NIIMBL Equipment Ontology
type: Ontology
label: 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: ReferenceOntologyCandidates
imports: Core
version IRI: Equipment
copyright: Copyright (c) 2022, 2023, 2024, 2025, 2026 Open Applications Group
maturity: Released

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; Sterptavidin agarose used for capturing biotinilyated 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 solutes, 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'

analytic chromatographic system
type: Class
subclass of: chromatography system
contributor: Merck KGaA
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: AnalyticChromatographySystem(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 'analytic 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'

bioproduction environment capability
type: Class
subclass of: ManufacturingCapability
subclass of: Restriction
  on property: capabilityOf
  some values from: EngineeredSystem
example: Capability to regulate nutrient feed rates for sustained protein expression; capability to continuously remove metabolic waste products while maintaining nutrient supply in perfusion culture to sustain high-density cell cultures with optimal product formation; capability to maintain continuous culture conditions for high product yield;
first order logic axiom: BioproductionEnvironmentCapability(x) → Capability(x) ∧ ∃z(EngineeredSystem(z) ∧ capabilityOf(x, z))
is primitive: true
natural language definition: capability that an engineered system has to provide a controlled environment in which biological entities can produce material products or process intermediates
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 'capability' that is the 'capability of' some 'engineered system'

bioreactor
type: Class
subclass of: EngineeredSystem
equivalent class: Class
  intersection of: EngineeredSystem
  intersection of: Restriction
    on property: hasCapability
    some values from: bioproduction environment capability
  intersection of: Restriction
    on property: hasFunction
    some values from: cultivation environment capability
equivalent class: Class
  intersection of: EngineeredSystem
  intersection of: Restriction
    on property: hasCapability
    some values from: cultivation environment capability
  intersection of: Restriction
    on property: hasFunction
    some values from: bioproduction environment capability
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) ∧ ( ∃c1∃f1 (BioproductionEnvironmentCapability(c1) ∧ hasCapability(x, c1) ∧ CultivationEnvironmentCapability(f1) ∧ hasFunction(x, f1)) ∨ ∃c2∃f2 (CultivationEnvironmentCapability(c2) ∧ hasCapability(x, c2) ∧ BioproductionEnvironmentCapability(f2) ∧ hasFunction(x, f2)) )
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 either has capability some 'bioproduction environment capability' and has function some 'cultivation environment capability', or has capability some 'cultivation environment capability' and has function some 'bioproduction environment capability'

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'

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: AFO_/equipment#AFE:0000217 and CHMO:0000997
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
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 capability
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(FlowRateControllingCapability(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 capability'

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: Capability to maintain optimal temperature and CO₂ levels for cell expansion; capability to provide stable nutrient and oxygen levels that support sustained cell viability and proliferation during expansion phases; capability to sustain controlled humidity for tissue culture; capability to regulate gas composition to support microbial growth; capability to maintain aseptic conditions for long-term cell maintenance.
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 that an engineered system has to provide a controlled environment suitable for the growth or maintenance of cells, tissues, or microorganisms
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'

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 have a defined pore size or structure and which 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'

filter
type: Class
subclass of: MaterialArtifact
example: depth filter; membrane 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'

flow rate controlling capability
type: Class
subclass of: Capability
subclass of: Restriction
  on property: BFO_0000054
  all values from: PlannedProcess
subclass of: Restriction
  on property: capabilityOf
  all values from: Class
    union of: Agent
    union of: PieceOfEquipment
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) → Capability(x) ∧ ∀z(capabilityOf(x, z) → (Agent(z) ∨ PieceOfEquipment(z))) ∧ ∀y(hasRealization(x, y) → PlannedProcess(y))
is primitive: true
natural language definition: capability that an agent or piece of equipment has to regulate the flow rate of a fluid when participating in a particular 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 'flow rate controlling capability' then x is a 'capability' such that x is the 'capability of' only an 'agent' or a 'piece of equipment' and whenever some y 'realizes' x that y must be a 'planned process'

hydrophobic chromatography medium
type: Class
subclass of: chromatography medium
contributor: Merck KGaA
example: Butyl Sepharose used for Hidrophobic Interaction Chromatography; C18 Silica resin used for reverse 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'

membrane filter
type: Class
subclass of: filter
example: “Regenerated cellulose;PES; Amicon® Ultra”
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 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'

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; gradient of water and acetonitrile as mobile phase in gradient elution; sodium chloride solution as mobile phase in size-exclusion chromatography
adapted from: AFO_/role#AFRL:0000011 and GE Protein Purification Handbook and https://goldbook.iupac.org/terms/view/M03952 and htps://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: 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; gradient of water and acetonitrile as mobile phase in gradient elution; sodium chloride solution as mobile phase in size-exclusion chromatography
adapted from: AFO_/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 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'

preparative chromatography system
type: Class
subclass of: chromatography system
contributor: Merck KGaA
alternative label: process chromatographic 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) proven design has been verified during development and can be user configured to meet specific process demands. 2) 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. 3) Preparative chromatography systems typically involving larger sample loads and scales than analytical chromatography systems, which primarily focus on identification and quantitation.
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'

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. Since currently there is no protein and antibody hierarchy present this capability has not been expanded to IgG specifically. This will be modeled in a future version
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 a protein A as a 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: Protein A resin capability to bind IgG molecules; Immobilized capture antibody on an ELISA plate capability to bind specific (target) protein; . FcRn Receptor capability to bind therapeutic IgG
counter example: non-specific binding of proteins to surfaces of plastic containers; covalent imobilization 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'

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 weight
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'

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: 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.
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.
explanatory note: AFO_/role#AFRL:0000032 and https://goldbook.iupac.org/terms/view/S05949 and “https://userpages.umbc.edu/~dfrey1/documents/lc_glossary.pd
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'

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 to maintain setpoint temperature in a recirculating warm water thawing system; capability to apply gentle ultrasonic energy for thawing frozen tissues without damaging structure; capability to regulate heated plate temperature for thawing cryovials in automated thawing devices
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 a 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 system
type: Class
subclass of: EngineeredSystem
equivalent class: Class
  intersection of: EngineeredSystem
  intersection of: Restriction
    on property: hasFunction
    some values from: thawing capability
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(ThawingCapability(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 capability'