NIIMBL Equipment Ontology
type: Ontology
label: Biopharma Equipment Ontology
abstract: This module contains terms and relations enabling representation of equipment types, properties (qualities, capabilities, and functions), equipment specifications and validation (e.g., methods, testing, reporting, etc.).
contributor: Adlane Rebai, Millipore Sigma
contributor: Ana Nikolov, OAGi
contributor: Boonserm Kulvatunyou, NIST
contributor: Cameron Gibbs, CrownPoint Technologies, LLC
contributor: Gabriela Henning, NIST
contributor: Jan Kemper, AstraZeneca
contributor: Marie-Aude Coutouly, Millipore Sigma
contributor: Melissa Weller, CrownPoint Technologies, LLC
contributor: Milos Drobnjakovic, OAGi
contributor: Stephen J. Granite, CrownPoint Technologies, LLC
contributor: Stephen Kahmann, CrownPoint Technologies, LLC
creator: NIIMBL BD-1 Ontology Group
license: http://opensource.org/licenses/MIT
imports: BiopharmaReferenceOntologyAttributes
imports: ReferenceOntologyCandidates
imports: Core
version IRI: BiopharmaEquipment
copyright: Copyright (c) 2022, 2023, 2024, 2025, 2026 Open Applications Group
maturity: Released

adherent cell culture holding capability
type: Class
subclass of: cell culture holding capability
example: Capability of a T-flask to contain adherent mammalian cells attached to its culture surface during incubation; Capability of a cell culture dish to contain adherent cells during expansion; Capability of a multilayer cell culture vessel to contain adherent cells and medium during scale-up; Capability of a microplate well to contain adherent cells during a cell-based assay.
first order logic axiom: AdherentCellCultureHoldingCapability(x) → CellCultureHoldingCapability(x)
is primitive: true
natural language definition: cell culture holding capability to contain an adherent cell culture during a cell cultivation process
primitive rationale: See the rationale under cell culture holding capability
semi formal natural language axiom: if x is an 'adherent cell culture holding capability' then x is a 'cell culture holding capability'

adherent cell culture holding function
type: Class
subclass of: adherent cell culture holding capability
equivalent class: Class
  intersection of: adherent cell culture holding capability
  intersection of: Restriction
    on property: functionOf
    some values from: BFO_0000040
example: the adherent cell culture holding function of a T-flask to contain cells attached to its culture surface; the adherent cell culture holding function of a multilayer cell-culture vessel to contain adherent cells and culture medium during scale-up; the adherent cell culture holding function of a fixed-bed bioreactor vessel to contain cells attached to its internal culture-support structure
first order logic definition: AdherentCellCultureHoldingFunction(x) ↔ AdherentCellCultureHoldingCapability(x) ∧ ∃m(MaterialEntity(m) ∧ functionOf(x,m))
natural language definition: adherent cell culture holding capability that is a function of a material entity
semi formal natural language definition: every instance of 'adherent cell culture holding function' is exactly an instance of 'adherent cell culture holding capability' that is the 'function of' some 'material entity'

aeration capability
type: Class
subclass of: gas transfer capability
example: the aeration capability of a bioreactor sparger to introduce air into a mammalian cell culture; the aeration capability of a microsparger to introduce oxygen-enriched gas into a production culture; the aeration capability of an overlay-gas assembly to introduce air into a vessel headspace
first order logic axiom: AerationCapability(x) → GasTransferCapability(x)
is primitive: true
natural language definition: gas transfer capability to enable introduction of oxygen-containing gas to a material entity or site
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is an 'aeration capability' then x is a 'gas transfer capability'

affinity chromatography medium
type: Class
subclass of: chromatography medium
contributor: Merck KGaA
example: Protein A Resin typically used for IgG capture; Con A Sepharose resin used for mannosylated and glucosylated glycoproteins; IMAC resins for capturing proteins with a his-tag as their part; Streptavidin agarose used for capturing biotinylated proteins or nucleic acids
adapted from: http://wolfson.huji.ac.il/purification/PDF/affinity/GE_Affinity_Chromatography_Handbook-Antibodies.pdf
explanatory note: In chromatography, functional groups refer broadly to chemical moieties attached to the stationary phase that provide general interaction types with entities transported by the mobile phase, such as ionic or hydrophobic interactions. Ligands are a specialized subset of functional groups, typically larger and more complex molecules covalently attached to the medium to enable highly selective and specific binding to target molecules through molecular recognition. In affinity chromatography, ligands are used rather than general functional groups to emphasize this specificity, reflecting the medium’s design for selective capture of particular biomolecules.
first order logic axiom: AffinityChromatographyMedium(x) → ChromatographyMedium(x)
is primitive: true
natural language definition: chromatography medium which has an immobilized ligand as its part which has reversible binding capability to a specific part of a biomolecule
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is an 'affinity chromatography medium' then x is a 'chromatography medium'

agitation rate controlling capability
type: Class
subclass of: control capability
example: the agitation rate controlling capability of a stirred-tank bioreactor control system to maintain a specified impeller agitation rate; the agitation rate controlling capability of a microbial fermenter control system to change agitation rate as part of a dissolved oxygen control cascade; the agitation rate controlling capability of an incubator shaker to maintain a specified orbital shaking rate
first order logic axiom: AgitationRateControllingCapability(x) → ControlCapability(x)
is primitive: true
natural language definition: control capability to carry out control of agitation rate
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is an 'agitation rate controlling capability' then x is a 'control capability'

analytical chromatography system
type: Class
subclass of: chromatography system
contributor: Merck KGaA
alternative label: analytic chromatographic system
example: Gas chromatography-mass spectrometry (GC-MS) system; High-performance liquid chromatography (HPLC) system with UV detection; Ultra-Performance Liquid Chromatography (UPLC) system
adapted from: https://www.emdmillipore.com/US/en/products/analytics-sample-prep/chromatography-for-analysis/4aOb.qB.GMkAAAE_NeF3.Lxi,nav
first order logic axiom: AnalyticalChromatographySystem(x) → ChromatographySystem(x)
is primitive: true
natural language definition: chromatography system designed to be used in chromatography processes with the primary objective of identifying or quantifying chemical or biological substances
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is an 'analytical chromatography system' then x is a 'chromatography system'

anion exchange chromatography medium
type: Class
subclass of: chromatography medium
contributor: Merck KGaA
example: DEAE-Sepharose; Q Sepharose
adapted from: http://wolfson.huji.ac.il/purification/PDF/affinity/GE_Affinity_Chromatography_Handbook-Antibodies.pdf
explanatory note: positively charged molecules that are chemically bound to the matrix serve as functional groups as they provide the material basis of the resin function
first order logic axiom: AnionExchangeChromatographyMedium(x) → ChromatographyMedium(x)
is primitive: true
natural language definition: chromatography medium consisting of a matrix and positively charged molecules that are chemically bound to it
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is an 'anion exchange chromatography medium' then x is a 'chromatography medium'

aseptic barrier capability
type: Class
subclass of: Capability
subclass of: Restriction
  on property: capabilityOf
  some values from: Class
    union of: EngineeredSystem
    union of: MaterialArtifact
example: the aseptic barrier capability of a sterile connector; the aseptic barrier capability of a sealed single-use bioprocess bag; the aseptic barrier capability of an isolator enclosure; the aseptic barrier capability of a vial septum
adapted from: https://www.sciencedirect.com/science/chapter/bookseries/abs/pii/S0065216408705926
first order logic axiom: AsepticBarrierCapability(x) → Capability(x) ∧ ∃b((MaterialArtifact(b) ∨ EngineeredSystem(b)) ∧ capabilityOf(x,b))
is primitive: true
natural language definition: capability of a material artifact or engineered system to prevent or limit transfer of contaminating material across a physical boundary separating protected material from potential contamination sources
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is an 'aseptic barrier capability' then x is a 'capability' that is the 'capability of' a 'material artifact' or an 'engineered system'

bioproduction environment capability
type: Class
subclass of: cultivation environment capability
example: the bioproduction environment capability of a production bioreactor to maintain conditions for monoclonal-antibody production by a CHO cell culture; the bioproduction environment capability of a perfusion bioreactor to maintain conditions for high-density recombinant-protein production
first order logic axiom: BioproductionEnvironmentCapability(x) → CultivationEnvironmentCapability(x)
is primitive: true
natural language definition: cultivation environment capability to provide a controlled environment in which biological entities generate, or are expanded as, a material product or process intermediate
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'bioproduction environment capability' then x is a 'cultivation environment capability'

bioreactor
type: Class
subclass of: EngineeredSystem
equivalent class: Class
  intersection of: EngineeredSystem
  intersection of: Restriction
    on property: BFO_0000115
    some values from: bioreactor vessel
  intersection of: Restriction
    on property: hasFunction
    some values from: cultivation environment function
example: Stainless steel production bioreactor with integrated agitation and feed control; 2000 L single-use production bioreactor for monoclonal antibody manufacturing; Stirred-tank seed bioreactor with automated pH and DO control; single-use seed bioreactor for mammalian cell expansion; small-scale glass seed bioreactor with temperature regulation; perfusion seed bioreactor with cell retention system
adapted from: https://www.sciencedirect.com/topics/earth-and-planetary-sciences/bioreactor and https://www.sciencedirect.com/topics/immunology-and-microbiology/bioreactor and https://www.sciencedirect.com/topics/agricultural-and-biological-sciences/bioreactor
counter example: Empty stainless steel vessel without integrated agitation, control skid, or single-use bag system; refrigerated storage unit maintaining cell viability; Incubator designed to maintain temperature and CO₂ for cell culture without agitation, feeding, or waste removal functions; static cell culture flask lacking active environmental controls
first order logic definition: Bioreactor(x) ↔ EngineeredSystem(x) ∧ ∃b(BioreactorVessel(b) ∧ hasMemberPartAtSomeTime(x,b)) ∧ ∃f(CultivationEnvironmentFunction(f) ∧ hasFunction(x,f))
natural language definition: engineered system designed to provide a controlled environment for the cultivation of cells, tissues, or microorganisms, or for the production of material products or process intermediate materials by those biological entities
semi formal natural language definition: every instance of 'bioreactor' is defined as exactly an instance of 'engineered system' that 'has member part at some time' some 'bioreactor vessel' and 'has function' some 'cultivation environment function'

