Triple
T17521734
| Position | Surface form | Disambiguated ID | Type / Status |
|---|---|---|---|
| Subject | Bioconductor |
E426691
|
entity |
| Predicate | hasComponent |
P35
|
FINISHED |
| Object | clusterProfiler 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: clusterProfiler package | Statement: [Bioconductor, hasComponent, clusterProfiler package]
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: clusterProfiler package Context triple: [Bioconductor, hasComponent, clusterProfiler package]
-
A.
Gene Ontology (GO)
Gene Ontology (GO) is a major bioinformatics initiative that provides a structured, controlled vocabulary to describe gene and gene product attributes across species in terms of their molecular functions, biological processes, and cellular components.
-
B.
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.
-
C.
KEGG pathways
KEGG pathways are curated biological pathway maps in the KEGG database that represent networks of molecular interactions, reactions, and relations involved in cellular and organismal processes.
-
D.
Reactome pathways
Reactome pathways are curated, peer-reviewed biological pathways that map molecular interactions and processes in human biology and other species.
-
E.
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.
- 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: clusterProfiler package Target entity description: The clusterProfiler package is an R/Bioconductor tool for statistical analysis and visualization of functional profiles, such as GO and pathway enrichment, of gene and gene clusters.
-
A.
Gene Ontology (GO)
Gene Ontology (GO) is a major bioinformatics initiative that provides a structured, controlled vocabulary to describe gene and gene product attributes across species in terms of their molecular functions, biological processes, and cellular components.
-
B.
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.
-
C.
KEGG pathways
KEGG pathways are curated biological pathway maps in the KEGG database that represent networks of molecular interactions, reactions, and relations involved in cellular and organismal processes.
-
D.
Reactome pathways
Reactome pathways are curated, peer-reviewed biological pathways that map molecular interactions and processes in human biology and other species.
-
E.
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.
- 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.