valuesets 0.3.1__py3-none-any.whl

valuesets/schema/bio/structural_biology.yaml

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+name: structural_biology
+title: Structural Biology Value Sets
+description: 'Value sets for structural biology techniques, including cryo-EM, X-ray crystallography, SAXS/SANS, mass spectrometry,
+  and related sample preparation and data processing methods.
+
+  '
+id: https://w3id.org/valuesets/bio/structural_biology
+imports:
+- linkml:types
+prefixes:
+  linkml: https://w3id.org/linkml/
+  EDAM: http://edamontology.org/
+  OBI: http://purl.obolibrary.org/obo/OBI_
+  CHMO: http://purl.obolibrary.org/obo/CHMO_
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  sample:
+    description: Types of biological samples used in structural biology
+    range: SampleType
+  structural_biology_technique:
+    description: Structural biology experimental techniques
+    range: StructuralBiologyTechnique
+  cryo_em_preparation:
+    description: Types of cryo-EM sample preparation
+    range: CryoEMPreparationType
+  cryo_em_grid:
+    description: Types of electron microscopy grids
+    range: CryoEMGridType
+  vitrification_method:
+    description: Methods for sample vitrification
+    range: VitrificationMethod
+  crystallization_method:
+    description: Methods for protein crystallization
+    range: CrystallizationMethod
+  x_ray_source:
+    description: Types of X-ray sources
+    range: XRaySource
+  detector:
+    description: Types of detectors for structural biology
+    range: Detector
+  workflow:
+    description: Types of computational processing workflows
+    range: WorkflowType
+  file_format:
+    description: File formats used in structural biology
+    range: FileFormat
+  data:
+    description: Types of structural biology data
+    range: DataType
+  processing_status:
+    description: Status of data processing workflows
+    range: ProcessingStatus
+enums:
+  SampleType:
+    description: Types of biological samples used in structural biology
+    permissible_values:
+      PROTEIN:
+        description: Purified protein sample
+      NUCLEIC_ACID:
+        description: Nucleic acid sample (DNA or RNA)
+      PROTEIN_COMPLEX:
+        description: Protein-protein or protein-nucleic acid complex
+      MEMBRANE_PROTEIN:
+        description: Membrane-associated protein sample
+      VIRUS:
+        description: Viral particle or capsid
+      ORGANELLE:
+        description: Cellular organelle (mitochondria, chloroplast, etc.)
+      CELL:
+        description: Whole cell sample
+      TISSUE:
+        description: Tissue sample
+  StructuralBiologyTechnique:
+    description: Structural biology experimental techniques
+    permissible_values:
+      CRYO_EM:
+        title: cryogenic electron microscopy
+        description: Cryo-electron microscopy
+        meaning: CHMO:0002413
+        annotations:
+          resolution_range: 2-30 Å typical
+          aliases: cryoEM, electron cryo-microscopy
+      CRYO_ET:
+        description: Cryo-electron tomography
+        annotations:
+          resolution_range: 20-100 Å typical
+          aliases: cryoET, electron cryo-tomography
+      X_RAY_CRYSTALLOGRAPHY:
+        title: single crystal X-ray diffraction
+        description: X-ray crystallography
+        meaning: CHMO:0000159
+        annotations:
+          resolution_range: 1-4 Å typical
+          aliases: XRC, macromolecular crystallography
+      NEUTRON_CRYSTALLOGRAPHY:
+        description: Neutron crystallography
+        annotations:
+          advantages: hydrogen positions, deuteration studies
+      SAXS:
+        title: small-angle X-ray scattering
+        description: Small-angle X-ray scattering
+        meaning: CHMO:0000204
+        annotations:
+          information: low-resolution structure, conformational changes
+      SANS:
+        description: Small-angle neutron scattering
+        annotations:
+          advantages: contrast variation with deuteration
+      WAXS:
+        description: Wide-angle X-ray scattering
+      NMR:
+        title: nuclear magnetic resonance spectroscopy
+        description: Nuclear magnetic resonance spectroscopy
+        meaning: CHMO:0000591
+        annotations:
+          information: solution structure, dynamics
+      MASS_SPECTROMETRY:
+        description: Mass spectrometry
+        meaning: CHMO:0000470
+        annotations:
+          applications: native MS, crosslinking, HDX
+      NEGATIVE_STAIN_EM:
+        description: Negative stain electron microscopy
+        annotations:
+          resolution_range: 15-30 Å typical
+  CryoEMPreparationType:
+    description: Types of cryo-EM sample preparation
+    permissible_values:
+      VITREOUS_ICE:
+        description: Sample embedded in vitreous ice
+      CRYO_SECTIONING:
+        description: Cryo-sectioned sample
+      FREEZE_SUBSTITUTION:
+        description: Freeze-substituted sample
+      HIGH_PRESSURE_FREEZING:
+        description: High-pressure frozen sample
+  CryoEMGridType:
+    description: Types of electron microscopy grids
+    permissible_values:
+      C_FLAT:
