PDBx/mmCIF dictionary
E736791
The PDBx/mmCIF dictionary is the standardized data schema used by the Protein Data Bank to define and organize macromolecular structure information in a machine-readable format.
All labels observed (4)
| Label | Occurrences |
|---|---|
| mmCIF dictionary | 2 |
| CIF macromolecular dictionary | 1 |
| PDBx/mmCIF dictionary canonical | 1 |
| PDBx/mmCIF format | 1 |
How this entity was disambiguated
This entity first appeared as the object of triple T8482561 — 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: PDBx/mmCIF dictionary Context triple: [Protein Data Bank, hasStandard, PDBx/mmCIF dictionary]
-
A.
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.
-
B.
Crystallographic Information Framework
The Crystallographic Information Framework is a standardized data format and ontology used worldwide for representing, exchanging, and archiving crystallographic and related structural science data.
-
C.
IUCrData
IUCrData is an open-access crystallography data journal published by the International Union of Crystallography, focusing on brief reports of crystal structure determinations and related datasets.
-
D.
PDB
PDB (Program Database) is a file format used by Microsoft development tools to store debugging and project state information for compiled programs.
-
E.
pdb
pdb is Python’s built-in interactive debugger, used to inspect and control the execution of Python programs for troubleshooting and development.
- 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: PDBx/mmCIF dictionary Target entity description: The PDBx/mmCIF dictionary is the standardized data schema used by the Protein Data Bank to define and organize macromolecular structure information in a machine-readable format.
-
A.
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.
-
B.
Crystallographic Information Framework
The Crystallographic Information Framework is a standardized data format and ontology used worldwide for representing, exchanging, and archiving crystallographic and related structural science data.
-
C.
IUCrData
IUCrData is an open-access crystallography data journal published by the International Union of Crystallography, focusing on brief reports of crystal structure determinations and related datasets.
-
D.
PDB
PDB (Program Database) is a file format used by Microsoft development tools to store debugging and project state information for compiled programs.
-
E.
pdb
pdb is Python’s built-in interactive debugger, used to inspect and control the execution of Python programs for troubleshooting and development.
- F. None of above. chosen
Statements (49)
| Predicate | Object |
|---|---|
| instanceOf |
data dictionary
ⓘ
data schema ⓘ ontology for macromolecular structure data ⓘ |
| appliesTo |
atomic coordinate data
ⓘ
biological assembly descriptions ⓘ chemical component descriptions ⓘ experimental conditions ⓘ refinement statistics ⓘ sequence information ⓘ validation metrics ⓘ |
| basedOn | mmCIF format ⓘ |
| compatibleWith | mmCIF data files ⓘ |
| contains |
categories
ⓘ
constraints on data values ⓘ data items ⓘ definitions of data types ⓘ enumeration ranges ⓘ relationships between categories ⓘ |
| defines |
categories of structural biology information
ⓘ
data items for 3DEM structure data ⓘ data items for NMR structure data ⓘ data items for macromolecular crystallography ⓘ relationships between structural data items ⓘ |
| designedFor |
extensibility of structural data representation
ⓘ
long-term archival of structural data ⓘ |
| enables |
automated parsing of PDB data
ⓘ
schema-driven data validation ⓘ software interoperability in structural biology ⓘ uniform representation of metadata ⓘ |
| extends | Crystallographic Information Framework ⓘ |
| formatFor | PDBx/mmCIF files ⓘ |
| goal |
to provide a comprehensive schema for macromolecular structure data
ⓘ
to replace legacy PDB format limitations ⓘ |
| implementedIn | STAR syntax ⓘ |
| maintainedBy |
wwPDB partners
ⓘ
linked to:
Protein Data Bank
|
| standardFor |
PDB archival data
ⓘ
PDB data deposition ⓘ PDB data exchange ⓘ |
| standardizedBy |
wwPDB
ⓘ
linked to:
Protein Data Bank
|
| supports |
complex biological assemblies
ⓘ
integrated experimental data descriptions ⓘ large macromolecular structures ⓘ rich annotation of structural data ⓘ validation of structural models ⓘ |
| usedBy |
Protein Data Bank
ⓘ
Worldwide Protein Data Bank ⓘ
linked to:
Protein Data Bank
|
| usedFor |
machine-readable description of structural biology data
ⓘ
organization of Protein Data Bank data ⓘ representation of macromolecular structure data ⓘ |
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: PDBx/mmCIF dictionary Description of subject: The PDBx/mmCIF dictionary is the standardized data schema used by the Protein Data Bank to define and organize macromolecular structure information in a machine-readable format.
Referenced by (5)
Full triples — surface form annotated when it differs from this entity's canonical label.
linked to: PDBx/mmCIF dictionary
linked to: PDBx/mmCIF dictionary
linked to: PDBx/mmCIF dictionary
linked to: PDBx/mmCIF dictionary