Changes in 🟢 Biopharma Manufacturing Execution Ontology

  • Maturity: 🟢 Released

Added

Classes

Construct Definition
AerationProcess material addition process in which an oxygen-containing gas is added to a defined recipient to provide oxygen or support gas exchange
AntifoamAdditionProcess material addition process in which an antifoam agent is introduced into a defined recipient to suppress, reduce, or prevent foam formation
BatchProcessOperatingMode process operating mode of a planned process in which a finite quantity of process material is introduced before or at the start of the main processing interval and processed as a single unit, without additional process material being introduced or removed during that interval
CellBleedProcess material removal process in which a portion of cell-containing culture material is withdrawn from a cell culture during an ongoing culture process to regulate culture properties such as viable cell density, biomass concentration, or metabolite accumulation
CellCultureInoculationProcess inoculation process in which a cell-containing inoculum is introduced to initiate a cell culture process
CellCultureRecoveryProcess planned process in which cells that have undergone a stress-inducing process are cultured under controlled conditions to restore or stabilize viability, metabolic activity, or growth potential
CellRetentionProcess planned process in which material is removed from a cell culture while cells are preferentially kept in or returned to the cell culture
CellTherapyProductionProcess biomanufacturing production process that results in a cell population which constitutes the targeted product material
ChemostatCultureProcessOperatingMode continuous culture process operating mode in which culture medium containing a growth-limiting component is introduced while culture material is concomitantly removed over an operating interval, with dilution rate used to regulate culture growth
ContinuousCultureProcessOperatingMode continuous process operating mode of a culture process in which culture medium or other input material is introduced while culture material, spent medium, or product-containing harvest material is concomitantly removed over an operating interval
ContinuousProcessOperatingMode process operating mode that characterizes a planned process in which input material is introduced into the process while output material is concomitantly removed from the same process over the whole operating interval
CultureFeedAdditionProcess material addition process in which a nutrient feed is added to a cell culture during a culture process
CultureFeedingStrategy plan specification that prescribes how one or more feeding processes are to be executed during a cell culture process, including scheduling and amounts or rates, and any specified triggering conditions
CultureMediumChargingProcess material addition process in which culture medium is added to a culture vessel in preparation for cell culture inoculation
CultureMediumExchangeProcess planned process in which part or all of the spent culture medium associated with a cell culture is removed and fresh culture medium is added
DegassingProcess planned process during which dissolved, entrained, or adsorbed gas is separated from a liquid or solid material
FedBatchProcessOperatingMode process operating mode of a planned process in which a finite quantity of process material is introduced before or at the start of the main processing interval, and additional process material is introduced during that interval while the process material is retained and processed as a single unit
InductionProcess planned process that is a part of a cultivation or production process and triggers a defined change in cellular function, pathway activity, production phase, or differentiation state
InoculationProcess material addition process in which cells, microorganisms, viruses, or biological preparations are deliberately introduced into a defined recipient to initiate growth, infection, testing, production, or a biological response
MixingProcess planned process that combines material entities or redistributes parts of a material entity to increase or maintain the homogeneity of the material being processed
PHAdjustmentAdditionProcess material addition process in which an acidifying or alkalizing material is introduced into a defined recipient to modify pH
PerfusionCultureProcessOperatingMode continuous culture process operating mode in which culture medium or other input material is introduced while spent medium or product-containing harvest material is concomitantly removed over an operating interval, with cell retention used to preferentially keep cells in the culture system
PerfusionMediumExchangeProcess culture medium exchange process in which fresh culture medium is added to a cell culture while material is continuously or quasi-continuously removed from the cell culture, with cell retention used to preferentially keep cells in the culture
PerpendicularFlowOrientation fluid flow orientation that is the perpendicular (normal) orientation of fluid movement in a process with respect to a defined surface
PlannedCellInfectionProcess planned process in which a cell culture is exposed to a virus inoculum under defined conditions in order to generate a population of infected host cells
PlannedProcessOperatingMode process characteristic of a planned process that characterizes the overall pattern by which process material is introduced into, retained in, and removed from the planned process over an operating interval
PlannedTransductionProcess genetic transformation process of introducing DNA or RNA into cells by a virus or viral vector to modify the cell’s genetic material
ProductionCultureGrowthPhase cell culture expansion process that is a temporal part of a production culture process
ProductionCultureProductionPhase manufacturing process that is a temporal part of a production culture process and during which process conditions are managed primarily to support target product production
SplittingProcess manufacturing process in which a batch or lot of a product or intermediate is divided into two or more separately managed portions for further processing, handling, storage or release
SterileMaterialState material state in which a participating material entity is free of viable microorganisms
SterilizationProcess planned process in which a material entity is rendered free of all viable microorganisms
UpstreamBiomanufacturingProcess manufacturing process that includes preparation, expansion, cultivation, or propagation of biological material under controlled conditions to produce a process intermediate material or material product
VirusInoculationProcess inoculation process in which a virus seed or infected host-cell-containing material is deliberately introduced into a cell culture to initiate viral propagation