+        description: C-flat holey carbon grid
+        annotations:
+          hole_sizes: 1.2/1.3, 2/1, 2/2 μm common
+          manufacturer: Protochips
+      QUANTIFOIL:
+        description: Quantifoil holey carbon grid
+        annotations:
+          hole_sizes: 1.2/1.3, 2/1, 2/2 μm common
+          manufacturer: Quantifoil
+      LACEY_CARBON:
+        description: Lacey carbon support film
+        annotations:
+          structure: irregular holes, thin carbon film
+      ULTRATHIN_CARBON:
+        description: Ultrathin carbon film on holey support
+        annotations:
+          thickness: 3-5 nm typical
+      GOLD_GRID:
+        description: Pure gold grid
+        annotations:
+          advantages: inert, high-resolution imaging
+      GRAPHENE_OXIDE:
+        description: Graphene oxide support
+        annotations:
+          advantages: atomically thin, good contrast
+  VitrificationMethod:
+    description: Methods for sample vitrification
+    permissible_values:
+      PLUNGE_FREEZING:
+        description: Plunge freezing in liquid ethane
+        annotations:
+          temperature: -180°C ethane
+          equipment: Vitrobot, Leica GP
+      HIGH_PRESSURE_FREEZING:
+        description: High pressure freezing
+        annotations:
+          pressure: 2100 bar typical
+          advantages: thick samples, no ice crystals
+      SLAM_FREEZING:
+        description: Slam freezing against metal block
+        annotations:
+          cooling_rate: 10,000 K/s
+      SPRAY_FREEZING:
+        description: Spray freezing into liquid nitrogen
+        annotations:
+          applications: large samples, tissues
+  CrystallizationMethod:
+    description: Methods for protein crystallization
+    permissible_values:
+      VAPOR_DIFFUSION_HANGING:
+        description: Vapor diffusion hanging drop method
+        annotations:
+          volume: 2-10 μL drops typical
+          advantages: visual monitoring, easy optimization
+      VAPOR_DIFFUSION_SITTING:
+        description: Vapor diffusion sitting drop method
+        annotations:
+          advantages: automated setup, stable drops
+      MICROBATCH:
+        description: Microbatch under oil method
+        annotations:
+          oil_type: paraffin, silicone oil
+          advantages: prevents evaporation
+      DIALYSIS:
+        description: Dialysis crystallization
+        annotations:
+          applications: large volume samples, gentle conditions
+      FREE_INTERFACE_DIFFUSION:
+        description: Free interface diffusion
+        annotations:
+          setup: capillary tubes, gel interface
+      LCP:
+        description: Lipidic cubic phase crystallization
+        annotations:
+          applications: membrane proteins
+          lipid: monoolein most common
+  XRaySource:
+    description: Types of X-ray sources
+    permissible_values:
+      SYNCHROTRON:
+        description: Synchrotron radiation source
+        annotations:
+          advantages: high intensity, tunable wavelength
+          brightness: 10^15-10^18 photons/s/mm²/mrad²
+      ROTATING_ANODE:
+        description: Rotating anode generator
+        annotations:
+          power: 3-18 kW typical
+          target: copper, molybdenum common
+      MICROFOCUS:
+        description: Microfocus sealed tube
+        annotations:
+          spot_size: 10-50 μm
+          applications: small crystals, in-house screening
+      METAL_JET:
+        description: Liquid metal jet source
+        annotations:
+          advantages: higher power density, longer lifetime
+          metals: gallium, indium
+  Detector:
+    description: Types of detectors for structural biology
+    permissible_values:
+      DIRECT_ELECTRON:
+        description: Direct electron detector (DED)
+        annotations:
+          examples: K2, K3, Falcon, DE-series
+          advantages: high DQE, fast readout
+      CCD:
+        description: Charge-coupled device camera
+        annotations:
+          applications: legacy EM, some crystallography
+      CMOS:
+        description: Complementary metal-oxide semiconductor detector
+        annotations:
+          advantages: fast readout, low noise
+      HYBRID_PIXEL:
+        description: Hybrid pixel detector
+        annotations:
+          examples: Pilatus, Eiger
+          advantages: photon counting, zero noise
+      PHOTOSTIMULABLE_PHOSPHOR:
+        description: Photostimulable phosphor (image plate)
+        annotations:
+          applications: legacy crystallography
+  WorkflowType:
+    description: Types of computational processing workflows
+    permissible_values:
+      MOTION_CORRECTION:
+        description: Motion correction for cryo-EM movies
+        annotations:
+          software: MotionCorr, Unblur, RELION
+      CTF_ESTIMATION:
+        description: Contrast transfer function estimation
+        annotations:
+          software: CTFFIND, Gctf, RELION
+      PARTICLE_PICKING:
+        description: Particle picking from micrographs
+        annotations:
+          methods: template matching, deep learning
+          software: RELION, cryoSPARC, Topaz