bioreactor vessel
type: Class
subclass of: Container
subclass of: Restriction
  on property: hasFunction
  some values from: cell culture holding function
example: A 200 L single-use polymer bioreactor vessel; A 2 L borosilicate glass bioreactor vessel with a stainless steel headplate
adapted from: https://www.cytivalifesciences.com/en/us/insights/single-use-or-stainless-steel-bioreactors and https://atlas-scientific.com/blog/how-to-set-up-a-bioreactor/#:~:text=The%20vessel%20is%20the%20main%20component%20of,and%20dissolved%20oxygen%20levels%20of%20the%20system.
explanatory note: The vessel is the primary containment unit of a bioreactor. It provides the physical space for cultivation (growth, maintenance, expansion) or production (of products or intermediates) while relying on integration with the bioreactor system for controlled conditions. Typical features include impellers, spargers, probes, and ports that allow interaction with system-level functions. Vessels may be constructed from stainless steel, glass, or single-use polymers depending on scale and application.
first order logic axiom: BioreactorVessel(x) → Container(x) ∧ ∃f (hasFunction(x, f) ∧ CellCultureHoldingFunction(f))
is primitive: true
natural language definition: container designed to contain material undergoing a cell cultivation process and to incorporate or interface with one or more components that provide mixing, aeration, monitoring, or control as part of a bioreactor
primitive rationale: There are insufficient constructs to create necessary and sufficient conditions, particularly for representing that a container is designed to incorporate or interface with components of a bioreactor during cell cultivation
semi formal natural language axiom: if x is a 'bioreactor vessel' then x is a 'container' that 'has function' some 'cell culture holding function'

cation exchange chromatography medium
type: Class
subclass of: chromatography medium
contributor: Merck KGaA
example: CM-Sepharose; SP-Sepharose
adapted from: http://wolfson.huji.ac.il/purification/PDF/affinity/GE_Affinity_Chromatography_Handbook-Antibodies.pdf
explanatory note: negatively charged molecules that are chemically bound to the matrix serve as functional groups as they provide the material basis of the resin function
first order logic axiom: CationExchangeChromatographyMedium(x) → ChromatographyMedium(x)
is primitive: true
natural language definition: chromatography medium consisting of a matrix and negatively charged molecules that are chemically bound to it
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'cation exchange chromatography medium' then x is a 'chromatography medium'

cell culture holding capability
type: Class
subclass of: MaterialContainmentCapability
example: Capability of a T-flask to contain an adherent mammalian cell culture during incubation; Capability of a shake flask to contain a microbial or mammalian suspension culture during shaking cultivation; Capability of a spinner flask to contain a suspension cell culture during stirred cultivation; Capability of a cell culture bag to contain cells and medium during expansion; Capability of a bioreactor vessel to contain a cell culture during a controlled cultivation process;
explanatory note: 1) This capability is specific to containing material while that material undergoes a cell cultivation process, rather than holding material in general. The cultivated material may include suspension or adherent cultures, microbial cultures, cell aggregates, tissues or other multicellular structures, culture-support materials, and culture medium. 2) The capability applies to vessels and vessel-like artifacts such as T-flasks, shake flasks, spinner flasks, culture bags, microplate wells, and bioreactor vessels. 3) It does not by itself imply temperature control, carbon-dioxide control, humidity control, agitation, aeration, sterility, or aseptic operation; those should be represented by separate capabilities where needed.
first order logic axiom: CellCultureHoldingCapability(x) → MaterialContainmentCapability(x)
is primitive: true
natural language definition: material containment capability to contain material undergoing a cell cultivation process
primitive rationale: The formalization of this term requires the processes that are in the manufacturing execution and material module
semi formal natural language axiom: if x is a 'cell culture holding capability' then x is a 'material containment capability'

cell culture holding function
type: Class
subclass of: cell culture holding capability
equivalent class: Class
  intersection of: cell culture holding capability
  intersection of: Restriction
    on property: functionOf
    some values from: BFO_0000040
example: the cell culture holding function of a T-flask to contain material undergoing adherent-cell cultivation; the cell culture holding function of a single-use bioprocess bag to contain material undergoing cell cultivation; the cell culture holding function of a bioreactor vessel to contain cultivated material during a controlled cultivation process
first order logic definition: CellCultureHoldingFunction(x) ↔ CellCultureHoldingCapability(x) ∧ ∃m(MaterialEntity(m) ∧ functionOf(x,m))
natural language definition: cell culture holding capability that is a function of a material entity
semi formal natural language definition: every instance of 'cell culture holding function' is exactly an instance of 'cell culture holding capability' that is the 'function of' some 'material entity'

centrifuge
type: Class
subclass of: EngineeredSystem
example: a benchtop centrifuge used to pellet cells from a suspension; a refrigerated floor centrifuge used to separate biomass from culture supernatant; a disc-stack centrifuge used for continuous separation of cells from cell-culture harvest; a microcentrifuge used to separate precipitated material from a liquid sample
adapted from: http://purl.obolibrary.org/obo/OBI_0400106 and https://goldbook.iupac.org/terms/view/C00933 and https://tsapps.nist.gov/publication/get_pdf.cfm?pub_id=936588
first order logic axiom: Centrifuge(x) → EngineeredSystem(x)
is primitive: true
natural language definition: engineered system designed to separate materials by subjecting them to centrifugal acceleration generated by rotation
primitive rationale: There are insufficient constructs to create a set of necessary and sufficient conditions
semi formal natural language axiom: if x is a 'centrifuge' then x is an 'engineered system'

chromatography column
type: Class
subclass of: MaterialArtifact
disjoint with: chromatography medium
example: Analytical stainless steel chromatography column; preparative glass chromatography column; high-pressure liquid chromatography (HPLC) column with silica resin; ion-exchange chromatography column with polymer resin; size-exclusion chromatography column with agarose-based resin;
adapted from: http://purl.allotrope.org/ontologies/equipment#AFE_0000217 and http://purl.obolibrary.org/obo/OBI_0000038
explanatory note: Columns vary in size and material depending on the application, such as analytical or preparative chromatography, and are selected based on factors like pressure tolerance, chemical compatibility, and flow dynamics.
first order logic axiom: ChromatographyColumn(x) → MaterialArtifact(x)
is primitive: true
natural language definition: material artifact that is a tube or a cylinder designed to house chromatography medium as the stationary phase during one or more chromatography processes
primitive rationale: There are currently insufficient constructs to adequately model the shape of a tube or a cylinder
semi formal natural language axiom: if x is a 'chromatography column' then x is a 'material artifact'

chromatography medium
type: Class
subclass of: BFO_0000040
example: affinity chromatography medium; size exclusion chromatography medium; anion exchange medium
explanatory note: 1) This material is typically engineered to enable separation based on physicochemical properties such as charge, size, hydrophobicity, or specific affinity. It functions by interacting with analytes in a mobile phase as they pass through or across the matrix. The material may be functionalized with ligands or surface groups to enhance selectivity and is commonly packed into columns or cartridges used in chromatographic systems. 2) Chromatography media can take various physical forms including resins, monoliths, and membranes. Resins typically consist of spherical or irregularly shaped porous beads that serve as the stationary phase. Monoliths are continuous, single-piece porous structures that allow high flow rates and low backpressure. Membranes are thin, porous films that enable selective retention based on size or chemical affinity, often used for rapid separations. All serve as porous matrices designed to selectively and reversibly retain target molecules during chromatography processes. 3) This definition reflects the canonical design of chromatography media, which are typically engineered to support selective and reversible interactions with molecular species, enabling separation, recovery, or analysis. In certain use cases, such as affinity depletion workflows, the chromatography medium may be operated in a process mode where bound targets are not eluted and are instead discarded with the medium. In such cases, the binding appears irreversible not because of a limitation in the medium’s capability, but because the process is intentionally run without an elution step. The underlying binding interactions remain chemically reversible and could be reversed under appropriate conditions.
first order logic axiom: ChromatographyMedium(x) → MaterialEntity(x)
is primitive: true
natural language definition: material entity designed to selectively and reversibly retain different molecules during one or more chromatography processes
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'chromatography medium' then x is a 'material entity'

