valuesets 0.3.1__py3-none-any.whl

valuesets/schema/bio/viral_genome_types.yaml

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+name: viral_genome_types
+id: https://w3id.org/linkml/valuesets/bio/viral_genome_types
+prefixes:
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  SO: http://purl.obolibrary.org/obo/SO_
+  mixs: https://genomicsstandardsconsortium.github.io/mixs/
+  valuesets: https://w3id.org/valuesets/
+default_prefix: valuesets
+slots:
+  viral_genome_type:
+    description: Types of viral genomes based on Baltimore classification
+    range: ViralGenomeTypeEnum
+enums:
+  ViralGenomeTypeEnum:
+    description: Types of viral genomes based on Baltimore classification
+    conforms_to: https://en.wikipedia.org/wiki/Baltimore_classification
+    permissible_values:
+      DNA:
+        description: Viral genome composed of DNA
+        meaning: CHEBI:16991
+        title: deoxyribonucleic acid
+      DSDNA:
+        description: Double-stranded DNA viral genome
+        meaning: NCIT:C14348
+        title: Double Stranded DNA Virus
+        is_a: DNA
+        aliases:
+        - Baltimore Group I
+        - Group I
+      SSDNA:
+        description: Single-stranded DNA viral genome
+        meaning: NCIT:C14350
+        title: Single Stranded DNA Virus
+        is_a: DNA
+        aliases:
+        - Baltimore Group II
+        - Group II
+      RNA:
+        description: Viral genome composed of RNA
+        meaning: CHEBI:33697
+        title: ribonucleic acid
+      DSRNA:
+        description: Double-stranded RNA viral genome
+        meaning: NCIT:C28518
+        title: Double Stranded RNA Virus
+        is_a: RNA
+        aliases:
+        - Baltimore Group III
+        - Group III
+      SSRNA:
+        description: Single-stranded RNA viral genome
+        meaning: NCIT:C95939
+        title: Single-Stranded RNA
+        is_a: RNA
+      SSRNA_POSITIVE:
+        description: Positive-sense single-stranded RNA viral genome
+        meaning: NCIT:C14351
+        title: Positive Sense ssRNA Virus
+        is_a: SSRNA
+        aliases:
+        - Baltimore Group IV
+        - Group IV
+        - (+)ssRNA
+      SSRNA_NEGATIVE:
+        description: Negative-sense single-stranded RNA viral genome
+        meaning: NCIT:C14346
+        title: Negative Sense ssRNA Virus
+        is_a: SSRNA
+        aliases:
+        - Baltimore Group V
+        - Group V
+        - (-)ssRNA
+      SSRNA_RT:
+        description: Single-stranded RNA viruses that replicate through a DNA intermediate (retroviruses)
+        meaning: NCIT:C14347
+        title: Deltaretrovirus
+        is_a: SSRNA
+        aliases:
+        - Baltimore Group VI
+        - Group VI
+        - Retroviruses
+      DSDNA_RT:
+        description: Double-stranded DNA viruses that replicate through a single-stranded RNA intermediate (pararetroviruses)
+        meaning: NCIT:C14349
+        title: Other Virus Grouping
+        is_a: DSDNA
+        aliases:
+        - Baltimore Group VII
+        - Group VII
+        - Pararetroviruses
+      MIXED:
+        description: Mixed or hybrid viral genome type
+        meaning: NCIT:C128790
+        title: Hybrid
+      UNCHARACTERIZED:
+        description: Viral genome type not yet characterized
+        meaning: NCIT:C17998
+        title: Unknown

valuesets/schema/bioprocessing/scale_up.yaml

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+name: scale_up
+title: Bioprocessing Scale-up Value Sets
+description: 'Value sets for bioprocessing scale-up facilities, fermentation, and biomanufacturing
+
+  operations like those at ABPDU (Advanced Biofuels and Bioproducts Process Development Unit)'
+id: https://w3id.org/linkml/valuesets/bioprocessing/scale_up
+imports:
+- linkml:types
+prefixes:
+  valuesets: https://w3id.org/valuesets/
+  NCIT: http://purl.obolibrary.org/obo/NCIT_
+  OBI: http://purl.obolibrary.org/obo/OBI_
+  ENVO: http://purl.obolibrary.org/obo/ENVO_
+  CHMO: http://purl.obolibrary.org/obo/CHMO_
+  CHEBI: http://purl.obolibrary.org/obo/CHEBI_
+  UO: http://purl.obolibrary.org/obo/UO_
+  BAO: http://www.bioassayontology.org/bao#BAO_
+  SBO: http://biomodels.net/SBO/SBO_
+  MSIO: http://purl.obolibrary.org/obo/MSIO_
+  mesh: http://id.nlm.nih.gov/mesh/
+  FOODON: http://purl.obolibrary.org/obo/FOODON_
+default_prefix: valuesets
+slots:
+  process_scale:
+    description: Scale of bioprocessing operations from lab bench to commercial production
+    range: ProcessScaleEnum
+  bioreactor_type:
+    description: Types of bioreactors used in fermentation and cell culture
+    range: BioreactorTypeEnum
+  fermentation_mode:
