Triple

T8482533
Position Surface form Disambiguated ID Type / Status
Subject Protein Data Bank E200553 entity
Predicate memberOrganization P10218 FINISHED
Object PDBe
PDBe (Protein Data Bank in Europe) is a major European resource that archives, curates, and provides access to three-dimensional biomolecular structure data.
 E200553 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: PDBe | Statement: [Protein Data Bank, memberOrganization, PDBe]
NED1 Entity disambiguation (via context triple) gpt-5-mini-2025-08-07 
Target entity: PDBe
Context triple: [Protein Data Bank, memberOrganization, PDBe]
  • A. Protein Data Bank
    The Protein Data Bank is a global repository that archives and provides open access to 3D structural data of biological macromolecules such as proteins and nucleic acids.
  • B. PDB
    PDB (Program Database) is a file format used by Microsoft development tools to store debugging and project state information for compiled programs.
  • C. EMBL-EBI AlphaFold Protein Structure Database
    The EMBL-EBI AlphaFold Protein Structure Database is a publicly accessible resource providing predicted 3D structures of proteins generated by DeepMind’s AlphaFold system.
  • D. pdb
    pdb is Python’s built-in interactive debugger, used to inspect and control the execution of Python programs for troubleshooting and development.
  • E. Protein database
    The Protein database is a curated collection of protein sequences and related functional, structural, and bibliographic information maintained by the National Center for Biotechnology Information (NCBI).
  • 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: PDBe
Triple: [Protein Data Bank, memberOrganization, PDBe]
Generated description
PDBe (Protein Data Bank in Europe) is a major European resource that archives, curates, and provides access to three-dimensional biomolecular structure data.
NED2 Entity disambiguation (via description) gpt-5-mini-2025-08-07 
Target entity: PDBe
Target entity description: PDBe (Protein Data Bank in Europe) is a major European resource that archives, curates, and provides access to three-dimensional biomolecular structure data.
  • A. Protein Data Bank chosen
    The Protein Data Bank is a global repository that archives and provides open access to 3D structural data of biological macromolecules such as proteins and nucleic acids.
  • B. PDB
    PDB (Program Database) is a file format used by Microsoft development tools to store debugging and project state information for compiled programs.
  • C. EMBL-EBI AlphaFold Protein Structure Database
    The EMBL-EBI AlphaFold Protein Structure Database is a publicly accessible resource providing predicted 3D structures of proteins generated by DeepMind’s AlphaFold system.
  • D. pdb
    pdb is Python’s built-in interactive debugger, used to inspect and control the execution of Python programs for troubleshooting and development.
  • E. Protein database
    The Protein database is a curated collection of protein sequences and related functional, structural, and bibliographic information maintained by the National Center for Biotechnology Information (NCBI).
  • F. None of above.

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_69cbe53638c48190b742fc51d1b4442a completed March 31, 2026, 3:16 p.m.
NED1 Entity disambiguation (via context triple) batch_69ce3a2b2e9081909f19712946c6ec20 completed April 2, 2026, 9:43 a.m.
NEDg Description generation batch_69ce3b4008a0819096bb44b46f510213 completed April 2, 2026, 9:47 a.m.
NED2 Entity disambiguation (via description) batch_69ce3c000e608190adf1b6499d382529 completed April 2, 2026, 9:50 a.m.
Created at: March 30, 2026, 6:12 p.m.