chromatography system
type: Class
subclass of: EngineeredSystem
contributor: Merck KGaA
disjoint with: incubator
equivalent class: Class
  intersection of: EngineeredSystem
  intersection of: Restriction
    on property: BFO_0000115
    some values from: stationary phase
  intersection of: Restriction
    on property: hasCapability
    some values from: MeasurementCapability
  intersection of: Restriction
    on property: hasFunction
    some values from: flow rate controlling function
example: AKTA FPLC Chromatography systems such as AKTA pure and AKTAprime plus; Agilent Gas Chromatography System; Vanquish HPLC and UHPLC Systems
adapted from: http://wolfson.huji.ac.il/purification/PDF/affinity/GE_Affinity_Chromatography_Handbook-Antibodies.pdf https://www.cytivalifesciences.com/en/us/shop/chromatography/chromatography-systems?sort=NameAsc&chunk=1 and https://biocev.lf1.cuni.cz/file/282/protein-purification-handbook.pdf
explanatory note: 1) Chromatography systems typically include hardware for sample introduction, flow control, and detection, as well as software interfaces for configuring, monitoring, and automating purification processes across research, clinical, and manufacturing scales. Monitoring may include pH, conductivity, pressure, temperature, or other relevant parameters associated with the separation process. 2) Chromatography systems are available as single-use or multi-use models to accommodate different operational requirements and separation needs across laboratory, clinical, and manufacturing scales. 3) The phrase “house or interface with the stationary phase” refers to the system's ability either to physically contain the stationary phase directly (e.g., in built-in columns or integrated cartridges) or to connect to and operate with external components that contain the stationary phase, such as detachable chromatography columns. This accommodates both fully integrated and modular system designs, ensuring that the stationary phase is part of the fluid path during the chromatography process
first order logic definition: ChromatographySystem(x) ↔ EngineeredSystem(x) ∧ ∃s(StationaryPhase(s) ∧ hasMemberPartAtSomeTime(x, s)) ∧ ∃c(MeasurementCapability(c) ∧ hasCapability(x, c)) ∧ ∃f(FlowRateControllingFunction(f) ∧ hasFunction(x, f))
natural language definition: engineered system designed to control the fluid flow of the mobile phase, provide monitoring or detection capabilities, and house or interface with the stationary phase for one or more chromatography processes
semi formal natural language definition: every instance of 'chromatography system' is defined as exactly an instance of 'engineered system' that 'has member part at some time' some 'stationary phase', 'has capability' some 'measurement capability', and 'has function' some 'flow rate controlling function'

control capability
type: Class
subclass of: Capability
subclass of: Restriction
  on property: BFO_0000054
  all values from: PlannedProcess
subclass of: Restriction
  on property: capabilityOf
  some values from: Class
    union of: Agent
    union of: EngineeredSystem
    union of: MaterialArtifact
example: the control capability of a bioreactor control system to carry out pH control during a production culture; the control capability of a mass-flow controller to carry out gas-flow control during aeration;
first order logic axiom: ControlCapability(x) → Capability(x) ∧ ∃b((MaterialArtifact(b) ∨ Agent(b) ∨ EngineeredSystem(b)) ∧ capabilityOf(x,b)) ∧ ∀p(hasRealization(x,p) → PlannedProcess(p))
is primitive: true
natural language definition: capability of a material artifact, agent, or engineered system to carry out control during a planned process
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'control capability' then x is a 'capability' that is the 'capability of' some entity that is a 'material artifact', an 'agent', or an 'engineered system', and whenever some p 'realizes' x, p is a 'planned process'

cryovial
type: Class
subclass of: vial
example: A 2 mL polypropylene cryovial with an O-ring screw cap designed for storing samples in vapor-phase liquid nitrogen.
adapted from: https://www.fishersci.com/us/en/browse/90168052/cryogenic-storage-vials
explanatory note: Cryovials are specialized small, sealable containers typically made of plastics (e.g., polypropylene) or glass designed to withstand liquid nitrogen or −80 °C conditions without compromising material integrity. They are commonly used in biomanufacturing and research to preserve cells, tissues, nucleic acids, or proteins.
first order logic axiom: Cryovial(x) → Vial(x)
is primitive: true
natural language definition: vial designed for storage of material at ultra-low temperatures
primitive rationale: There are insufficient constructs present to create a set of necessary and sufficient conditions. In particular the required capabilities and functions are missing.
semi formal natural language axiom: if x is a 'cryovial' then x is a 'vial'

cultivation environment capability
type: Class
subclass of: Capability
subclass of: Restriction
  on property: BFO_0000054
  all values from: PlannedProcess
subclass of: Restriction
  on property: capabilityOf
  some values from: EngineeredSystem
example: the cultivation environment capability of a CO₂ incubator to maintain temperature, carbon-dioxide concentration, and humidity for adherent mammalian-cell culture; the cultivation environment capability of a seed bioreactor to maintain temperature, pH, dissolved oxygen, mixing, and nutrient supply during cell expansion;
first order logic axiom: CultivationEnvironmentCapability(x) → Capability(x) ∧ ∃z(EngineeredSystem(z) ∧ capabilityOf(x, z)) ∧ ∀y(hasRealization(x, y) → PlannedProcess(y))
is primitive: true
natural language definition: capability of an engineered system to provide a controlled environment suitable for the growth or maintenance of cells, tissues, or microorganisms, or for the production of material products or process intermediates by those entities
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'cultivation environment capability' then x is a 'capability' that is the 'capability of' some 'engineered system' and whenever some y 'realizes' x that y must be a 'planned process'

cultivation environment function
type: Class
subclass of: cultivation environment capability
equivalent class: Class
  intersection of: cultivation environment capability
  intersection of: Restriction
    on property: functionOf
    some values from: EngineeredSystem
example: the cultivation environment function of a CO₂ incubator to provide controlled temperature, carbon-dioxide concentration, and humidity for adherent mammalian-cell cultivation; the cultivation environment function of a seed bioreactor to provide suitable temperature, pH, dissolved oxygen, mixing, and nutrient supply during cell expansion
first order logic definition: CultivationEnvironmentFunction(x) ↔ CultivationEnvironmentCapability(x) ∧ ∃e(EngineeredSystem(e) ∧ functionOf(x,e))
natural language definition: cultivation environment capability that is a function of an engineered system
semi formal natural language definition: every instance of 'cultivation environment function' is exactly an instance of 'cultivation environment capability' that is the 'function of' some 'engineered system'

depth filter
type: Class
subclass of: filter
contributor: Merck KGaA
disjoint with: membrane filter
example: Cellulose-based depth filter; polypropylene depth filter; glass fiber depth filter; cellulose acetate depth filter; polyester depth filter; diatomaceous earth (DE) depth filter; mixed cellulose ester depth filter; cellulose nitrate depth filter
adapted from: https://www.cytivalifesciences.com/en/us/solutions/lab-filtration/knowledge-center/glossary/depth-filter and https://www.iso.org/obp/ui#iso:std:iso:3857:-4:ed-1:v1:en:term:2.25
explanatory note: Particles are entrapped or adsorbed both within and on the filter due to a randomly arranged matrix or structure that creates a tortuous flow path through the filter medium. This enables the retention of a broad range of particle sizes throughout the depth of the filter.
first order logic axiom: DepthFilter(x) → Filter(x)
is primitive: true
natural language definition: filter that does not rely on a uniform, defined pore size and that is designed to retain particles both on its surface and within its internal matrix
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'depth filter' then x is a 'filter'

dissolved oxygen controlling capability
type: Class
subclass of: control capability
example: the dissolved oxygen controlling capability of a stirred-tank bioreactor control system to control dissolved oxygen by adjusting agitation and gas flow; the dissolved oxygen controlling capability of a microbial fermenter control system to control dissolved oxygen by cascading air flow and oxygen enrichment
abbreviation: DO control capability
first order logic axiom: DissolvedOxygenControllingCapability(x) → ControlCapability(x)
is primitive: true
natural language definition: control capability to carry out control of dissolved oxygen concentration within a particular liquid
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'dissolved oxygen controlling capability' then x is a 'control capability'

exhaust gas removal capability
type: Class
subclass of: gas transfer capability
example: the exhaust gas removal capability of a bioreactor exhaust assembly to remove off-gas from the vessel headspace; the exhaust gas removal capability of a microbial fermenter exhaust line to remove process gas; the exhaust gas removal capability of an incubator exhaust assembly to remove chamber gas
first order logic axiom: ExhaustGasRemovalCapability(x) → GasTransferCapability(x)
is primitive: true
natural language definition: gas transfer capability to enable removal of gas from a material entity or site
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is an 'exhaust gas removal capability' then x is a 'gas transfer capability'

filter
type: Class
subclass of: MaterialArtifact
example: Polyvinylidene Fluoride (PVDF) membrane filter; Hollow-fiber Polyethersulfone (PES) membrane filter; Aramid/Nomex dust collector heat-resistant filter bag; Millistak+® HC Pro Pod Depth Filter
adapted from: https://www.sciencedirect.com/topics/engineering/filtration-process
explanatory note: 1) Retention is achieved either by deposition of suspended particles on the filter surface or by capture of particles in the porous medium 2) This definition uses "retain" to indicate the physical exclusion or capture of particles above a defined size. In the case of filters, this retention is achieved through structural exclusion or entrapment and is not reversible under normal operating conditions.
first order logic axiom: Filter(x) → MaterialArtifact(x)
is primitive: true
natural language definition: material artifact that is porous and designed to retain particles above a certain size threshold when a fluid is passed through it
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'filter' then x is a 'material artifact'

flask
type: Class
subclass of: Container
example: a 2 L baffled Erlenmeyer flask holding a CHO seed culture; a 250 mL spinner flask containing a suspension cell culture; a T75 tissue-culture flask containing adherent HEK293 cells
adapted from: http://purl.obolibrary.org/obo/PROCO_0000191
explanatory note: 1) Flasks are often made of glass or plastic. 2) They are commonly conical (e.g., Erlenmeyer flask) or spherical (e.g., round-bottom flask) in form. 3) Many flasks are designed to allow heating, cooling, or shaking during use.
first order logic axiom: Flask(x) → Container(x)
is primitive: true
natural language definition: container that has a body wider than its neck and is designed to contain material during a material transformation, separation, measurement, or cultivation process
primitive rationale: There are insufficient constructs present to create a set of necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'flask' then x is a 'container'

flow rate controlling capability
type: Class
subclass of: control capability
example: capability to control buffer flow rate during chromatography column equilibration; capability to adjust feed solution flow rate in a fed-batch fermentation process; capability to maintain consistent gas flow rate in a bioreactor sparging system; capability to modulate liquid flow rate in an ultrafiltration unit; capability to regulate mobile phase flow rate during chromatography column elution
counter example: capability to measure flow rate passively without adjusting it; capability to maintain structural integrity of a pipe during fluid transfer
first order logic axiom: FlowRateControllingCapability(x) → ControlCapability(x)
is primitive: true
natural language definition: control capability to carry out control of flow rate
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'flow rate controlling capability' then x is a 'control capability'

