Triple
T8482784
| Position | Surface form | Disambiguated ID | Type / Status |
|---|---|---|---|
| Subject | UniProt protein sequences |
E200557
|
entity |
| Predicate | linkedTo |
P37
|
FINISHED |
| Object |
Pfam domains
Pfam domains are conserved protein regions defined in the Pfam database that represent functional and structural units shared across different proteins.
|
E736821
|
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: Pfam domains | Statement: [UniProt protein sequences, linkedTo, Pfam domains]
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: Pfam domains Context triple: [UniProt protein sequences, linkedTo, Pfam domains]
-
A.
Conserved Domain Database
The Conserved Domain Database is an NCBI-curated resource that catalogs and annotates conserved protein domains to support functional and evolutionary analysis of protein sequences.
-
B.
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).
-
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.
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.
-
E.
UniProt protein sequences
UniProt protein sequences are a comprehensive, curated collection of protein sequence data that serves as a primary reference resource for protein information in biological and biomedical research.
- 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: Pfam domains Triple: [UniProt protein sequences, linkedTo, Pfam domains]
Generated description
Pfam domains are conserved protein regions defined in the Pfam database that represent functional and structural units shared across different proteins.
NED2
Entity disambiguation (via description)
gpt-5-mini-2025-08-07
Target entity: Pfam domains Target entity description: Pfam domains are conserved protein regions defined in the Pfam database that represent functional and structural units shared across different proteins.
-
A.
Conserved Domain Database
The Conserved Domain Database is an NCBI-curated resource that catalogs and annotates conserved protein domains to support functional and evolutionary analysis of protein sequences.
-
B.
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).
-
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.
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.
-
E.
UniProt protein sequences
UniProt protein sequences are a comprehensive, curated collection of protein sequence data that serves as a primary reference resource for protein information in biological and biomedical research.
- 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_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.