Triple
T17521735
| Position | Surface form | Disambiguated ID | Type / Status |
|---|---|---|---|
| Subject | Bioconductor |
E426691
|
entity |
| Predicate | hasComponent |
P35
|
FINISHED |
| Object | biomaRt package |
—
|
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: biomaRt package | Statement: [Bioconductor, hasComponent, biomaRt package]
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: biomaRt package Context triple: [Bioconductor, hasComponent, biomaRt package]
-
A.
Ensembl
Ensembl is a comprehensive genome annotation and browsing platform that provides detailed, regularly updated genomic data for a wide range of species.
-
B.
NCBI E-utilities API
The NCBI E-utilities API is a set of programmatic web services that allow automated querying, retrieval, and integration of data from NCBI databases such as PubMed.
-
C.
Taxonomy Browser
Taxonomy Browser is an online NCBI tool that allows users to explore and retrieve information about the classification and nomenclature of organisms across the tree of life.
-
D.
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.
-
E.
GEO DataSets
GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
- F. None of above. chosen
- G. Unsure - the case is ambiguous/there is not enough information to decide.
NED2
Entity disambiguation (via description)
gpt-5-mini-2025-08-07
Target entity: biomaRt package Target entity description: The biomaRt package is an R/Bioconductor tool that provides programmatic access to a wide range of biological databases via the BioMart data management system, enabling flexible retrieval and integration of genomic annotation data.
-
A.
Ensembl
Ensembl is a comprehensive genome annotation and browsing platform that provides detailed, regularly updated genomic data for a wide range of species.
-
B.
NCBI E-utilities API
The NCBI E-utilities API is a set of programmatic web services that allow automated querying, retrieval, and integration of data from NCBI databases such as PubMed.
-
C.
Taxonomy Browser
Taxonomy Browser is an online NCBI tool that allows users to explore and retrieve information about the classification and nomenclature of organisms across the tree of life.
-
D.
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.
-
E.
GEO DataSets
GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
- F. None of above. chosen
Provenance (2 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. |
Created at: April 10, 2026, 5:49 a.m.