Triple

T17521734
Position Surface form Disambiguated ID Type / Status
Subject Bioconductor E426691 entity
Predicate hasComponent P35 FINISHED
Object clusterProfiler package
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.
E1274394 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: 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.
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: clusterProfiler package
Triple: [Bioconductor, hasComponent, clusterProfiler package]
Generated 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.
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 (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.