-
B.
lme4
lme4 is a widely used R package for fitting linear and generalized linear mixed-effects models using efficient numerical optimization methods.
-
C.
GEO DataSets
GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
-
D.
OncoAnalytics
OncoAnalytics is a data and analytics platform by Flatiron Health that provides real-world oncology insights to support cancer research and clinical decision-making.
-
E.
NGS
NGS is the National Geodetic Survey, the U.S. federal agency responsible for defining and managing the national coordinate system used for mapping, navigation, and surveying.
- F. None of above. chosen
- G. Unsure - the case is ambiguous/there is not enough information to decide.
NEDg
Description generation
gpt-5.1
Instruction
Generate a one-sentence description of the target entity. You are given a context triple in the form (subject, predicate, object), where the object is the target entity. # Instructions Use the triple to infer relevant information about the entity. Describe the entity based on what is most defining, well-known. Avoid repeating the information from the triple, unless really essential. # Response Format Return only the sentence: "Description: [one-sentence description of the target entity]"
Input
Entity: edgeR package Triple: [Bioconductor, hasComponent, edgeR package]
Generated description
The edgeR package is a Bioconductor software tool for statistical analysis of differential expression in count-based genomics data, particularly RNA-seq.
NED2
Entity disambiguation (via description)
gpt-5-mini-2025-08-07
Target entity: edgeR package Target entity description: The edgeR package is a Bioconductor software tool for statistical analysis of differential expression in count-based genomics data, particularly RNA-seq.
-
A.
Bioconductor
Bioconductor is an open-source project that provides R packages and tools for the analysis and comprehension of high-throughput genomic and biological data.
-
B.
lme4
lme4 is a widely used R package for fitting linear and generalized linear mixed-effects models using efficient numerical optimization methods.
-
C.
GEO DataSets
GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
-
D.
OncoAnalytics
OncoAnalytics is a data and analytics platform by Flatiron Health that provides real-world oncology insights to support cancer research and clinical decision-making.
-
E.
NGS
NGS is the National Geodetic Survey, the U.S. federal agency responsible for defining and managing the national coordinate system used for mapping, navigation, and surveying.
- F. None of above. chosen
Provenance (5 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_69d889de677081909b22d2657b1f0292 |
completed | April 10, 2026, 5:25 a.m. |
| NER | Named-entity recognition | batch_69e452d2f79881909556894728e255ab |
completed | April 19, 2026, 3:58 a.m. |
| NED1 | Entity disambiguation (via context triple) | batch_6a01c94237d08190bb1f874735c87803 |
completed | May 11, 2026, 12:19 p.m. |
| NEDg | Description generation | batch_6a01cabea2b48190a690b17a88d45b40 |
completed | May 11, 2026, 12:25 p.m. |
| NED2 | Entity disambiguation (via description) | batch_6a01cefa08f8819086cb86ce22193baa |
completed | May 11, 2026, 12:43 p.m. |
Created at: April 10, 2026, 5:49 a.m.