Protein database
E569466
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).
All labels observed (1)
| Label | Occurrences |
|---|---|
| Protein database canonical | 1 |
How this entity was disambiguated
This entity first appeared as the object of triple T6098380 — resolving that mention is where its identity was fixed. The disambiguator weighed these candidate entities and picked the highlighted one (or “None”, minting a new entity). This is how homonymy is resolved: the same surface form can point to different entities.
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.
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
Statements (48)
| Predicate | Object |
|---|---|
| instanceOf |
biological database
ⓘ
protein sequence database ⓘ |
| accessibleVia |
Entrez search interface
NERFINISHED
ⓘ
NCBI website ⓘ |
| containsInformationOn |
bibliographic references
ⓘ
literature citations ⓘ protein annotations ⓘ protein domains ⓘ protein function ⓘ protein identifiers ⓘ protein motifs ⓘ protein structure ⓘ sequence features ⓘ |
| hasAbbreviation | Protein ⓘ |
| hasFullName | NCBI Protein database NERFINISHED ⓘ |
| hasScope |
model organisms
ⓘ
multiple species ⓘ pathogens ⓘ |
| integratedWith |
BLAST
NERFINISHED
ⓘ
GenBank NERFINISHED ⓘ PubMed NERFINISHED ⓘ RefSeq NERFINISHED ⓘ |
| isCurated | true ⓘ |
| isFreelyAvailable | true ⓘ |
| isPubliclyAccessible | true ⓘ |
| linkedTo |
3D structure databases
ⓘ
conserved domain database ⓘ nucleotide sequence records ⓘ taxonomy database ⓘ |
| locatedIn |
United States of America
ⓘ
surface form:
United States
|
| maintainedBy |
NCBI
NERFINISHED
ⓘ
National Center for Biotechnology Information NERFINISHED ⓘ |
| operatedBy | U.S. National Library of Medicine NERFINISHED ⓘ |
| partOf | NCBI Entrez system NERFINISHED ⓘ |
| stores |
amino acid sequences
ⓘ
protein sequences ⓘ |
| supports |
BLAST protein searches
ⓘ
FASTA downloads ⓘ programmatic access via E-utilities ⓘ sequence similarity searches ⓘ |
| usedBy |
bioinformaticians
ⓘ
molecular biologists ⓘ structural biologists ⓘ |
| usedFor |
comparative genomics
ⓘ
evolutionary studies ⓘ functional annotation of proteins ⓘ protein characterization ⓘ sequence analysis ⓘ |
How these facts were elicited
The pipeline generated the facts above by prompting gpt-5.1 with this entity's name + description and the instruction below.
Instruction
You are a knowledge base construction expert. Given a subject entity and a description of it, return factual statements that you know for the subject as a JSON list of dictionaries(triples), where keys must be "subject", "predicate" and "object". The number of facts may be very high, between 25 to 50 or more, for very popular subjects. For less popular subjects, the number of facts can be very low, like 5 or 10. # Requirements - If you don't know the subject at all, return an empty list. - If the subject is not a named entity, return an empty list. - Include at least one triple where predicate is "instanceOf". - Do not get too wordy. - Separate several objects into multiple triples with one object.
Input
Subject: Protein database Description of subject: 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).
Referenced by (1)
Full triples — surface form annotated when it differs from this entity's canonical label.