Triple
T6098380
| Position | Surface form | Disambiguated ID | Type / Status |
|---|---|---|---|
| Subject | NCBI E-utilities API |
E135932
|
entity |
| Predicate | providesAccessTo |
P1985
|
FINISHED |
| Object |
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).
|
E569466
|
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: Protein database | Statement: [NCBI E-utilities API, providesAccessTo, Protein database]
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: Protein database Context triple: [NCBI E-utilities API, providesAccessTo, Protein database]
-
A.
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.
-
B.
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.
-
C.
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.
-
D.
NCBI E-utilities API
The NCBI E-utilities API is a set of programmatic web services that allow automated querying, retrieval, and integration of data from NCBI databases such as PubMed.
-
E.
DBIO
DBIO is the Division of Biological Physics within the American Physical Society, focusing on research at the interface of physics and the life sciences.
- 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: Protein database Triple: [NCBI E-utilities API, providesAccessTo, Protein database]
Generated description
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).
NED2
Entity disambiguation (via description)
gpt-5-mini-2025-08-07
Target entity: Protein database Target entity description: 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).
-
A.
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.
-
B.
BioProject database
The BioProject database is an NCBI resource that organizes and links together data from large-scale biological research projects, such as genome sequencing and functional genomics studies.
-
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.
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.
-
E.
NCBI E-utilities API
The NCBI E-utilities API is a set of programmatic web services that allow automated querying, retrieval, and integration of data from NCBI databases such as PubMed.
- 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_69c0087cd3c48190b459848c72d84eb1 |
completed | March 22, 2026, 3:19 p.m. |
| NER | Named-entity recognition | batch_69c05a9a02888190ac201acd14c3fc31 |
completed | March 22, 2026, 9:09 p.m. |
| NED1 | Entity disambiguation (via context triple) | batch_69c125475548819086b733a80056eba5 |
completed | March 23, 2026, 11:34 a.m. |
| NEDg | Description generation | batch_69c128753cd8819096edb3c817bfae10 |
completed | March 23, 2026, 11:48 a.m. |
| NED2 | Entity disambiguation (via description) | batch_69c129134ce08190ada54a7b3eda27f4 |
completed | March 23, 2026, 11:50 a.m. |
Created at: March 22, 2026, 4:12 p.m.