Triple
T17521736
| Position | Surface form | Disambiguated ID | Type / Status |
|---|---|---|---|
| Subject | Bioconductor |
E426691
|
entity |
| Predicate | hasComponent |
P35
|
FINISHED |
| Object |
GEOquery package
The GEOquery package is an R/Bioconductor tool that facilitates downloading and importing gene expression and other functional genomics data from NCBI’s Gene Expression Omnibus (GEO) into R for analysis.
|
E1274396
|
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: GEOquery package | Statement: [Bioconductor, hasComponent, GEOquery package]
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: GEOquery package Context triple: [Bioconductor, hasComponent, GEOquery package]
-
A.
GEO DataSets
GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
-
B.
GEO reports
GEO reports are flagship United Nations environmental assessment publications that periodically evaluate the state of the global environment, emerging trends, and policy options for sustainable development.
-
C.
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.
-
D.
Genome Data Viewer
Genome Data Viewer is an NCBI web-based genome browser that allows users to visualize, explore, and analyze annotated genomic sequences and features.
-
E.
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.
- 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: GEOquery package Triple: [Bioconductor, hasComponent, GEOquery package]
Generated description
The GEOquery package is an R/Bioconductor tool that facilitates downloading and importing gene expression and other functional genomics data from NCBI’s Gene Expression Omnibus (GEO) into R for analysis.
NED2
Entity disambiguation (via description)
gpt-5-mini-2025-08-07
Target entity: GEOquery package Target entity description: The GEOquery package is an R/Bioconductor tool that facilitates downloading and importing gene expression and other functional genomics data from NCBI’s Gene Expression Omnibus (GEO) into R for analysis.
-
A.
GEO DataSets
GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
-
B.
GEO reports
GEO reports are flagship United Nations environmental assessment publications that periodically evaluate the state of the global environment, emerging trends, and policy options for sustainable development.
-
C.
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.
-
D.
Genome Data Viewer
Genome Data Viewer is an NCBI web-based genome browser that allows users to visualize, explore, and analyze annotated genomic sequences and features.
-
E.
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.
- 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.