Removed

Classes

Construct Definition
PerpendicularlFlowOrientation fluid flow orientation that is the perpendicular (normal) orientation of fluid movement in a process with respect to a defined surface

Changed

Classes

BiomanufacturingProductionProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/BiomanufacturingProductionProcess

Annotations

  • example = “recombinant protein expression using CHO cells; monoclonal antibody production in a bioreactor; viral vector production using HEK293 cells; fermentation process for production of penicillin by Penicillium chrysogenum; mRNA synthesis using enzymatic in vitro transcription;”

  • example = “Biomanufacturing production process where Chinese Hamster Ovary (CHO) cells serve as the mammalian host platform for producing recombinant protein therapeutics; monoclonal antibody production in a bioreactor; viral vector production using HEK293 cells; fermentation process for production of penicillin by Penicillium chrysogenum; mRNA synthesis using enzymatic in vitro transcription;”

CellBanking

  • IRI: https://spec.industrialontologies.org/ontology/construct/CellBanking

Annotations

  • example = “establishing a master cell bank by freezing aliquots of a cloned HEK293 cell line under GMP conditions; banking the Vero cell line in cryopreservation medium supplemented with DMSO and storing it in vapor-phase liquid nitrogen for future vaccine manufacturing; banking a hybridoma cell line after single-cell cloning and characterization to preserve monoclonal antibody production capability”

  • explanatoryNote = “1) It ensures a reliable, consistent, and well-characterized source of cells, reducing the need for constant cell culture and mitigating risks associated with genetic drift or contamination. 2) Examples of future use include research, drug development, and manufacturing of biopharmaceuticals”

  • firstOrderLogicAxiom = “CellBankingProcess(x) → StorageProcess(x) ∧ ∃y (CellLine(y) ∧ hasParticipantAtSomeTime(x, y))”

  • naturalLanguageDefinition = “storage process of preserving and maintaining cell lines for future use”@en-US

  • semiFormalNaturalLanguageAxiom = “if x is a ‘cell banking process’ then x is a ‘storage process’ that ‘has participant at some time’ some ‘cell line’”

  • example = “establishing a master cell bank by freezing portions of a cloned HEK293 cell line under GMP conditions; banking the Vero cell line in cryopreservation medium supplemented with DMSO (dimethyl sulfoxide) and storing it in vapor-phase liquid nitrogen for future vaccine manufacturing; banking a hybridoma cell line after single-cell cloning and characterization to provide a preserved source of cells for monoclonal antibody production”

  • explanatoryNote = “1) Cell banking provides a reliable and consistent source of a cell line for future use, reducing the need for continued propagation and helping to mitigate risks associated with genetic drift or contamination. 2) Examples of future use include research, drug development, and manufacturing of biopharmaceuticals.”

