Triple

T8482783
Position Surface form Disambiguated ID Type / Status
Subject UniProt protein sequences E200557 entity
Predicate linkedTo P37 FINISHED
Object Reactome pathways
Reactome pathways are curated, peer-reviewed biological pathways that map molecular interactions and processes in human biology and other species.
 E739006 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: Reactome pathways | Statement: [UniProt protein sequences, linkedTo, Reactome pathways]
NED1 Entity disambiguation (via context triple) gpt-5-mini-2025-08-07 
Target entity: Reactome pathways
Context triple: [UniProt protein sequences, linkedTo, Reactome pathways]
  • A. 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.
  • B. 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.
  • C. LifeWiki
    LifeWiki is a comprehensive online encyclopedia dedicated to documenting patterns, terminology, and research related to Conway's Game of Life and other cellular automata.
  • D. Molecular Systems Biology
    Molecular Systems Biology is a peer-reviewed scientific journal focusing on systems-level analysis of molecular and cellular processes in biology.
  • E. Protein Information Resource
    Protein Information Resource is a bioinformatics resource center that curates, annotates, and provides access to comprehensive protein sequence and functional information for the scientific community.
  • 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: Reactome pathways
Triple: [UniProt protein sequences, linkedTo, Reactome pathways]
Generated description
Reactome pathways are curated, peer-reviewed biological pathways that map molecular interactions and processes in human biology and other species.
NED2 Entity disambiguation (via description) gpt-5-mini-2025-08-07 
Target entity: Reactome pathways
Target entity description: Reactome pathways are curated, peer-reviewed biological pathways that map molecular interactions and processes in human biology and other species.
  • A. 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.
  • B. 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.
  • C. LifeWiki
    LifeWiki is a comprehensive online encyclopedia dedicated to documenting patterns, terminology, and research related to Conway's Game of Life and other cellular automata.
  • D. Molecular Systems Biology
    Molecular Systems Biology is a peer-reviewed scientific journal focusing on systems-level analysis of molecular and cellular processes in biology.
  • E. Protein Information Resource
    Protein Information Resource is a bioinformatics resource center that curates, annotates, and provides access to comprehensive protein sequence and functional information for the scientific community.
  • 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_69ca831b17988190a1f3f3413d57b820 completed March 30, 2026, 2:05 p.m.
NER Named-entity recognition batch_69cbe53845e881909eeb32863c7aa942 completed March 31, 2026, 3:16 p.m.
NED1 Entity disambiguation (via context triple) batch_69ce4de95e3081908277c65598f3884a completed April 2, 2026, 11:07 a.m.
NEDg Description generation batch_69ce5028c38c81908e81390d0be21387 completed April 2, 2026, 11:16 a.m.
NED2 Entity disambiguation (via description) batch_69ce517fea7c819098d0343fd2c4ccdd completed April 2, 2026, 11:22 a.m.
Created at: March 30, 2026, 6:12 p.m.