Equipment Ontology
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.).
Cameron Gibbs, CrownPoint Technologies, LLC
Melissa Weller, CrownPoint Technologies, LLC
Stephen J. Granite, CrownPoint Technologies, LLC
Stephen Kahmann, CrownPoint Technologies, LLC
Copyright (c) 2022, 2023, 2024, 2025, 2026 Open Applications Group
affinity chromatography medium
Merck KGaA
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
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.
AffinityChromatographyMedium(x) → ChromatographyMedium(x)
chromatography medium which has an immobilized ligand as its part which has reversible binding capability to a specific part of a biomolecule
There are insufficient constructs in the ontology to create necessary and sufficient conditions.
if x is an 'affinity chromatography medium' then x is a 'chromatography medium'
analytic chromatographic system
Gas chromatography-mass spectrometry (GC-MS) system;High-performance liquid chromatography (HPLC) system with UV detection; Ultra-Performance Liquid Chromatography (UPLC) system
AnalyticChromatographySystem(x) → ChromatographySystem(x)
chromatography system designed to be used in chromatography processes with the primary objective of identifying or quantifying chemical or biological substances
if x is an 'analytic chromatography system' then x is a 'chromatography system'
anion exchange chromatography medium
positively charged molecules that are chemically bound to the matrix serve as functional groups as they provide the material basis of the resin function
AnionExchangeChromatographyMedium(x) → ChromatographyMedium(x)
chromatography medium consisting of a matrix and positively charged molecules that are chemically bound to it
if x is an 'anion exchange chromatography medium' then x is a 'chromatography medium'
bioproduction environment capability
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;
BioproductionEnvironmentCapability(x) → Capability(x) ∧ ∃z(EngineeredSystem(z) ∧ capabilityOf(x, z))
capability that an engineered system has to provide a controlled environment in which biological entities can produce material products or process intermediates
if x is a 'bioproduction environment capability' then x is a 'capability' that is the 'capability of' some 'engineered system'
bioreactor
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
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
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
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)) )
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
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
negatively charged molecules that are chemically bound to the matrix serve as functional groups as they provide the material basis of the resin function
CationExchangeChromatographyMedium(x) → ChromatographyMedium(x)
chromatography medium consisting of a matrix and negatively charged molecules that are chemically bound to it
if x is a 'cation exchange chromatography medium' then x is a 'chromatography medium'
chromatography column
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;
AFO_/equipment#AFE:0000217 and CHMO:0000997
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.
ChromatographyColumn(x) → MaterialArtifact(x)
material artifact that is a tube or a cylinder designed to house chromatography medium as the stationary phase during one or more chromatography processes
There are currently insufficient constructs to adequately model the shape of a tube or a cylinder
if x is a 'chromatography column' then x is a 'material artifact'
chromatography medium
affinity chromatography medium; size exclusion chromatography medium; anion exchange medium
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.
ChromatographyMedium(x) → MaterialEntity(x)
material entity designed to selectively and reversibly retain different molecules during one or more chromatography processes
if x is a 'chromatography medium' then x is a 'material entity'
chromatography system
AKTA FPLC Chromatography systems such as AKTA pure and AKTAprime plus; Agilent Gas Chromatography System; Vanquish HPLC and UHPLC Systems
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
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
ChromatographySystem(x) ↔ EngineeredSystem(x) ∧ ∃s(StationaryPhase(s) ∧ hasMemberPartAtSomeTime(x, s)) ∧ ∃c(MeasurementCapability(c) ∧ hasCapability(x, c)) ∧ ∃f(FlowRateControllingCapability(f) ∧ hasFunction(x, f))
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
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
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.
CultivationEnvironmentCapability(x) → Capability(x) ∧ ∃z(EngineeredSystem(z) ∧ capabilityOf(x, z)) ∧ ∀y(hasRealization(x, y) → PlannedProcess(y))
capability that an engineered system has to provide a controlled environment suitable for the growth or maintenance of cells, tissues, or microorganisms
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
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
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
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.
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
if x is a 'depth filter' then x is a 'filter'
filter
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.
material artifact that is porous and designed to retain particles above a certain size threshold when a fluid is passed through it
if x is a 'filter' then x is a 'material artifact'
flow rate controlling capability
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
capability to measure flow rate passively without adjusting it; capability to maintain structural integrity of a pipe during fluid transfer
FlowRateControllingCapability(x) → Capability(x) ∧ ∀z(capabilityOf(x, z) → (Agent(z) ∨ PieceOfEquipment(z))) ∧ ∀y(hasRealization(x, y) → PlannedProcess(y))
capability that an agent or piece of equipment has to regulate the flow rate of a fluid when participating in a particular planned process
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
Butyl Sepharose used for Hidrophobic Interaction Chromatography; C18 Silica resin used for reverse phase chromatography
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
HydrophobicChromatographyMedium(x) → ChromatographyMedium(x)
chromatography medium consisting of a matrix and hydrophobic molecules that are chemically bound to it
if x is a 'hydrophobic chromatography medium' then x is a 'chromatography medium'
membrane filter
“Regenerated cellulose;PES; Amicon® Ultra”
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
Metal filters;Activated carbon sheets;Glass fibers
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
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
if x is a 'membrane filter' then x is a 'filter'
mixed mode chromatography medium
Hydroxyapatite (CHT/CFT/Bio-Gel HT/HTP) Resins that interact through electrostatic and calcium coordination complexes; Resins with hydrophobic ion exchange ligands
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
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.