  • firstOrderLogicAxiom = “CellBanking(x) → PlannedProcess(x) ∧ ∃y (CellLine(y) ∧ hasParticipantAtSomeTime(x, y))”

  • naturalLanguageDefinition = “planned process of preserving and maintaining a cell line for future use”@en-US

  • semiFormalNaturalLanguageAxiom = “if x is a ‘cell banking’ then x is a ‘planned process’ that ‘has participant at some time’ some ‘cell line’”

Parents

  • StorageProcess (https://spec.industrialontologies.org/ontology/construct/StorageProcess)

  • PlannedProcess (https://spec.industrialontologies.org/ontology/construct/PlannedProcess)

Axioms

  • SubClassOf: constr:StorageProcess

  • SubClassOf: constr:PlannedProcess

CellCultureExpansionProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/CellCultureExpansionProcess

Annotations

  • firstOrderLogicAxiom = “if x is a ‘cell culture expansion process’ then x is a ‘planned process’ that ‘has input’ some ‘cell culture’ and ‘has occurrent part’ some ‘cell population proliferation’”

  • naturalLanguageDefinition = “planned process in which cells within a cell culture proliferate, resulting in an increase in the total cell number”@en-US

  • semiFormalNaturalLanguageAxiom = “CellCultureExpansionProcess(x) → PlannedProcess(x) ∧ ∃y (CellCulture(y) ∧ hasInput(x, y)) ∧ ∃z (CellPopulationProliferation(z) ∧ hasOccurrentPart(x, z))”

  • explanatoryNote = “Incidental or secondary cell proliferation during a cell culture recovery process or production culture production phase does not by itself make that process a cell culture expansion process.”

  • firstOrderLogicAxiom = “CellCultureExpansionProcess(x) → PlannedProcess(x) ∧ ∃p (CellPopulationProliferation(p) ∧ hasOccurrentPart(x, p)) ∧ ∃c (CellCulture(c) ∧ hasParticipantAtSomeTime(x, c))”

  • naturalLanguageDefinition = “planned cell culture process during which cultivation is managed primarily to increase the total number of cells through cell proliferation”@en-US

  • semiFormalNaturalLanguageAxiom = “if x is a ‘cell culture expansion process’ then x is a ‘planned process’ that ‘has occurrent part’ some ‘cell population proliferation’ and ‘has participant at some time’ some ‘cell culture’”

Disjoint With

  • CellCultureRecoveryProcess (https://spec.industrialontologies.org/ontology/construct/CellCultureRecoveryProcess)

  • ProductionCultureProductionPhase (https://spec.industrialontologies.org/ontology/construct/ProductionCultureProductionPhase)

Axioms

  • SubClassOf: constr:hasInput some constr:CellCulture

  • SubClassOf: bfo:has_participant_at_some_time some constr:CellCulture

  • constr:CellCultureExpansionProcess DisjointWith: (constr:CellCultureRecoveryProcess, constr:ProductionCultureProductionPhase)

CellLineDevelopment

  • IRI: https://spec.industrialontologies.org/ontology/construct/CellLineDevelopment

Annotations

  • explanatoryNote = “1) Cell line development involves one or more clonal selection processes to isolate and expand a genetically stable monoclonal population with desirable traits. 2) Cell line development process ends with the banking of the particular cell line 3) Cell line development is one of the first steps in the process of developing a biopharmaceutical product. This step is time consuming and resource-intense. 4) Engineering in this context means that the cell line is created, either through passaging of a primary cell culture to relative genetic stability and compositional homogeneity, or through some experimental modification of an existing cell line to produce a new line with novel characteristics (e.g. immortalization or some other stable genetic modification). 5) Regulatory standards in biologics require proof of monoclonality for a production cell line. This implies that it originates from a single progenitor cell, regardless of whether one calls it a clone or a line. In practice, a clone is the starting point for development: once selected and scaled, it becomes a permanent cell line with specific attributes used for product manufacture.”

  • firstOrderLogicAxiom = “CellLineDevelopment(x) → ManufacturingProcess(x) ∧ ∃g ∃c (GeneticTransformationProcess(g) ∧ CloneSelectionProcess(c) ∧ hasOccurrentPart(x, g) ∧ hasOccurrentPart(x, c) ∧ precedes(g, c)) ∧ ∃o (CellLine(o) ∧ hasSpecifiedOutput(x, o)) ∧ temporallyStartedBy(x, g) ∧ (∃b (CellBanking(b) ∧ meets(x, b)) ∨ ∃b (CellBanking(b) ∧ temporallyOverlaps(x, b)))”

