Enum: FileFormat

File formats used in structural biology

URI: valuesets:FileFormat

Permissible Values

Value	Meaning	Description	Exact Mappings	Applications	Extension
MRC		MRC format for EM density maps		EM volumes, tomograms	.mrc, .map
TIFF	EDAM:format_3591	Tagged Image File Format		micrographs, general imaging	.tif, .tiff
HDF5	EDAM:format_3590	Hierarchical Data Format 5		large datasets, metadata storage	.h5, .hdf5
STAR		Self-defining Text Archival and Retrieval format		RELION metadata, particle parameters	.star
PDB	EDAM:format_1476	Protein Data Bank coordinate format	OBI:0001525	atomic coordinates, legacy format	.pdb
MMCIF	EDAM:format_1477	Macromolecular Crystallographic Information File	NCIT:C133997	atomic coordinates, modern PDB format	.cif
MTZ		MTZ reflection data format		crystallographic reflections, phases	.mtz
CBF		Crystallographic Binary Format		detector images, diffraction data	.cbf
DM3		Digital Micrograph format		FEI/Thermo Fisher EM data	.dm3, .dm4
SER		FEI series format		FEI movie stacks	.ser

Slots

Name	Description
file_format	File formats used in structural biology

Identifier and Mapping Information

Schema Source

• from schema: https://w3id.org/linkml/valuesets

LinkML Source

name: FileFormat
instantiates:
- valuesets_meta:ValueSetEnumDefinition
description: File formats used in structural biology
title: File Format
from_schema: https://w3id.org/linkml/valuesets
contributors:
- orcid:0000-0002-6601-2165
- https://github.com/anthropics/claude-code
status: DRAFT
rank: 1000
permissible_values:
  MRC:
    text: MRC
    description: MRC format for EM density maps
    annotations:
      extension:
        tag: extension
        value: .mrc, .map
      applications:
        tag: applications
        value: EM volumes, tomograms
  TIFF:
    text: TIFF
    description: Tagged Image File Format
    meaning: EDAM:format_3591
    annotations:
      extension:
        tag: extension
        value: .tif, .tiff
      applications:
        tag: applications
        value: micrographs, general imaging
  HDF5:
    text: HDF5
    description: Hierarchical Data Format 5
    meaning: EDAM:format_3590
    annotations:
      extension:
        tag: extension
        value: .h5, .hdf5
      applications:
        tag: applications
        value: large datasets, metadata storage
  STAR:
    text: STAR
    description: Self-defining Text Archival and Retrieval format
    annotations:
      extension:
        tag: extension
        value: .star
      applications:
        tag: applications
        value: RELION metadata, particle parameters
  PDB:
    text: PDB
    description: Protein Data Bank coordinate format
    meaning: EDAM:format_1476
    annotations:
      extension:
        tag: extension
        value: .pdb
      applications:
        tag: applications
        value: atomic coordinates, legacy format
    exact_mappings:
    - OBI:0001525
  MMCIF:
    text: MMCIF
    description: Macromolecular Crystallographic Information File
    meaning: EDAM:format_1477
    annotations:
      extension:
        tag: extension
        value: .cif
      applications:
        tag: applications
        value: atomic coordinates, modern PDB format
    exact_mappings:
    - NCIT:C133997
  MTZ:
    text: MTZ
    description: MTZ reflection data format
    annotations:
      extension:
        tag: extension
        value: .mtz
      applications:
        tag: applications
        value: crystallographic reflections, phases
  CBF:
    text: CBF
    description: Crystallographic Binary Format
    annotations:
      extension:
        tag: extension
        value: .cbf
      applications:
        tag: applications
        value: detector images, diffraction data
  DM3:
    text: DM3
    description: Digital Micrograph format
    annotations:
      extension:
        tag: extension
        value: .dm3, .dm4
      applications:
        tag: applications
        value: FEI/Thermo Fisher EM data
  SER:
    text: SER
    description: FEI series format
    annotations:
      extension:
        tag: extension
        value: .ser
      applications:
        tag: applications
        value: FEI movie stacks