Enum: FileFormat

File formats used in structural biology

Permissible Values

Value	Meaning	Description
MRC	EDAM:3842	MRC format for EM density maps
TIFF	EDAM:3591	Tagged Image File Format
HDF5	EDAM:3590	Hierarchical Data Format 5
STAR	EDAM:3906	Self-defining Text Archival and Retrieval format
PDB	EDAM:1476	Protein Data Bank coordinate format
MMCIF	EDAM:1477	Macromolecular Crystallographic Information File
MTZ	EDAM:3816	MTZ reflection data format
CBF	EDAM:3874	Crystallographic Binary Format
DM3	None	Digital Micrograph format
SER	None	FEI series format

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
    meaning: EDAM:3842
    annotations:
      extension:
        tag: extension
        value: .mrc, .map
      applications:
        tag: applications
        value: EM volumes, tomograms
  TIFF:
    text: TIFF
    description: Tagged Image File Format
    meaning: EDAM: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: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
    meaning: EDAM:3906
    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: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: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
    meaning: EDAM:3816
    annotations:
      extension:
        tag: extension
        value: .mtz
      applications:
        tag: applications
        value: crystallographic reflections, phases
  CBF:
    text: CBF
    description: Crystallographic Binary Format
    meaning: EDAM:3874
    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