  • naturalLanguageDefinition = “manufacturing process in which a cell line is engineered to produce a therapeutic biomolecule or biologic”@en-US

  • semiFormalNaturalLanguageAxiom = “if x is a ‘cell line development’ then x is a ‘manufacturing process’ and ‘has occurrent part’ some ‘genetic transformation process’ that ‘precedes’ some ‘clone selection process’ and ‘has occurrent part’ some ‘clone selection process’ and ‘has specified output’ some ‘cell line’ and is ‘temporally started by’ some ‘genetic transformation process’ and either ‘meets’ some ‘cell banking’ or ‘temporally overlaps’ some ‘cell banking’”

  • explanatoryNote = “1) Cell line development involves one or more clonal selection processes to isolate and expand a genetically stable monoclonal population with desirable traits. 2) A cell line development process ends with the banking of the resulting cell line. 3) Cell line development is one of the first steps in the process of developing a biopharmaceutical product. This step is time consuming and resource-intensive. 4) Engineering in this context includes experimental modification of an existing cell population or cell line to establish a new cell line with desired characteristics, such as introduction of genetic material, immortalization, or another stable genetic modification. 5) Regulatory standards in biologics require proof of monoclonality for a production cell line. This implies that it originates from a single progenitor cell, regardless of whether one calls it a clone or a line. In practice, a clone is the starting point for development: once selected and scaled, it becomes a permanent cell line with specific attributes used for product manufacture.”

  • firstOrderLogicAxiom = “CellLineDevelopment(x) → PlannedProcess(x) ∧ ∃g∃c∃l∃b(GeneticTransformationProcess(g) ∧ CloneSelectionProcess(c) ∧ ClonedCellLine(l) ∧ CellBanking(b) ∧ hasOccurrentPart(x,g) ∧ hasOccurrentPart(x,c) ∧ precedes(g,c) ∧ temporallyStartedBy(x,g) ∧ hasSpecifiedOutput(c,l) ∧ hasSpecifiedOutput(x,l) ∧ hasParticipantAtSomeTime(b,l) ∧ (meets(x,b) ∨ temporallyOverlaps(x,b)))”

  • naturalLanguageDefinition = “planned process in which a cell line is engineered to produce a therapeutic biomolecule or biologic”@en-US

  • semiFormalNaturalLanguageAxiom = “if x is a ‘cell line development’ then x is a ‘planned process’ that is ‘temporally started by’ some ‘genetic transformation process’ g and ‘has occurrent part’ g and some ‘clone selection process’ c, where g ‘precedes’ c, and c ‘has specified output’ some ‘cloned cell line’ l that is also the ‘specified output’ of x, and x either ‘meets’ or ‘temporally overlaps’ some ‘cell banking’ that ‘has participant at some time’ that same l”

Parents

  • ManufacturingProcess (https://spec.industrialontologies.org/ontology/construct/ManufacturingProcess)

  • PlannedProcess (https://spec.industrialontologies.org/ontology/construct/PlannedProcess)

Axioms

  • SubClassOf: constr:ManufacturingProcess

  • SubClassOf: constr:PlannedProcess

CellPopulationProliferation

  • IRI: https://spec.industrialontologies.org/ontology/construct/CellPopulationProliferation

Annotations

  • primitiveRationale = “This term is expected to remain primitive. Details of cellular reproduction or multiplications are out of scope and should be utilized if needed from a biological ontology.”

  • primitiveRationale = “This term is expected to remain primitive. Details of cellular reproduction or multiplication are out of scope and should be utilized if needed from a biological ontology.”

CentrifugationProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/CentrifugationProcess

Annotations

  • firstOrderLogicAxiom = “CentrifugationProcess(x) → PlannedProcess(x)”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘centrifugation process’ then x is a ‘planned process’”

  • firstOrderLogicAxiom = “CentrifugationProcess(x) → PlannedProcess(x) ∧ ∃c(Centrifuge(c) ∧ hasParticipantAtSomeTime(x,c))”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘centrifugation process’ then x is a ‘planned process’ that ‘has participant at some time’ some ‘centrifuge’”

Axioms

  • SubClassOf: bfo:has_participant_at_some_time some constr:Centrifuge

CloneSelectionProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/CloneSelectionProcess

