OneDep
E736792
OneDep is the unified deposition and annotation system used by the Protein Data Bank for submitting and curating macromolecular structure data.
All labels observed (1)
| Label | Occurrences |
|---|---|
| OneDep canonical | 1 |
How this entity was disambiguated
This entity first appeared as the object of triple T8482578 — 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: OneDep Context triple: [Protein Data Bank, hasDepositionSystem, OneDep]
-
A.
Depend
Depend is a leading adult incontinence product brand known for its disposable underwear and protective garments designed to manage bladder leakage.
-
B.
GitHub Packages
GitHub Packages is a software package hosting and management service integrated into GitHub, enabling developers to publish, share, and reuse packages alongside their source code and workflows.
-
C.
Hackage
Hackage is the central online package repository and distribution platform for the Haskell programming language’s libraries and tools.
-
D.
Gitgit Waterfall
Gitgit Waterfall is a popular scenic cascade in northern Bali, Indonesia, known for its lush jungle surroundings and easy accessibility to visitors.
-
E.
Apt
Apt is a historic market town in southeastern France’s Vaucluse department, known for its candied fruit production and Provençal charm.
- 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: OneDep Target entity description: OneDep is the unified deposition and annotation system used by the Protein Data Bank for submitting and curating macromolecular structure data.
-
A.
Depend
Depend is a leading adult incontinence product brand known for its disposable underwear and protective garments designed to manage bladder leakage.
-
B.
GitHub Packages
GitHub Packages is a software package hosting and management service integrated into GitHub, enabling developers to publish, share, and reuse packages alongside their source code and workflows.
-
C.
Hackage
Hackage is the central online package repository and distribution platform for the Haskell programming language’s libraries and tools.
-
D.
Gitgit Waterfall
Gitgit Waterfall is a popular scenic cascade in northern Bali, Indonesia, known for its lush jungle surroundings and easy accessibility to visitors.
-
E.
Apt
Apt is a historic market town in southeastern France’s Vaucluse department, known for its candied fruit production and Provençal charm.
- F. None of above. chosen
Statements (47)
| Predicate | Object |
|---|---|
| instanceOf |
deposition and annotation system
ⓘ
scientific data curation system ⓘ software platform ⓘ |
| accessModel | online portal ⓘ |
| associatedWith |
PDB format
ⓘ
PDBx/mmCIF format ⓘ
linked to:
PDBx/mmCIF dictionary
wwPDB validation reports ⓘ
linked to:
Protein Data Bank
|
| domain |
3D biostructure data management
ⓘ
macromolecular crystallography ⓘ structural biology ⓘ |
| feature |
automated validation tools
ⓘ
curator annotation workflows ⓘ version-controlled data management ⓘ web-based deposition interface ⓘ |
| goal |
ensure consistency of biostructure annotations
ⓘ
improve data quality for the Protein Data Bank ⓘ provide a single global system for PDB depositions ⓘ |
| handlesDataType |
PDB entries
ⓘ
macromolecular complexes ⓘ nucleic acid structures ⓘ protein structures ⓘ protein–nucleic acid complexes ⓘ |
| language | web technologies ⓘ |
| maintainsRelationshipWith |
Protein Data Bank archive
ⓘ
linked to:
Protein Data Bank
|
| operatedBy |
PDBc
ⓘ
PDBe ⓘ
linked to:
Protein Data Bank
PDBj ⓘ
linked to:
Protein Data Bank
RCSB PDB ⓘ
linked to:
PDB
wwPDB partner sites ⓘ |
| purpose |
annotation of macromolecular structure data
ⓘ
curation of macromolecular structure data ⓘ unified deposition of macromolecular structure data ⓘ validation of macromolecular structure data ⓘ |
| supportsMethod |
NMR spectroscopy
ⓘ
X-ray crystallography ⓘ cryo-electron microscopy ⓘ integrative or hybrid methods ⓘ |
| usedBy |
Protein Data Bank
ⓘ
Worldwide Protein Data Bank ⓘ
linked to:
Protein Data Bank
wwPDB ⓘ
linked to:
Protein Data Bank
|
| usedFor |
managing deposition metadata
ⓘ
submission of new PDB entries ⓘ updating existing PDB entries ⓘ |
| user |
NMR spectroscopists
ⓘ
cryo-EM researchers ⓘ crystallographers ⓘ structural biologists ⓘ |
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: OneDep Description of subject: OneDep is the unified deposition and annotation system used by the Protein Data Bank for submitting and curating macromolecular structure data.
Referenced by (1)
Full triples — surface form annotated when it differs from this entity's canonical label.