flow rate controlling function
type: Class
subclass of: flow rate controlling capability
equivalent class: Class
  intersection of: flow rate controlling capability
  intersection of: Restriction
    on property: functionOf
    some values from: Class
      union of: EngineeredSystem
      union of: MaterialArtifact
example: the flow rate controlling function of a chromatography system to control mobile-phase flow during column operation; the flow rate controlling function of a mass-flow controller to control gas flow into a bioreactor; the flow rate controlling function of a feed-pump system to control nutrient-feed flow during a fed-batch cultivation process
first order logic definition: FlowRateControllingFunction(x) ↔ FlowRateControllingCapability(x) ∧ ∃b((MaterialArtifact(b) ∨ EngineeredSystem(b)) ∧ functionOf(x,b))
natural language definition: flow rate controlling capability that is a function of a material artifact or engineered system
semi formal natural language definition: every instance of 'flow rate controlling function' is exactly an instance of 'flow rate controlling capability' that is the 'function of' some entity that is a 'material artifact' or an 'engineered system'

fluid transfer capability
type: Class
subclass of: material transfer capability
subclass of: Restriction
  on property: BFO_0000054
  all values from: Class
    intersection of: PlannedProcess
    intersection of: Restriction
      on property: BFO_0000057
      some values from: Class
        intersection of: BFO_0000040
        intersection of: Restriction
example: the fluid transfer capability of a peristaltic-pump assembly to transfer nutrient feed into a bioreactor; the fluid transfer capability of a gas-delivery assembly to supply oxygen to a bioreactor; the fluid transfer capability of a transfer skid to move cell-culture harvest to a hold vessel
first order logic axiom: FluidTransferCapability(x) → MaterialTransferCapability(x) ∧ ∀y(hasRealization(x,y) → (PlannedProcess(y) ∧ ∃m(MaterialEntity(m) ∧ hasParticipant(y,m) ∧ ∃q(FluidAggregateState(q) ∧ hasQuality(m,q)) ∧ ∃r(TransferredMaterialRole(r) ∧ hasRole(m,r)))))
is primitive: true
natural language definition: material transfer capability to enable movement of a fluid to or from a material entity or site
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'fluid transfer capability' then x is a 'material transfer capability' and whenever some y 'realizes' x then y is a 'planned process' that 'has participant' some 'material entity' that 'has quality' some 'fluid aggregate state' and 'has role' some 'transferred material role'

foam level controlling capability
type: Class
subclass of: control capability
example: the foam level controlling capability of a bioreactor control system to control foam through automated antifoam addition; the foam level controlling capability of a microbial fermenter equipped with a mechanical foam breaker; the foam level controlling capability of an operator to control foam by adjusting gas flow and antifoam addition
first order logic axiom: FoamLevelControllingCapability(x) → ControlCapability(x)
is primitive: true
natural language definition: control capability to carry out control of foam level
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'foam level controlling capability' then x is a 'control capability'

gas transfer capability
type: Class
subclass of: fluid transfer capability
subclass of: Restriction
  on property: BFO_0000054
  all values from: Class
    intersection of: PlannedProcess
    intersection of: Restriction
      on property: BFO_0000057
      some values from: Class
        intersection of: BFO_0000040
        intersection of: Restriction
example: the gas transfer capability of a gas-delivery assembly to supply air to a bioreactor; the gas transfer capability of a nitrogen-supply assembly to introduce nitrogen into a buffer-vessel headspace; the gas transfer capability of a bioreactor exhaust assembly to remove off-gas
first order logic axiom: GasTransferCapability(x) → FluidTransferCapability(x) ∧ ∀y(hasRealization(x,y) → (PlannedProcess(y) ∧ ∃m(MaterialEntity(m) ∧ hasParticipant(y,m) ∧ ∃q(GaseousAggregateState(q) ∧ hasQuality(m,q)) ∧ ∃r(TransferredMaterialRole(r) ∧ hasRole(m,r)))))
is primitive: true
natural language definition: fluid transfer capability to enable movement of a gas to or from a material entity or site
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'gas transfer capability' then x is a 'fluid transfer capability' and whenever some y 'realizes' x then y is a 'planned process' that 'has participant' some 'material entity' that 'has quality' some 'gaseous aggregate state' and 'has role' some 'transferred material role'

heat exchange capability
type: Class
subclass of: Capability
subclass of: Restriction
  on property: capabilityOf
  some values from: Class
    union of: EngineeredSystem
    union of: MaterialArtifact
example: the heat exchange capability of a jacketed bioreactor vessel; the heat exchange capability of a plate heat exchanger; the heat exchange capability of a water bath; the heat exchange capability of a single-use bioreactor heating blanket
first order logic axiom: HeatExchangeCapability(x) → Capability(x) ∧ ∃b((MaterialArtifact(b) ∨ EngineeredSystem(b)) ∧ capabilityOf(x,b))
is primitive: true
natural language definition: capability of a material artifact or engineered system to enable transfer of thermal energy between material entities
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'heat exchange capability' then x is a 'capability' that is the 'capability of' some 'material artifact' or an 'engineered system'

hydrophobic chromatography medium
type: Class
subclass of: chromatography medium
contributor: Merck KGaA
example: Butyl Sepharose used for Hydrophobic Interaction Chromatography; C18 Silica resin used for reversed-phase chromatography
explanatory note: In this case hydrophobic molecules that are chemically bound to the matrix serve as functional groups as they provide the material basis of the medium function
first order logic axiom: HydrophobicChromatographyMedium(x) → ChromatographyMedium(x)
is primitive: true
natural language definition: chromatography medium consisting of a matrix and hydrophobic molecules that are chemically bound to it
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'hydrophobic chromatography medium' then x is a 'chromatography medium'

incubator
type: Class
subclass of: EngineeredSystem
example: CO₂ incubator for mammalian cell culture. A stainless-steel laboratory incubator with HEPA filtration and automated humidity control, maintaining 37 °C and 5 percent CO₂, used for cultivating CHO cells in research and production.
adapted from: http://purl.obolibrary.org/obo/OBI_0000136 and https://en.wikipedia.org/wiki/Incubator_(culture) and https://documents.thermofisher.com/TFS-Assets/LED/manuals/7053110r9-EN-3100-Series-Water-Jacket.pdf
counter example: a shaking water bath used to heat and mix samples in tubes, because it does not provide the enclosed and regulated chamber environment characteristic of an incubator; a bioreactor, because it provides controlled conditions directly for material within its integrated bioreactor vessel rather than maintaining a chamber environment around separately placed vessels
explanatory note: 1) Incubators may regulate environmental parameters such as temperature, humidity, CO₂, oxygen, or light conditions, depending on their design. 2) In cultivation or storage contexts, incubators provide environmental control around material entities placed inside the chamber, such as flasks, plates, bags, tubes, vials, or the materials contained in them. 3) An incubator should be distinguished from the vessel or other artifact that directly holds the material. For example, a T-flask contains the cell culture, while the incubator maintains the surrounding controlled chamber environment. 4) Incubators differ from bioreactors in how the controlled cultivation environment is provided. An incubator controls the surrounding chamber environment for vessels or other material entities placed inside it. A bioreactor controls process conditions for the culture within the bioreactor vessel, for example through agitation, aeration, pH control, dissolved oxygen control, or temperature control.
first order logic axiom: Incubator(x) → EngineeredSystem(x)
is primitive: true
natural language definition: engineered system designed to maintain controlled environmental conditions within an enclosed chamber for material entities placed within that chamber
primitive rationale: There are insufficient constructs to create a set of necessary and sufficient conditions
semi formal natural language axiom: if x is an 'incubator' then x is an 'engineered system'

liquid transfer capability
type: Class
subclass of: fluid transfer capability
subclass of: Restriction
  on property: BFO_0000054
  all values from: Class
    intersection of: PlannedProcess
    intersection of: Restriction
      on property: BFO_0000057
      some values from: Class
        intersection of: BFO_0000040
        intersection of: Restriction
example: the liquid transfer capability of a peristaltic pump to transfer nutrient feed into a bioreactor; the liquid transfer capability of a transfer assembly to move cell-culture harvest into a hold bag; the liquid transfer capability of an operator using a pipette to transfer a liquid sample into an analytical vial
first order logic axiom: LiquidTransferCapability(x) → FluidTransferCapability(x) ∧ ∀y(hasRealization(x,y) → (PlannedProcess(y) ∧ ∃m(MaterialEntity(m) ∧ hasParticipant(y,m) ∧ ∃q(LiquidAggregateState(q) ∧ hasQuality(m,q)) ∧ ∃r(TransferredMaterialRole(r) ∧ hasRole(m,r)))))
is primitive: true
natural language definition: fluid transfer capability to enable movement of a liquid to or from a material entity or site
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'liquid transfer capability' then x is a 'fluid transfer capability' and whenever some y 'realizes' x then y is a 'planned process' that 'has participant' some 'material entity' that 'has quality' some 'liquid aggregate state' and 'has role' some 'transferred material role'