Annotations

  • naturalLanguageDefinition = “planned processs in which an optimal set of cell clones is identified and isolated based on the clones exibiting desirable characteristics”@en-US

  • naturalLanguageDefinition = “planned process in which an optimal set of cell clones is identified and isolated based on the clones exhibiting desirable characteristics”@en-US

DiafiltrationProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/DiafiltrationProcess

Annotations

  • explanatoryNote = “Diafiltration can be conducted either in a continous or discontinous manner: Continuous diafiltration: Buffer is added continuously as filtrate is removed, maintaining a constant volume and concentration of the target molecule. Discontinuous diafiltration: Involves diluting the sample, concentrating it back, and repeating this process multiple times.”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘diafiltration process’ then x is a ‘planned process’ and ‘has occurrent part’ some ‘dilution process’ and ‘has occurrent part’ some ‘filtration process’ and the ‘dilution process’ ‘occurs before’ the ‘filtration process’ or ‘occurs simultaneously with’ the ‘filtration process’”

  • explanatoryNote = “Diafiltration can be conducted either in a continuous or discontinuous manner: Continuous diafiltration: Buffer is added continuously as filtrate is removed, maintaining a constant volume and concentration of the target molecule. Discontinuous diafiltration: Involves diluting the sample, concentrating it back, and repeating this process multiple times.”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘diafiltration process’ then x is a ‘planned process’ and ‘has occurrent part’ some ‘dilution process’ and ‘has occurrent part’ some ‘filtration process’ and the ‘dilution process’ is such that it either ‘occurs before’ the ‘filtration process’ or ‘occurs simultaneously with’ the ‘filtration process’”

DilutionProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/DilutionProcess

Annotations

  • firstOrderLogicAxiom = “DilutionProcess(x) → SolutionPreparationProcess(x)”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘dilution process’ then x is a ‘solution preparation process’”

  • firstOrderLogicAxiom = “DilutionProcess(x) → SolutionPreparationProcess(x) ∧ ∃s∃v(Solution(s) ∧ Solvent(v) ∧ hasInput(x,s) ∧ hasInput(x,v))”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘dilution process’ then x is a ‘solution preparation process’ that ‘has input’ some ‘solution’ and ‘has input’ some ‘solvent’”

Axioms

  • SubClassOf: constr:hasInput some constr:Solution

  • SubClassOf: constr:hasInput some constr:Solvent

DirectFlowFiltration

  • IRI: https://spec.industrialontologies.org/ontology/construct/DirectFlowFiltration

Annotations

  • firstOrderLogicDefinition = “DirectFlowFiltrationProcess(x) ↔ FiltrationProcess(x) ∧ ∃y (PerpendicularFlowOrientation(y) ∧ hasProperOccurrentPart(x, y))”

  • semiFormalNaturalLanguageDefinition = “if x is a ‘direct flow filtration process’ then x is a ‘filtration process’ that ‘has proper occurrent part’ some ‘perpendicular flow orientation’”

  • firstOrderLogicDefinition = “DirectFlowFiltration(x) ↔ FiltrationProcess(x) ∧ ∃y (PerpendicularFlowOrientation(y) ∧ hasProcessProfile(x, y))”

  • semiFormalNaturalLanguageDefinition = “every instance of ‘direct flow filtration’ is defined as exactly an instance of ‘filtration process’ that ‘has process profile’ some ‘perpendicular flow orientation’”

Disjoint With

  • TangentialFlowFiltration (https://spec.industrialontologies.org/ontology/construct/TangentialFlowFiltration)

Axioms

  • EquivalentTo: constr:FiltrationProcess and bfo:has_proper_occurrent_part some constr:PerpendicularlFlowOrientation

  • constr:DirectFlowFiltration DisjointWith: constr:TangentialFlowFiltration

  • EquivalentTo: constr:FiltrationProcess and constr:hasProcessProfile some constr:PerpendicularFlowOrientation

FiltrationProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/FiltrationProcess