+    description: Modes of fermentation operation
+    range: FermentationModeEnum
+  oxygenation_strategy:
+    description: Oxygen supply strategies for fermentation
+    range: OxygenationStrategyEnum
+  agitation_type:
+    description: Types of agitation/mixing in bioreactors
+    range: AgitationTypeEnum
+  downstream_process:
+    description: Downstream processing unit operations
+    range: DownstreamProcessEnum
+  feedstock_type:
+    description: Types of feedstocks for bioprocessing
+    range: FeedstockTypeEnum
+  product_type:
+    description: Types of products from bioprocessing
+    range: ProductTypeEnum
+  sterilization_method:
+    description: Methods for sterilization in bioprocessing
+    range: SterilizationMethodEnum
+enums:
+  ProcessScaleEnum:
+    description: Scale of bioprocessing operations from lab bench to commercial production
+    permissible_values:
+      BENCH_SCALE:
+        description: Laboratory bench scale (typically < 10 L)
+        annotations:
+          volume_range: 0.1-10 L
+          typical_volume: 1-5 L
+          purpose: Initial development and screening
+      PILOT_SCALE:
+        description: Pilot plant scale (10-1000 L)
+        annotations:
+          volume_range: 10-1000 L
+          typical_volume: 50-500 L
+          purpose: Process development and optimization
+      DEMONSTRATION_SCALE:
+        description: Demonstration scale (1000-10000 L)
+        annotations:
+          volume_range: 1000-10000 L
+          typical_volume: 2000-5000 L
+          purpose: Technology demonstration and validation
+      PRODUCTION_SCALE:
+        description: Commercial production scale (>10000 L)
+        related_mappings:
+        - NCIT:C112927
+        annotations:
+          volume_range: '>10000 L'
+          typical_volume: 20000-200000 L
+          purpose: Commercial manufacturing
+      MICROFLUIDIC_SCALE:
+        description: Microfluidic scale (<1 mL)
+        related_mappings:
+        - mesh:D044085
+        annotations:
+          volume_range: <1 mL
+          typical_volume: 1-1000 μL
+          purpose: High-throughput screening
+  BioreactorTypeEnum:
+    description: Types of bioreactors used in fermentation and cell culture
+    permissible_values:
+      STIRRED_TANK:
+        description: Stirred tank reactor (STR/CSTR)
+        related_mappings:
+        - OBI:0001046
+        annotations:
+          mixing: Mechanical agitation
+          common_volumes: 1-200000 L
+      AIRLIFT:
+        description: Airlift bioreactor
+        related_mappings:
+        - ENVO:00002125
+        - OBI:0001046
+        annotations:
+          mixing: Gas sparging
+          advantages: Low shear, no mechanical parts
+      BUBBLE_COLUMN:
+        description: Bubble column bioreactor
+        related_mappings:
+        - OBI:0001046
+        annotations:
+          mixing: Gas bubbling
+          advantages: Simple design, good mass transfer
+      PACKED_BED:
+        description: Packed bed bioreactor
+        annotations:
+          configuration: Fixed bed of immobilized cells/enzymes
+          flow: Continuous
+      FLUIDIZED_BED:
+        description: Fluidized bed bioreactor
+        annotations:
+          configuration: Suspended solid particles
+          mixing: Fluid flow
+      MEMBRANE:
+        title: membrane bioreactor
+        description: Membrane bioreactor
+        meaning: ENVO:03600010
+        annotations:
+          feature: Integrated membrane separation
+          application: Cell retention, product separation
+      WAVE_BAG:
+        description: Wave/rocking bioreactor
+        annotations:
+          mixing: Rocking motion
+          advantages: Single-use, low shear
+      HOLLOW_FIBER:
+        description: Hollow fiber bioreactor
+        annotations:
+          configuration: Hollow fiber membranes
+          application: High-density cell culture
+      PHOTOBIOREACTOR:
+        description: Photobioreactor for photosynthetic organisms
+        annotations:
+          light_source: Required
+          organisms: Algae, cyanobacteria
+  FermentationModeEnum:
+    description: Modes of fermentation operation
+    permissible_values:
+      BATCH:
+        title: batch cell culture
+        description: Batch fermentation
+        meaning: MSIO:0000181
+        annotations:
+          operation: All nutrients added at start
+          duration: Fixed time period
+      FED_BATCH:
+        description: Fed-batch fermentation
+        related_mappings:
+        - MSIO:0000165
+        - MSIO:0000166
+        annotations:
+          operation: Nutrients added during run
+          advantage: Control of growth rate