material transfer capability
type: Class
subclass of: Capability
subclass of: Restriction
  on property: BFO_0000054
  all values from: Class
    union of: MaterialAdditionProcess
    union of: MaterialRemovalProcess
    union of: MaterialTransferProcess
subclass of: Restriction
  on property: capabilityOf
  some values from: Class
    union of: Agent
    union of: EngineeredSystem
    union of: MaterialArtifact
example: the material transfer capability of an operator to charge weighed buffer salt into a mixing vessel; the material transfer capability of a peristaltic pump to transfer feed solution into a bioreactor; the material transfer capability of a gas-delivery system to supply oxygen to a bioreactor
first order logic axiom: MaterialTransferCapability(x) → Capability(x) ∧ ∃b((Agent(b) ∨ MaterialArtifact(b) ∨ EngineeredSystem(b)) ∧ capabilityOf(x,b) ∧ ∀p(hasRealization(x,p) → ((MaterialAdditionProcess(p) ∨ MaterialRemovalProcess(p) ∨ MaterialTransferProcess(p)) ∧ ∃m∃r(MaterialEntity(m) ∧ TransferredMaterialRole(r) ∧ hasParticipant(p,m) ∧ hasRole(m,r)) ∧ ∀n((MaterialEntity(n) ∧ hasParticipant(p,n) ∧ ∃s(TransferredMaterialRole(s) ∧ hasRole(n,s))) → n ≠ b))))
is primitive: true
natural language definition: capability of an agent, material artifact, or engineered system to enable movement of material distinct from the capability bearer to or from a material entity or site
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'material transfer capability' then x is a 'capability' that is the 'capability of' some entity b that is an 'agent', a 'material artifact', or an 'engineered system', and whenever some p 'realizes' x, p is a 'material addition process', a 'material removal process', or a 'material transfer process' that 'has participant' some 'material entity' that 'has role' some 'transferred material role', and every material entity that participates in p and has some 'transferred material role' is distinct from b

membrane filter
type: Class
subclass of: filter
example: Regenerated cellulose membrane filter; PES (Polyethersulfone) membrane filter; Amicon® Ultra Centrifugal Filter, 10 kDa MWCO
adapted from: https://link.springer.com/chapter/10.1007/978-1-4615-0549-5_5 and https://www.biopharminternational.com/view/advances-in-filtration-technology and https://www.iso.org/obp/ui#iso:std:iso:7704:ed-2:v1:en:term:3.1.1
counter example: Metal filters; Activated carbon sheets; Glass fibers
explanatory note: 1) Typical requirements of membrane filters used in the production of protein pharmaceuticals are (1) low adsorption of protein to the filter membrane, (2) high total liquid throughput, (3) minimum fouling of the filter, and (4) fulfillment of all applicable regulatory requirements. 2) These filters are used in biopharmaceutical manufacturing for purposes including bioburden control, virus retention, concentration, and buffer exchange. They are employed across multiple unit operations, including sterilizing filtration (e.g., 0.2-micron for aseptic processing), mycoplasma protection (e.g., 0.1-micron), and high-throughput buffer filtration, and may feature multi-layer or single-layer constructions to meet specific performance requirements such as flux and capacity 3) Examples of polymers used for membrane filters are surface-modified polyether sulfones
first order logic axiom: MembraneFilter(x) → Filter(x)
is primitive: true
natural language definition: filter consisting of one or more flat or pleated porous layers made from polymers, that has a defined pore size enabling the removal of particles from liquids by (physical exclusion) sieving or surface adsorption
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'membrane filter' then x is a 'filter'

mixed mode chromatography medium
type: Class
subclass of: chromatography medium
contributor: Merck KGaA
alternative label: multimodal chromatography medium
example: Hydroxyapatite (CHT/CFT/Bio-Gel HT/HTP) Resins that interact through electrostatic and calcium coordination complexes; Resins with hydrophobic ion exchange ligands
adapted from: http://wolfson.huji.ac.il/purification/PDF/HCIC/GE_MultimodalChromat.pdf and https://www.bio-rad.com/en-rs/applications-technologies/introduction-multimodal-or-mixed-mode-chromatography?ID=LUSN9AKG4
explanatory note: Different modes of interaction can occur between the chromatographic ligand and the target molecule depending on the experimental or operating conditions. These interactions may function cooperatively or independently. For example, in the case of mixed-mode pH-controllable sorbents, the ligand 4-mercaptoethylpyridine (MEP) exhibits condition-dependent binding behavior. At neutral and basic pH, the pyridine ring remains uncharged, enabling the ligand to act as a hydrophobic binding moiety. As the pH decreases, the nitrogen in the pyridine ring becomes protonated, introducing a positive charge and thereby enabling ionic interactions. This transformation renders the resin a mixed-mode medium. The dual functionality of MEP under different pH conditions exemplifies a chromatographic mode known as hydrophobic charge induction chromatography (HCIC), where hydrophobic binding at neutral pH transitions to charge-mediated elution at lower pH.
first order logic axiom: MixedModeChromatographyMedium(x) → ChromatographyMedium(x)
is primitive: true
natural language definition: chromatography medium with immobilized functional groups designed to selectively interact with molecules through multiple distinct interaction mechanisms
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'mixed mode chromatography medium' then x is a 'chromatography medium'

mixing capability
type: Class
subclass of: Capability
subclass of: Restriction
  on property: capabilityOf
  some values from: Class
    union of: EngineeredSystem
    union of: MaterialArtifact
example: Capability of an impeller to agitate cell culture contents in a stirred-tank bioreactor; Capability of a magnetic stir bar to agitate buffer in a flask; Capability of a rocking platform to agitate liquid in a single-use bag; Capability of a spinner flask stirrer to agitate a suspension cell culture during cultivation; Capability of a V-Blender that mixes ibuprofen powder with excipients; Capability of a ribbon blender that mixes wheat flour, baking powder, salt, and flavoring ingredients to produce pre-mixed baking flour
adapted from: http://purl.allotrope.org/ontologies/function#AFFN_0000119
first order logic axiom: MixingCapability(x) → Capability(x) ∧ ∃y (capabilityOf(x, y) ∧ (EngineeredSystem(y) ∨ MaterialArtifact(y)))
is primitive: true
natural language definition: capability of a material artifact or engineered system to combine or redistribute material contents to produce a more uniform material mixture or maintain its uniformity
primitive rationale: There are insufficient constructs to create a set of necessary and sufficient conditions
semi formal natural language axiom: if x is a 'mixing capability' then x is a 'capability' and x is a 'capability of' some 'engineered system' or 'material artifact'

mixing function
type: Class
subclass of: mixing capability
equivalent class: Class
  intersection of: mixing capability
  intersection of: Restriction
    on property: functionOf
    some values from: Class
      union of: EngineeredSystem
      union of: MaterialArtifact
example: the mixing function of a bioreactor impeller to redistribute cells and medium within a stirred-tank vessel; the mixing function of a rocking platform to redistribute material contents within a single-use bag; the mixing function of a magnetic stirrer to combine and redistribute buffer components within a preparation vessel
first order logic definition: MixingFunction(x) ↔ MixingCapability(x) ∧ ∃b((MaterialArtifact(b) ∨ EngineeredSystem(b)) ∧ functionOf(x,b))
natural language definition: mixing capability that is a function of a material artifact or engineered system
semi formal natural language definition: every instance of 'mixing function' is exactly an instance of 'mixing capability' that is the 'function of' some entity that is a 'material artifact' or an 'engineered system'

mobile phase
type: Class
subclass of: BFO_0000040
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: hasRole
    some values from: mobile phase role
example: Water as mobile phase in reverse-phase chromatography; acetonitrile used as mobile phase in HPLC; phosphate buffer as mobile phase in ion-exchange chromatography; methanol serving as mobile phase in normal-phase chromatography; a water-acetonitrile mixture serving as the mobile phase during gradient elution; sodium chloride solution as mobile phase in size-exclusion chromatography
adapted from: http://purl.allotrope.org/ontologies/role#AFRL_0000011 and GE Protein Purification Handbook and https://goldbook.iupac.org/terms/view/M03952 and https://www.sartorius.com/en/knowledge/resources/chromatography-glossary
counter example: Liquid used for column cleaning or sanitization after chromatography is completed; Air or nitrogen gas used for drying the column after elution (not used as percolating fluid during chromatography)
first order logic definition: MobilePhase(x) ↔ MaterialEntity(x) ∧ ∃r(MobilePhaseRole(r) ∧ hasRole(x, r))
natural language definition: material entity with a mobile phase role
semi formal natural language definition: every instance of 'mobile phase' is defined as exactly an instance of 'material entity' that 'has role' some 'mobile phase role'

mobile phase role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: roleOf
  some values from: BFO_0000040
disjoint with: stationary phase role
example: the mobile phase role borne by phosphate buffer during ion-exchange chromatography; the mobile phase role borne by a water-acetonitrile mixture during reversed-phase liquid chromatography; the mobile phase role borne by helium during gas chromatography
adapted from: http://purl.allotrope.org/ontologies/role#AFRL_0000011 and GE Protein Purification Handbook and https://goldbook.iupac.org/terms/view/M03952
explanatory note: In gas chromatography, the expression 'carrier gas' may be used for the mobile phase. In an elution process, the expression 'eluent' is also used for the mobile phase.
first order logic axiom: MobilePhaseRole(x) → Role(x) ∧ ∃y(MaterialEntity(y) ∧ roleOf(x, y))
is primitive: true
natural language definition: role held by a fluid when it is planned to be or is used in a chromatography process to percolate through or along the stationary phase
primitive rationale: There are insufficient constructs to create necessary and sufficient conditions. In particular modeling of fluid is required.
semi formal natural language axiom: if x is a 'mobile phase role' then x is a 'role' and x is the 'role of' some 'material entity'

pH controlling capability
type: Class
subclass of: control capability
example: the pH controlling capability of a mammalian-cell bioreactor control system to control culture pH through carbon-dioxide and base addition; the pH controlling capability of a microbial fermenter control system to control pH through acid and base addition; the pH controlling capability of an operator to control buffer pH during preparation
first order logic axiom: PHControllingCapability(x) → ControlCapability(x)
is primitive: true
natural language definition: control capability to carry out control of pH
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'pH controlling capability' then x is a 'control capability'

