Triple
T23466904
| Position | Surface form | Disambiguated ID | Type / Status |
|---|---|---|---|
| Subject | GEO DataSets |
E569121
|
entity |
| Predicate | linkedTo |
P37
|
FINISHED |
| Object | NCBI SRA |
—
|
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: NCBI SRA | Statement: [GEO DataSets, linkedTo, NCBI SRA]
NED1
Entity disambiguation (via context triple)
gpt-5-mini-2025-08-07
Target entity: NCBI SRA Context triple: [GEO DataSets, linkedTo, NCBI SRA]
-
A.
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.
-
B.
GEO DataSets
GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
-
C.
NCBI databases
NCBI databases are a collection of publicly accessible biological data resources, including nucleotide and protein sequences, genomes, and literature, maintained by the U.S. National Center for Biotechnology Information.
-
D.
GenBank
GenBank is a comprehensive public database of nucleotide sequences and their associated annotation, widely used as a primary resource for genetic and genomic research.
-
E.
DNAnexus
DNAnexus is a cloud-based genomics and bioinformatics platform that enables large-scale DNA data analysis, management, and collaboration for research and clinical applications.
- 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: NCBI SRA Target entity description: NCBI SRA (Sequence Read Archive) is a major public repository that stores and provides access to raw high-throughput sequencing data from a wide range of genomic and transcriptomic studies.
-
A.
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.
-
B.
GEO DataSets
GEO DataSets is a public NCBI repository that organizes and provides access to curated gene expression and other functional genomics experiment data.
-
C.
NCBI databases
NCBI databases are a collection of publicly accessible biological data resources, including nucleotide and protein sequences, genomes, and literature, maintained by the U.S. National Center for Biotechnology Information.
-
D.
GenBank
GenBank is a comprehensive public database of nucleotide sequences and their associated annotation, widely used as a primary resource for genetic and genomic research.
-
E.
DNAnexus
DNAnexus is a cloud-based genomics and bioinformatics platform that enables large-scale DNA data analysis, management, and collaboration for research and clinical applications.
- 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_69e2458ebd808190b3298163132cfb0b |
completed | April 17, 2026, 2:37 p.m. |
| NER | Named-entity recognition | batch_69f1a6fc35c48190a67614fb4170f15b |
completed | April 29, 2026, 6:36 a.m. |
Created at: April 17, 2026, 5:54 p.m.