+      CONTINUOUS:
+        title: continuous fermentation cell culture
+        description: Continuous fermentation (chemostat)
+        meaning: MSIO:0000155
+        annotations:
+          operation: Continuous feed and harvest
+          steady_state: true
+      PERFUSION:
+        description: Perfusion culture
+        annotations:
+          operation: Continuous media exchange with cell retention
+          application: High-density cell culture
+      REPEATED_BATCH:
+        description: Repeated batch fermentation
+        annotations:
+          operation: Sequential batches with partial harvest
+          advantage: Reduced downtime
+      SEMI_CONTINUOUS:
+        description: Semi-continuous operation
+        annotations:
+          operation: Periodic harvest and refill
+          advantage: Extended production
+  OxygenationStrategyEnum:
+    description: Oxygen supply strategies for fermentation
+    permissible_values:
+      AEROBIC:
+        description: Aerobic with active aeration
+        related_mappings:
+        - ENVO:00002126
+        annotations:
+          oxygen: Required
+          typical_DO: 20-80% saturation
+      ANAEROBIC:
+        description: Anaerobic (no oxygen)
+        related_mappings:
+        - ENVO:00002124
+        annotations:
+          oxygen: Excluded
+          atmosphere: N2 or CO2
+      MICROAEROBIC:
+        description: Microaerobic (limited oxygen)
+        annotations:
+          oxygen: Limited
+          typical_DO: <5% saturation
+      FACULTATIVE:
+        description: Facultative (with/without oxygen)
+        annotations:
+          oxygen: Optional
+          flexibility: Organism-dependent
+  AgitationTypeEnum:
+    description: Types of agitation/mixing in bioreactors
+    permissible_values:
+      RUSHTON_TURBINE:
+        description: Rushton turbine impeller
+        annotations:
+          type: Radial flow
+          power_number: 5-6
+      PITCHED_BLADE:
+        description: Pitched blade turbine
+        annotations:
+          type: Axial flow
+          angle: 45 degrees
+      MARINE_PROPELLER:
+        description: Marine propeller
+        annotations:
+          type: Axial flow
+          low_shear: true
+      ANCHOR:
+        description: Anchor impeller
+        annotations:
+          type: Close clearance
+          viscous_fluids: true
+      HELICAL_RIBBON:
+        description: Helical ribbon impeller
+        annotations:
+          type: Close clearance
+          high_viscosity: true
+      MAGNETIC_BAR:
+        description: Magnetic stir bar
+        annotations:
+          scale: Laboratory
+          volume: <5 L
+      ORBITAL_SHAKING:
+        description: Orbital shaking
+        annotations:
+          type: Platform shaker
+          application: Shake flasks
+      NO_AGITATION:
+        description: No mechanical agitation
+        annotations:
+          mixing: Gas sparging or static
+  DownstreamProcessEnum:
+    description: Downstream processing unit operations
+    permissible_values:
+      CENTRIFUGATION:
+        title: analytical centrifugation
+        description: Centrifugal separation
+        meaning: CHMO:0002010
+        annotations:
+          principle: Density difference
+          types: Disk stack, tubular, decanter
+      FILTRATION:
+        description: Filtration (micro/ultra/nano)
+        meaning: CHMO:0001640
+        annotations:
+          types: Dead-end, crossflow, depth
+      CHROMATOGRAPHY:
+        description: Chromatographic separation
+        meaning: CHMO:0001000
+        annotations:
+          types: Ion exchange, affinity, size exclusion
+      EXTRACTION:
+        description: Liquid-liquid extraction
+        meaning: CHMO:0001577
+        annotations:
+          principle: Partitioning between phases
+      PRECIPITATION:
+        description: Precipitation/crystallization
+        meaning: CHMO:0001688
+        annotations:
+          agents: Salts, solvents, pH
+      EVAPORATION:
+        description: Evaporation/concentration
+        meaning: CHMO:0001574
+        annotations:
+          types: Falling film, MVR, TVR
+      DISTILLATION:
+        description: Distillation
+        meaning: CHMO:0001534
+        title: continuous distillation
+        annotations:
+          principle: Boiling point difference
+      DRYING:
+        description: Drying operations
+        meaning: CHMO:0001551
+        title: direct drying
+        annotations:
+          types: Spray, freeze, vacuum
+      HOMOGENIZATION:
+        description: Cell disruption/homogenization
+        annotations:
+          methods: High pressure, bead mill