port
type: Class
subclass of: BFO_0000029
example: Sampling port used to withdraw culture samples from a bioreactor vessel; Addition port used to introduce feed or reagent into a single-use bioreactor bag; Harvest port used to remove process material from a vessel; Gas inlet port used to introduce air, oxygen, nitrogen, or CO₂ into a bioreactor; Exhaust port used to remove off-gas from a bioreactor; Probe port used for insertion or connection of a pH, dissolved oxygen, or temperature sensor to a bioreactor; Communication-connector port through which a controller exchanges data with a supervisory control system
first order logic axiom: Port(x) → Site(x)
is primitive: true
natural language definition: site that serves as an interface through which material, energy, or information may enter or leave
primitive rationale: There are insufficient constructs present to create a set of necessary and sufficient conditions. It is expected that further formalization of this term will be conducted in the Systems Engineering WG.
semi formal natural language axiom: if x is a 'port' then x is a 'site'

preparative chromatography system
type: Class
subclass of: chromatography system
contributor: Merck KGaA
alternative label: preparative chromatographic system
alternative label: process chromatography system
example: Stainless steel preparative HPLC system with large-diameter column; single-use preparative chromatography skid for monoclonal antibody purification; pilot-scale preparative ion-exchange chromatography system; large-scale preparative size-exclusion chromatography system with automated fraction collection; preparative affinity chromatography system with protein A resin; expanded bed adsorption chromatography system for feedstock clarification
adapted from: https://www.cytivalifesciences.com/en/us/shop/chromatography/chromatography-systems/akta-process-chromatography-system-p-25741
explanatory note: 1) Preparative chromatography systems are commonly used for purification of target components, but can also be employed for fractionation or other separation purposes where multiple fractions may be collected and retained for further processing. 2) Preparative chromatography systems typically involve larger sample loads and scales than analytical chromatography systems, which primarily focus on identification and quantification.
first order logic axiom: PreparativeChromatographySystem(x) → ChromatographySystem(x)
is primitive: true
natural language definition: chromatography system designed to be used in chromatography processes that produce fractions for further downstream processing, such as purification, formulation, or additional separations
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'preparative chromatography system' then x is a 'chromatography system'

pressure controlling capability
type: Class
subclass of: control capability
example: the pressure controlling capability of a backpressure regulator to control bioreactor vessel pressure; the pressure controlling capability of a pressure regulator to control gas-supply pressure; the pressure controlling capability of an operator to control vessel pressure by adjusting a vent valve
first order logic axiom: PressureControllingCapability(x) → ControlCapability(x)
is primitive: true
natural language definition: control capability to carry out control of pressure
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'pressure controlling capability' then x is a 'control capability'

production bioreactor
type: Class
subclass of: bioreactor
equivalent class: Class
  intersection of: bioreactor
  intersection of: Restriction
    on property: hasRole
    some values from: production bioreactor role
example: a 2,000 L stirred-tank bioreactor bearing a production bioreactor role during a monoclonal-antibody production culture; a 500 L single-use bioreactor bearing a production bioreactor role during a recombinant-protein production culture; a microbial fermenter bearing a production bioreactor role during enzyme production
explanatory note: See the expanded definition under the corresponding role class. The term is formalized here as a defined class by referring to its corresponding role class and exists primarily for ontological modeling and implementation convenience.
first order logic definition: ProductionBioreactor(x) ↔ Bioreactor(x) ∧ ∃r(ProductionBioreactorRole(r) ∧ hasRole(x,r))
natural language definition: bioreactor which has a production bioreactor role
semi formal natural language definition: every instance of 'production bioreactor' is defined as exactly an instance of 'bioreactor' that 'has role' some 'production bioreactor role'

production bioreactor role
type: Class
subclass of: EquipmentRole
subclass of: Restriction
  on property: roleOf
  some values from: bioreactor
example: the production bioreactor role borne by a 2,000 L stirred-tank bioreactor during a monoclonal-antibody production culture; the production bioreactor role borne by a single-use bioreactor during a fed-batch CHO production culture; the production bioreactor role borne by a microbial fermenter during an enzyme-production culture
first order logic axiom: ProductionBioreactorRole(x) → EquipmentRole(x) ∧ ∃b (roleOf(x, b) ∧ Bioreactor(b))
is primitive: true
natural language definition: equipment role held by a bioreactor when it is used or planned to be used to carry out a biomanufacturing production process
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'production bioreactor role' then x is an 'equipment role' and x is a 'role of' some 'bioreactor'

protein A chromatography medium
type: Class
subclass of: affinity chromatography medium
subclass of: Restriction
  on property: hasCapability
  some values from: protein binding capability
example: Protein A immobilized on cross-linked agarose beads; Recombinant Protein A immobilized on methacrylate beads
explanatory note: 1) Protein A is a bacterial cell wall protein derived from Staphylococcus aureus that specifically binds to the Fc region of IgG antibodies. This property enables the selective capture of antibodies from complex mixtures. Affinity chromatography using Protein A ligands is widely employed in the biopharmaceutical industry as a primary capture step in monoclonal antibody purification due to its high selectivity and strong binding capacity 2) It should be noted that the dominant use of protein A resin is IgG capture from a mixture. However, to keep this concept “future proof” and given the predominantly structure-based definitions of the resin this has not been included in the definition. Instead a ‘protein binding capability’ has been introduced and added as an axiom.
first order logic axiom: ProteinAChromatographyMedium(x) → AffinityChromatographyMedium(x) ∧ ∃c(ProteinBindingCapability(c) ∧ hasCapability(x, c))
is primitive: true
natural language definition: affinity chromatography medium which has protein A as an immobilized ligand
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions. Specifically Protein A ligand is missing
semi formal natural language axiom: if x is a 'protein A chromatography medium' then x is an 'affinity chromatography medium' that 'has capability' some 'protein binding capability'

protein binding capability
type: Class
subclass of: Capability
subclass of: Restriction
  on property: capabilityOf
  some values from: BFO_0000040
example: the protein binding capability of Protein A resin to bind IgG molecules; the protein binding capability of an immobilized capture antibody on an ELISA plate to bind its target protein; the protein binding capability of an FcRn-bearing surface to bind IgG
counter example: non-specific binding of proteins to surfaces of plastic containers; covalent immobilization of Protein A on agarose resin; non-specific aggregation of proteins; gel filtration resins - while used for protein purification the interaction mechanism is not binding
first order logic axiom: ProteinBindingCapability(x) → Capability(x) ∧ ∃z(MaterialEntity(z) ∧ capabilityOf(x, z))
is primitive: true
natural language definition: capability of a material entity to selectively and reversibly interact with one or more protein molecules through non-covalent molecular interactions
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'protein binding capability' then x is a 'capability' that is the 'capability of' some 'material entity'

rocker bag
type: Class
subclass of: Container
subclass of: Restriction
  on property: hasFunction
  some values from: cell culture holding function
example: Flexsafe RM bag
adapted from: https://link.springer.com/chapter/10.1007/10_2008_15 and https://www.sartorius.com/en/products/fermentation-bioreactors/single-use-bioreactors/biostat-rm-flexsafe-rm
explanatory note: 1) Rocker bags are single-use or disposable flexible culture chambers typically made from inert plastic film. 2) They may be used with full rocker-motion bioreactors, as well as simpler incubator rockers or trays 3) Their design enables mixing and gas transfer by wave or rocking motion rather than by impellers, reducing shear stress.
first order logic axiom: LA1:RockerBag(x) → Container(x) ∧ ∃f (hasFunction(x, f) ∧ CellCultureHoldingFunction(f))
first order logic axiom: LA2: RockerBag(x) ∧ ∃b (Bioreactor(b) ∧ memberPartOfAtAllTimes(x, b)) → BioreactorVessel(x)
is primitive: true
natural language definition: container that is a flexible bag designed for rocking or wave-motion mixing, gently agitating its contents to provide mixing and gas transfer that enable controlled cultivation of cells or microorganisms under low-shear conditions
primitive rationale: There are insufficient constructs to create necessary and sufficient conditions, particularly for representing the flexible bag construction and the rocking or wave-motion configuration.
semi formal natural language axiom: LA2: if x is a 'rocker bag' and x is a 'member part of at all times' some 'bioreactor', then x is a 'bioreactor vessel'
semi formal natural language axiom: if x is a 'rocker bag' then x is a 'container' that 'has function' some 'cell culture holding function'

seed bioreactor
type: Class
subclass of: bioreactor
equivalent class: Class
  intersection of: bioreactor
  intersection of: Restriction
    on property: hasRole
    some values from: seed bioreactor role
example: a 20 L stirred-tank bioreactor bearing a seed bioreactor role during cell expansion before inoculation of a 200 L production bioreactor; an N-1 perfusion bioreactor bearing a seed bioreactor role before inoculation of a production culture; a 2 L single-use bioreactor bearing a seed bioreactor role during an early seed-train stage
explanatory note: See the expanded definition under the corresponding role class. The term is formalized here as a defined class by referring to its corresponding role class and exists primarily for ontological modeling and implementation convenience.
first order logic definition: SeedBioreactor(x) ↔ Bioreactor(x) ∧ ∃r(SeedBioreactorRole(r) ∧ hasRole(x,r))
natural language definition: bioreactor which has a seed bioreactor role
semi formal natural language definition: every instance of 'seed bioreactor' is defined as exactly an instance of 'bioreactor' that 'has role' some 'seed bioreactor role'

