Triple

T17521718
Position Surface form Disambiguated ID Type / Status
Subject Bioconductor E426691 entity
Predicate hasComponent P35 FINISHED
Object limma 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: limma package | Statement: [Bioconductor, hasComponent, limma package]
NED1 Entity disambiguation (via context triple) gpt-5-mini-2025-08-07 
Target entity: limma package
Context triple: [Bioconductor, hasComponent, limma 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. Tukey's honestly significant difference test
    Tukey's honestly significant difference test is a statistical post-hoc procedure used to determine which specific group means differ after an ANOVA indicates a significant overall effect.
  • D. GEO DataSets
    GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
  • E. 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.
  • 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: limma package
Target entity description: The limma package is a widely used Bioconductor R toolkit for analyzing gene expression data, particularly for differential expression in microarray and RNA-seq experiments.
  • 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. Tukey's honestly significant difference test
    Tukey's honestly significant difference test is a statistical post-hoc procedure used to determine which specific group means differ after an ANOVA indicates a significant overall effect.
  • D. GEO DataSets
    GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
  • E. 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.
  • 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.