+  FeedstockTypeEnum:
+    description: Types of feedstocks for bioprocessing
+    permissible_values:
+      GLUCOSE:
+        description: Glucose/dextrose
+        meaning: CHEBI:17234
+        annotations:
+          source: Corn, sugarcane
+          carbon_source: true
+      SUCROSE:
+        description: Sucrose
+        meaning: CHEBI:17992
+        annotations:
+          source: Sugarcane, sugar beet
+          carbon_source: true
+      GLYCEROL:
+        description: Glycerol
+        meaning: CHEBI:17754
+        annotations:
+          source: Biodiesel byproduct
+          carbon_source: true
+      MOLASSES:
+        description: Molasses
+        meaning: CHEBI:83163
+        annotations:
+          source: Sugar processing byproduct
+          complex_medium: true
+      CORN_STEEP_LIQUOR:
+        description: Corn steep liquor
+        annotations:
+          source: Corn wet milling
+          nitrogen_source: true
+      YEAST_EXTRACT:
+        description: Yeast extract
+        meaning: FOODON:03315426
+        annotations:
+          source: Autolyzed yeast
+          complex_nutrient: true
+      LIGNOCELLULOSIC:
+        description: Lignocellulosic biomass
+        annotations:
+          source: Agricultural residues, wood
+          pretreatment: Required
+      METHANOL:
+        description: Methanol
+        meaning: CHEBI:17790
+        annotations:
+          carbon_source: true
+          methylotrophic: true
+      WASTE_STREAM:
+        description: Industrial waste stream
+        annotations:
+          variable_composition: true
+          sustainability: Circular economy
+  ProductTypeEnum:
+    description: Types of products from bioprocessing
+    permissible_values:
+      BIOFUEL:
+        title: fuel
+        description: Biofuel (ethanol, biodiesel, etc.)
+        meaning: CHEBI:33292
+        annotations:
+          category: Energy
+      PROTEIN:
+        description: Recombinant protein
+        meaning: NCIT:C17021
+        annotations:
+          category: Biopharmaceutical
+      ENZYME:
+        description: Industrial enzyme
+        meaning: NCIT:C16554
+        annotations:
+          category: Biocatalyst
+      ORGANIC_ACID:
+        description: Organic acid (citric, lactic, etc.)
+        meaning: CHEBI:64709
+        annotations:
+          category: Chemical
+      AMINO_ACID:
+        description: Amino acid
+        meaning: CHEBI:33709
+        annotations:
+          category: Nutritional
+      ANTIBIOTIC:
+        description: Antibiotic
+        meaning: CHEBI:33281
+        title: antimicrobial agent
+        annotations:
+          category: Pharmaceutical
+      VITAMIN:
+        description: Vitamin
+        meaning: CHEBI:33229
+        title: vitamin (role)
+        annotations:
+          category: Nutritional
+      BIOPOLYMER:
+        description: Biopolymer (PHA, PLA, etc.)
+        meaning: CHEBI:33694
+        title: biomacromolecule
+        annotations:
+          category: Material
+      BIOMASS:
+        description: Microbial biomass
+        meaning: ENVO:01000155
+        title: organic material
+        annotations:
+          category: Feed/food
+      SECONDARY_METABOLITE:
+        description: Secondary metabolite
+        meaning: CHEBI:25212
+        title: metabolite
+        annotations:
+          category: Specialty chemical
+  SterilizationMethodEnum:
+    description: Methods for sterilization in bioprocessing
+    permissible_values:
+      STEAM_IN_PLACE:
+        description: Steam in place (SIP)
+        annotations:
+          temperature: 121-134°C
+          time: 15-30 min
+      AUTOCLAVE:
+        title: autoclaving
+        description: Autoclave sterilization
+        meaning: CHMO:0002846
+        annotations:
+          temperature: 121°C
+          pressure: 15 psi
+      FILTER_STERILIZATION:
+        description: Filter sterilization (0.2 μm)
+        annotations:
+          pore_size: 0.2 μm
+          heat_labile: true
+      GAMMA_IRRADIATION:
+        description: Gamma irradiation
+        annotations:
+          dose: 25-40 kGy
+          single_use: true
+      ETHYLENE_OXIDE:
+        description: Ethylene oxide sterilization
+        annotations:
+          temperature: 30-60°C
+          plastic_compatible: true
+      UV_STERILIZATION:
+        description: UV sterilization
+        annotations:
+          wavelength: 254 nm
+          surface_only: true
+      CHEMICAL_STERILIZATION:
+        description: Chemical sterilization
+        annotations:
+          agents: Bleach, alcohol, peroxide
+          contact_time: Variable