seed bioreactor role
type: Class
subclass of: EquipmentRole
subclass of: Restriction
  on property: roleOf
  some values from: bioreactor
example: the seed bioreactor role borne by a 2 L stirred-tank bioreactor during CHO-cell expansion before transfer to a 20 L seed bioreactor; the seed bioreactor role borne by an N-1 perfusion bioreactor before inoculation of a production bioreactor; the seed bioreactor role borne by a single-use bioreactor during an intermediate seed-train stage
first order logic axiom: SeedBioreactorRole(x) → EquipmentRole(x) ∧ ∃b (roleOf(x, b) ∧ Bioreactor(b))
is primitive: true
natural language definition: equipment role held by a bioreactor that is involved or planned to be involved in carrying out a cell culture expansion process that is part of a seed train
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'seed bioreactor role' then x is an 'equipment role' and x is a 'role of' some 'bioreactor'

shake flask
type: Class
subclass of: flask
example: A 2 L baffled PETG Erlenmeyer flask used in small-scale mammalian cell culture, with vented cap and controlled shaking
adapted from: https://pmc.ncbi.nlm.nih.gov/articles/PMC11773345/ and https://www.eppendorf.com/no-en/industries-solutions/lab-solutions/other/shake-flasks-more-than-just-filling-volumes/
counter example: Test tubes placed on a shaker: although agitation is present, test tubes lack the flask geometry, venting options, and mixing dynamics of shake flasks. They can be used for cultivation, but they are not shake flasks as defined in laboratory and regulatory practice.
explanatory note: 1) Shake flasks are often based on Erlenmeyer flask geometry. 2) They may include baffles to improve mixing and oxygen transfer. 3) They are usually closed with breathable stoppers, foam plugs, or vented caps to allow gas exchange while limiting contamination. 4) They are commonly used for inoculum preparation, strain screening, and preliminary optimization of process parameters before scaling up to bioreactors. The geometry of the flask (e.g., baffled vs. non-baffled) and the shaking conditions influence oxygen transfer rates, mixing efficiency, and overall culture performance. 5) They are typically made of glass or plastic and range in volume from milliliters to liters.
first order logic axiom: ShakeFlask(x) → Flask(x)
is primitive: true
natural language definition: flask designed for cultivating biological material or conducting chemical reactions that require aeration and mixing under agitated conditions with a shape that minimizes spillage during shaking
primitive rationale: There are insufficient constructs present to create a set of necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'shake flask' then x is a 'flask'

shaker
type: Class
subclass of: EngineeredSystem
subclass of: Restriction
  on property: hasFunction
  some values from: mixing function
example: Orbital shaker used to agitate shake flasks during microbial cultivation; Platform shaker used to agitate tubes or plates during sample preparation; Rocking shaker used to move liquid in a single-use bag; Incubator shaker used to shake culture vessels while maintaining controlled temperature.
adapted from: https://en.wikipedia.org/wiki/Shaker_(laboratory)
first order logic axiom: Shaker(x) → EngineeredSystem(x) ∧ ∃c (hasFunction(x, c) ∧ MixingFunction(c))
is primitive: true
natural language definition: engineered system designed to apply shaking motion to material entities placed on or in it
primitive rationale: There are insufficient constructs to create a set of necessary and sufficient conditions
semi formal natural language axiom: if x is a 'shaker' then x is an 'engineered system' that 'has function' some 'mixing function'

single use role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: roleOf
  some values from: Class
    union of: PieceOfEquipment
    union of: ProductionConsumable
example: the single use role borne by a bioreactor bag used for one cell-culture batch and then discarded; the single use role borne by a mixing bag used for one buffer-preparation operation and then discarded; the single use role borne by a tubing assembly qualified for one manufacturing campaign
adapted from: https://ispe.org/topics/single-use-technologies-disposables
explanatory note: A single use role applies to production consumables or equipment items whose use pattern limits them to a single defined use, such as a batch run or manufacturing campaign.
first order logic axiom: SingleUseRole(x) → Role(x) ∧ ∃z (roleOf(x, z) ∧ (PieceOfEquipment(z) ∨ ProductionConsumable(z)))
is primitive: true
natural language definition: role held by a production consumable or piece of equipment that is used or planned to be used for a single defined use before being discarded or removed from further qualified use
primitive rationale: There are insufficient constructs present to fully formalize this construct
semi formal natural language axiom: if x is a 'single use role' then x is a 'role' that is a 'role of' some 'piece of equipment' or 'production consumable'

size exclusion chromatography medium
type: Class
subclass of: chromatography medium
contributor: Merck KGaA
example: Sephacryl resins; Biogel Agarose Gel resins; Biogel P Polyacrylamide Gel Resins
adapted from: http://wolfson.huji.ac.il/purification/PDF/affinity/GE_Affinity_Chromatography_Handbook-Antibodies.pdf
first order logic axiom: SizeExclusionChromatographyMedium(x) → ChromatographyMedium(x)
is primitive: true
natural language definition: chromatography medium designed to selectively and reversibly retain molecules based on differences in their size, shape, or molecular mass
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'size exclusion chromatography medium' then x is a 'chromatography medium'

solid transfer capability
type: Class
subclass of: material transfer capability
subclass of: Restriction
  on property: BFO_0000054
  all values from: Class
    intersection of: PlannedProcess
    intersection of: Restriction
      on property: BFO_0000057
      some values from: Class
        intersection of: BFO_0000040
        intersection of: Restriction
example: the solid transfer capability of an operator to charge powdered medium into a mixing vessel; the solid transfer capability of a powder-transfer system to move buffer salt into a dispensing container; the solid transfer capability of a vacuum-transfer system to move powdered buffer component from a dispensing container into a preparation vessel
first order logic axiom: SolidTransferCapability(x) → MaterialTransferCapability(x) ∧ ∀y(hasRealization(x,y) → (PlannedProcess(y) ∧ ∃m(MaterialEntity(m) ∧ hasParticipant(y,m) ∧ ∃q(SolidAggregateState(q) ∧ hasQuality(m,q)) ∧ ∃r(TransferredMaterialRole(r) ∧ hasRole(m,r)))))
is primitive: true
natural language definition: material transfer capability to enable movement of a solid to or from a material entity or site
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'solid transfer capability' then x is a 'material transfer capability' and whenever some y 'realizes' x then y is a 'planned process' that 'has participant' some 'material entity' that 'has quality' some 'solid aggregate state' and 'has role' some 'transferred material role'

spinner flask
type: Class
subclass of: flask
disjoint with: T-flask
equivalent class: Class
  intersection of: flask
  intersection of: Restriction
    on property: hasComponentPartAtAllTimes
    some values from: Class
      intersection of: MaterialComponent
      intersection of: Restriction
        on property: hasFunction
        some values from: mixing function
  intersection of: Restriction
    on property: hasFunction
    some values from: suspension cell culture holding function
example: A 250 mL glass spinner flask with a magnetic stirring bar
adapted from: https://www.sciencedirect.com/topics/engineering/spinner-flask
counter example: T-flask for adherent cell culture, which lacks any internal component with a mixing function
explanatory note: The mixing component is typically a magnetic stir bar, paddle, or impeller built into the vessel and externally driven to keep cells and medium evenly agitated. This prevents cell settling and improves oxygen and nutrient distribution. Spinner flasks are commonly used for small-scale suspension cultures (e.g., hybridomas, CHO cells) prior to scale-up into bioreactors.
first order logic definition: SpinnerFlask(x) ↔ Flask(x) ∧ ∃c (MaterialComponent(c) ∧ hasComponentPartAtAllTimes(x, c) ∧ ∃a (MixingFunction(a) ∧ hasFunction(c, a))) ∧ ∃h (SuspensionCellCultureHoldingFunction(h) ∧ hasFunction(x, h))
natural language definition: flask designed for cultivating cells in suspension that has as part a component with a mixing function to keep the culture uniformly agitated
semi formal natural language definition: every instance of 'spinner flask' is defined as exactly an instance of 'flask' that 'has component part at all times' some 'material component' that 'has function' some 'mixing function', and x 'has function' some 'suspension cell culture holding function'

stationary phase
type: Class
subclass of: BFO_0000040
equivalent class: Class
  intersection of: BFO_0000040
  intersection of: Restriction
    on property: hasRole
    some values from: stationary phase role
example: Silica gel as stationary phase in normal-phase chromatography; C18 bonded silica as stationary phase in reverse-phase chromatography; agarose bead gel as stationary phase in size-exclusion chromatography; ion-exchange resin as stationary phase in ion-exchange chromatography; protein A immobilized on resin as stationary phase in affinity chromatography; polymeric resin as stationary phase in hydrophobic interaction chromatography.
counter example: an unpacked chromatography column; chromatography medium when it is offered for sale by its manufacturer
explanatory note: Common terms such as “chromatographic bed” or “sorbent” may refer to its various physical forms. To avoid ambiguity, expressions like “liquid stationary phase” or “solid stationary phase” are preferred when specifying its physical state.
first order logic definition: StationaryPhase(x) ↔ MaterialEntity(x) ∧ ∃r(StationaryPhaseRole(r) ∧ hasRole(x, r))
natural language definition: material entity with a stationary phase role
semi formal natural language definition: every instance of 'stationary phase' is defined as exactly an instance of 'material entity' that 'has role' some 'stationary phase role'

stationary phase role
type: Class
subclass of: BFO_0000023
subclass of: Restriction
  on property: roleOf
  some values from: BFO_0000040
example: the stationary phase role borne by Protein A resin during affinity chromatography; the stationary phase role borne by C18-bonded silica during reversed-phase chromatography; the stationary phase role borne by agarose gel during size-exclusion chromatography
adapted from: http://purl.allotrope.org/ontologies/role#AFRL_0000032 and https://goldbook.iupac.org/terms/view/S05949 and https://userpages.umbc.edu/~dfrey1/documents/lc_glossary.pdf
explanatory note: 1) Common terms such as “chromatographic bed” or “sorbent” may refer to its various physical forms. To avoid ambiguity, expressions like “liquid stationary phase” or “solid stationary phase” are preferred when specifying its physical state 2) The stationary phase selectively and reversibly retains solutes, enabling their separation during chromatography through differential interactions with both the stationary and mobile phases. This includes mechanisms such as size exclusion, ion exchange, and affinity binding.
first order logic axiom: StationaryPhaseRole(x) → Role(x) ∧ ∃y(MaterialEntity(y) ∧ roleOf(x, y))
is primitive: true
natural language definition: role held by a solid, gel, or liquid that is planned to be or used in a chromatography process as the immobilized material which selectively and reversibly retains solutes in the mobile phase
primitive rationale: There are insufficient constructs to create necessary and sufficient conditions. In particular modeling of solid, gel or liquid is required.
semi formal natural language axiom: if x is a 'stationary phase role' then x is a 'role' and x is the 'role of' some 'material entity'