MixedModeChromatographyMedium(x) → ChromatographyMedium(x)
chromatography medium with immobilized functional groups designed to selectively interact with molecules through multiple distinct interaction mechanisms
if x is a 'mixed mode chromatography medium' then x is a 'chromatography medium'
mobile phase
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
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
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)
MobilePhase(x) ↔ MaterialEntity(x) ∧ ∃r(MobilePhaseRole(r) ∧ hasRole(x, r))
material entity with a mobile phase role
every instance of 'mobile phase' is defined as exactly an instance of 'material entity' that 'has role' some 'mobile phase role'
mobile phase role
AFO_/role#AFRL:0000011 and GE Protein Purification Handbook and https://goldbook.iupac.org/terms/view/M03952
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.
MobilePhaseRole(x) → Role(x) ∧ ∃y(MaterialEntity(y) ∧ roleOf(x, y))
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
There are insufficient constructs to create necessary and sufficient conditions. In particular modeling of fluid is required.
if x is a 'mobile phase role' then x is a 'role' and x is the 'role of' some 'material entity'
preparative chromatography system
process chromatographic system
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
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.
PreparativeChromatographySystem(x) → ChromatographySystem(x)
chromatography system designed to be used in chromatography processes that produce fractions for further downstream processing, such as purification, formulation, or additional separations
if x is a 'preparative chromatography system' then x is a 'chromatography system'
protein A chromatography medium
Protein A immobilized on cross-linked agarose beads; Recombinant Protein A immobilized on methacrylate beads
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
ProteinAChromatographyMedium(x) → AffinityChromatographyMedium(x) ∧ ∃c(ProteinBindingCapability(c) ∧ hasCapability(x, c))
affinity chromatography medium which has a protein A as a ligand
There are insufficient constructs in the ontology to create necessary and sufficient conditions. Specifically Protein A ligand is missing
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
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
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
ProteinBindingCapability(x) → Capability(x) ∧ ∃z(MaterialEntity(z) ∧ capabilityOf(x, z))
capability of a material entity to selectively and reversibly interact with one or more protein molecules through non-covalent molecular interactions
if x is a 'protein binding capability' then x is a 'capability' that is the 'capability of' some 'material entity'
size exclusion chromatography medium
Sephacryl resins; Biogel Agarose Gel resins; Biogel P Polyacrylamide Gel Resins
SizeExclusionChromatographyMedium(x) → ChromatographyMedium(x)
chromatography medium designed to selectively and reversibly retain molecules based on differences in their size, shape, or molecular weight
if x is a 'size exclusion chromatography medium' then x is a 'chromatography medium'
stationary phase
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.
an unpacked chromatography column; chromatography medium when it is offered for sale by its manufacturer
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.
StationaryPhase(x) ↔ MaterialEntity(x) ∧ ∃r(StationaryPhaseRole(r) ∧ hasRole(x, r))
material entity with a stationary phase role
every instance of 'stationary phase' is defined as exactly an instance of 'material entity' that 'has role' some 'stationary phase role'
stationary phase role
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.
AFO_/role#AFRL:0000032 and https://goldbook.iupac.org/terms/view/S05949 and “https://userpages.umbc.edu/~dfrey1/documents/lc_glossary.pd
StationaryPhaseRole(x) → Role(x) ∧ ∃y(MaterialEntity(y) ∧ roleOf(x, y))
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
There are insufficient constructs to create necessary and sufficient conditions. In particular modeling of solid,gel or liquid is required.
if x is a 'stationary phase role' then x is a 'role' and x is the 'role of' some 'material entity'
thawing capability
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
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.
ThawingCapability(x) → Capability(x) ∧ ∃z((EngineeredSystem(z) ∨ MaterialArtifact(z)) ∧ capabilityOf(x, z)) ∧ ∀y(hasRealization(x, y) → PlannedProcess(y))
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
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
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
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/
Thawing systems can be applied directly to a material or indirectly by heating the container in which the material is held.
ThawingSystem(x) ↔ EngineeredSystem(x) ∧ ∃f(ThawingCapability(f) ∧ hasFunction(x, f))
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
every instance of 'thawing system' is defined as exactly an instance of 'engineered system' that 'has function' some 'thawing capability'