+      CLASSIFICATION_2D:
+        description: 2D classification of particles
+        annotations:
+          purpose: sorting, cleaning particle dataset
+      CLASSIFICATION_3D:
+        description: 3D classification of particles
+        annotations:
+          purpose: conformational sorting, resolution improvement
+      REFINEMENT_3D:
+        description: 3D refinement of particle orientations
+        annotations:
+          algorithms: expectation maximization, gradient descent
+      MODEL_BUILDING:
+        description: Atomic model building into density
+        annotations:
+          software: Coot, ChimeraX, Isolde
+      MODEL_REFINEMENT:
+        description: Atomic model refinement
+        annotations:
+          software: PHENIX, REFMAC, Buster
+      PHASING:
+        description: Phase determination for crystallography
+        annotations:
+          methods: SAD, MAD, MR, MIR
+      DATA_INTEGRATION:
+        description: Integration of diffraction data
+        annotations:
+          software: XDS, DIALS, HKL
+      DATA_SCALING:
+        description: Scaling and merging of diffraction data
+        annotations:
+          software: SCALA, AIMLESS, XSCALE
+      SAXS_ANALYSIS:
+        description: SAXS data analysis and modeling
+        annotations:
+          software: PRIMUS, CRYSOL, FoXS
+  FileFormat:
+    description: File formats used in structural biology
+    permissible_values:
+      MRC:
+        description: MRC format for EM density maps
+        annotations:
+          extension: .mrc, .map
+          applications: EM volumes, tomograms
+      TIFF:
+        description: Tagged Image File Format
+        annotations:
+          extension: .tif, .tiff
+          applications: micrographs, general imaging
+      HDF5:
+        description: Hierarchical Data Format 5
+        annotations:
+          extension: .h5, .hdf5
+          applications: large datasets, metadata storage
+      STAR:
+        description: Self-defining Text Archival and Retrieval format
+        annotations:
+          extension: .star
+          applications: RELION metadata, particle parameters
+      PDB:
+        description: Protein Data Bank coordinate format
+        annotations:
+          extension: .pdb
+          applications: atomic coordinates, legacy format
+      MMCIF:
+        description: Macromolecular Crystallographic Information File
+        annotations:
+          extension: .cif
+          applications: atomic coordinates, modern PDB format
+      MTZ:
+        description: MTZ reflection data format
+        annotations:
+          extension: .mtz
+          applications: crystallographic reflections, phases
+      CBF:
+        description: Crystallographic Binary Format
+        annotations:
+          extension: .cbf
+          applications: detector images, diffraction data
+      DM3:
+        description: Digital Micrograph format
+        annotations:
+          extension: .dm3, .dm4
+          applications: FEI/Thermo Fisher EM data
+      SER:
+        description: FEI series format
+        annotations:
+          extension: .ser
+          applications: FEI movie stacks
+  DataType:
+    description: Types of structural biology data
+    permissible_values:
+      MICROGRAPH:
+        description: Electron micrograph image
+        annotations:
+          typical_size: 4k x 4k pixels
+      MOVIE:
+        description: Movie stack of frames
+        annotations:
+          applications: motion correction, dose fractionation
+      DIFFRACTION:
+        description: X-ray diffraction pattern
+        annotations:
+          information: structure factors, crystal lattice
+      SCATTERING:
+        description: Small-angle scattering data
+        annotations:
+          information: I(q) vs scattering vector
+      PARTICLES:
+        description: Particle stack for single particle analysis
+        annotations:
+          format: boxed particles, aligned
+      VOLUME:
+        description: 3D electron density volume
+        annotations:
+          applications: cryo-EM maps, crystallographic maps
+      TOMOGRAM:
+        description: 3D tomographic reconstruction
+        annotations:
+          resolution: 5-50 Å typical
+      MODEL:
+        description: Atomic coordinate model
+        annotations:
+          formats: PDB, mmCIF
+      METADATA:
+        description: Associated metadata file
+        annotations:
+          formats: STAR, XML, JSON
+  ProcessingStatus:
+    description: Status of data processing workflows
+    permissible_values:
+      RAW:
+        description: Raw unprocessed data
+      PREPROCESSING:
+        description: Initial preprocessing in progress
+      PROCESSING:
+        description: Main processing workflow running
+      COMPLETED:
+        description: Processing completed successfully
+      FAILED:
+        description: Processing failed with errors
+      QUEUED:
+        description: Queued for processing
+      PAUSED:
+        description: Processing paused by user
+      CANCELLED:
+        description: Processing cancelled by user