suspension cell culture holding capability
type: Class
subclass of: cell culture holding capability
example: Capability of a shake flask to contain a suspension culture during shaking cultivation; Capability of a spinner flask to contain a suspension cell culture during stirred cultivation; Capability of a bioreactor vessel to contain a suspension cell culture during a controlled cultivation process;
first order logic axiom: SuspensionCellCultureHoldingCapability(x) → CellCultureHoldingCapability(x)
is primitive: true
natural language definition: cell culture holding capability to contain a suspension cell culture during a cell cultivation process
primitive rationale: See the rationale under cell culture holding capability
semi formal natural language axiom: if x is a 'suspension cell culture holding capability' then x is a 'cell culture holding capability'

suspension cell culture holding function
type: Class
subclass of: suspension cell culture holding capability
equivalent class: Class
  intersection of: suspension cell culture holding capability
  intersection of: Restriction
    on property: functionOf
    some values from: BFO_0000040
example: the suspension cell culture holding function of a shake flask to contain a suspension culture during shaking cultivation; the suspension cell culture holding function of a spinner flask to contain a suspension cell culture during stirred cultivation; the suspension cell culture holding function of a stirred-tank bioreactor vessel to contain a suspension cell culture during controlled cultivation
first order logic definition: SuspensionCellCultureHoldingFunction(x) ↔ SuspensionCellCultureHoldingCapability(x) ∧ ∃m(MaterialEntity(m) ∧ functionOf(x,m))
natural language definition: suspension cell culture holding capability that is a function of a material entity
semi formal natural language definition: every instance of 'suspension cell culture holding function' is exactly an instance of 'suspension cell culture holding capability' that is the 'function of' some 'material entity'

T-flask
type: Class
subclass of: flask
subclass of: Restriction
  on property: hasFunction
  some values from: adherent cell culture holding function
example: A T75 polystyrene tissue culture flask with vented cap, used for adherent HEK293 cell expansion.
adapted from: https://www.abdoslifesciences.com/how-to-choose-the-right-t-flask-for-your-cell-culture-needs/
counter example: A spinner flask for suspension cell culture, which lacks a flat surface for cell attachment and instead has an internal stirring element
first order logic axiom: TFlask(x) → Flask(x) ∧ ∃f (hasFunction(x, f) ∧ AdherentCellCultureHoldingFunction(f))
is primitive: true
natural language definition: flask designed for cultivating adherent cells that has as part a flat growth surface for cell attachment and a narrow neck for adding or removing material while reducing contamination risk
primitive rationale: There are insufficient constructs present to create a set of necessary and sufficient conditions. In particular the constructs for representing flask geometry (shape) are missing.
semi formal natural language axiom: if x is a 'T-flask' then x is a 'flask' and x 'has function' some 'adherent cell culture holding function'

temperature controlling capability
type: Class
subclass of: control capability
example: the temperature controlling capability of a bioreactor temperature-control system to control culture temperature; the temperature controlling capability of a CO₂ incubator to control chamber temperature; the temperature controlling capability of a dry thawing system to control the temperature of the process material to be unfrozen during thawing
first order logic axiom: TemperatureControllingCapability(x) → ControlCapability(x)
is primitive: true
natural language definition: control capability to carry out control of temperature
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'temperature controlling capability' then x is a 'control capability'

thawing capability
type: Class
subclass of: Capability
subclass of: Restriction
  on property: BFO_0000054
  all values from: PlannedProcess
subclass of: Restriction
  on property: capabilityOf
  some values from: Class
    union of: EngineeredSystem
    union of: MaterialArtifact
example: Capability to uniformly raise temperature of cryopreserved cells in a sterile water bath; capability to provide precise temperature control for thawing frozen culture media in a dry thawing system; capability to deliver controlled microwave heating for rapid thawing of biological samples; capability of a recirculating warm water thawing system able to maintain its setpoint temperature; capability to apply gentle ultrasonic energy for thawing frozen tissues without damaging structure; capability of an automated thawing device for thawing cryovials by regulating its heated plate temperature; capability of a hot-air thawing tunnel that circulates hot air with precisely controlled temperature and flow rate to safely pre-thaw deep-frozen food products
explanatory note: It may be exhibited by complex engineered thawing systems or simpler material artifacts like warm water baths. Precise temperature control and monitoring are important to prevent damage to the material during thawing.
first order logic axiom: ThawingCapability(x) → Capability(x) ∧ ∃z((EngineeredSystem(z) ∨ MaterialArtifact(z)) ∧ capabilityOf(x, z)) ∧ ∀y(hasRealization(x, y) → PlannedProcess(y))
is primitive: true
natural language definition: capability that an engineered system or material artifact has to provide controlled heating to raise the temperature of a material to a specified setpoint, typically to transition the material from a solid or frozen state to a soft or liquid state
primitive rationale: There are insufficient constructs in the ontology to create necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'thawing capability' then x is a 'capability' that is the 'capability of' some 'engineered system' or 'material artifact' and whenever some y 'realizes' x that y must be a 'planned process'

thawing function
type: Class
subclass of: thawing capability
equivalent class: Class
  intersection of: thawing capability
  intersection of: Restriction
    on property: functionOf
    some values from: Class
      union of: EngineeredSystem
      union of: MaterialArtifact
example: the thawing function of a temperature-controlled water bath to thaw closed cryovials containing cryopreserved cells from a cell bank; the thawing function of a controlled-rate freeze-and-thaw system to thaw frozen bulk drug substance
first order logic definition: ThawingFunction(x) ↔ ThawingCapability(x) ∧ ∃b((MaterialArtifact(b) ∨ EngineeredSystem(b)) ∧ functionOf(x,b))
natural language definition: thawing capability that is a function of a material artifact or engineered system
semi formal natural language definition: every instance of 'thawing function' is exactly an instance of 'thawing capability' that is the 'function of' some entity that is a 'material artifact' or an 'engineered system'

thawing system
type: Class
subclass of: EngineeredSystem
equivalent class: Class
  intersection of: EngineeredSystem
  intersection of: Restriction
    on property: hasFunction
    some values from: thawing function
example: Controlled-rate water bath thawing system; sterile dry thawing system with temperature control; microwave-assisted thawing system with setpoint regulation; ultrasonic thawing system with precise temperature monitoring; recirculating warm water thawing system with feedback control; heated plate thawing system with programmable temperature setpoint; single-use thawing chamber with integrated temperature sensors; automated cryopreserved cell thawing device with controlled ramp rates
adapted from: https://dictionary.cambridge.org/dictionary/english/thawing, http://purl.obolibrary.org/obo/NCIT_C48165 and https://www.biolifesolutions.com/blog/thawing/how-does-a-water-free-automated-thawing-system-improve-your-cryopreservation-process/
explanatory note: Thawing systems can be applied directly to a material or indirectly by heating the container in which the material is held.
first order logic definition: ThawingSystem(x) ↔ EngineeredSystem(x) ∧ ∃f(ThawingFunction(f) ∧ hasFunction(x, f))
natural language definition: engineered system designed to raise the temperature of a material in a controlled manner to reach a specified setpoint, typically to transition it from a solid or frozen state to a soft or liquid state
semi formal natural language definition: every instance of 'thawing system' is defined as exactly an instance of 'engineered system' that 'has function' some 'thawing function'

vessel headspace
type: Class
subclass of: BFO_0000029
example: The gas-filled space above the liquid culture in a stirred-tank bioreactor; The air space above buffer solution in a storage bottle; The nitrogen-blanketed space above a liquid medium in a mixing vessel; The gas space above a cell culture medium in a shake flask
first order logic axiom: VesselHeadspace(x) → Site(x)
is primitive: true
natural language definition: site within the interior of a vessel that is not occupied by the contained bulk material and is bounded by the vessel walls and, when contents are present, by a surface of those contents
primitive rationale: There are insufficient constructs to create a set of necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'vessel headspace' then x is a 'site'

vial
type: Class
subclass of: Container
example: glass reagent vial used for chemical or media samples; autosampler vial used in analytical chromatography systems; cryovial used for frozen storage of a cryopreserved cell suspension
adapted from: https://www.fda.gov/drugs/data-standards-manual-monographs/data-standards-manual-monographs-package-type and http://purl.allotrope.org/ontologies/equipment#AFE_0000329
explanatory note: 1) Vials are often cylindrical in form. 2) They are typically made of glass or plastic. 3) They are commonly used to hold pharmaceutical preparations, injectable drugs, biological products, cryopreserved cells or cell suspensions, or laboratory samples. 4) Some vials are used for headspace analysis, containing gas or the gaseous headspace above a liquid or solid. 5) They are usually sealed with a stopper, screw cap, or crimp closure to protect the contents.
first order logic axiom: Vial(x) → Container(x)
is primitive: true
natural language definition: container that is small, sealable, and designed for holding, storing, or dispensing small quantities of material
primitive rationale: There are insufficient constructs present to create a set of necessary and sufficient conditions.
semi formal natural language axiom: if x is a 'vial' then x is a 'container'