Annotations

  • explanatoryNote = “1) Passing can be conducted by using gravity or by using pressure. 2) According to the direction of the fluid feed in relation to the filter medium there are two broad types of filtrations. In conventional (a.k.a normal, direct, perpendicular) l filtration, the fluid flows perpendicular to the medium which results in a cake of solids depositing on the filter medium. In tangential flow filtration the fluid flows parallel to the medium to minimize buildup of solids on the medium. Given that flow direction is the key differentiating characteristic, tangential flow filtration and normal flow filtration are modeled as defined subclasses of filtration. 3) Filtration is a separation technique predominantly based on particle size, where components are retained or passed through a porous medium depending on their dimensions relative to the pore size. However, in some cases, additional characteristics such as particle shape and electrostatic charge can significantly influence retention behavior and selectivity of the filter used in the process.”

  • adaptedFrom = “http://purl.obolibrary.org/obo/CHMO_0001640”

  • explanatoryNote = “1) Passing can be conducted by using gravity or by using pressure. 2) According to the direction of the fluid feed in relation to the filter medium there are two broad types of filtrations. In conventional (a.k.a normal, direct, perpendicular) filtration, the fluid flows perpendicular to the medium which results in a cake of solids depositing on the filter medium. In tangential flow filtration the fluid flows parallel to the medium to minimize buildup of solids on the medium. Given that flow direction is the key differentiating characteristic, tangential flow filtration and normal flow filtration (direct flow filtration) are modeled as defined subclasses of filtration. 3) Filtration is a separation technique predominantly based on particle size, where components are retained or passed through a porous medium depending on their dimensions relative to the pore size. However, in some cases, additional characteristics such as particle shape and electrostatic charge can significantly influence retention behavior and selectivity of the filter used in the process.”

GeneticTransformationProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/GeneticTransformationProcess

Annotations

  • example = “transfection of a mammalian cell; transduction of a CHO cell by a retrovirus containing a genetic sequence of a particular mAb; Gene deletion by CRISPR-CAS9; introducing mutation in the cells by error prone PCR”

  • example = “transfection of a mammalian cell; transduction of a CHO cell by a retrovirus containing a genetic sequence of a particular mAb; Gene deletion by using the CRISPR-CAS9 gene editing technology;”

HarvestingProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/HarvestingProcess

Annotations

  • adaptedFrom = “https://books.google.rs/books?hl=sr&lr=&id=p-rKBQAAQBAJ&oi=fnd&pg=PP1&dq=bioseparation+processes+harvesting&ots=eFDtLSUJ0I&sig=XjzTFnAmknXNjFlSWHpkkTtpHg0&redir_esc=y#v=onepage&q=bioseparation%20processes%20harvesting&f=false””

  • adaptedFrom = “https://books.google.rs/books?hl=sr&lr=&id=p-rKBQAAQBAJ&oi=fnd&pg=PP1&dq=bioseparation+processes+harvesting&ots=eFDtLSUJ0I&sig=XjzTFnAmknXNjFlSWHpkkTtpHg0&redir_esc=y#v=onepage&q=bioseparation%20processes%20harvesting&f=false”

LiquidChromatographyProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/LiquidChromatographyProcess

Annotations

  • example = “separating protein isoforms using ion exchange chromatography with a buffered liquid mobile phase; analyzing small molecule impurities in a drug product using reversed-phase HPLC; quantifying monoclonal antibody titer using protein A affinity chromatography;”

  • example = “separating protein isoforms using ion exchange chromatography with a buffered liquid mobile phase; analyzing small molecule impurities in a drug product using reversed-phase High-Performance Liquid Chromatography (HPLC); quantifying monoclonal antibody titer using protein A affinity chromatography;”

MediaSolutionPreparation

  • IRI: https://spec.industrialontologies.org/ontology/construct/MediaSolutionPreparation

Annotations

  • example = “dissolving CHO cell culture media powder in water for use in a fed-batch bioreactor; diluting a 10× DMEM stock solution with water to prepare a 1× working media solution; preparing Glasgow Minimum Essential Medium (GMEM) by dissolving powdered GMEM in a sodium bicarbonate buffer”

  • firstOrderLogicAxiom = “MediaSolutionProcess(x) → SolutionPreparationProcess(x) ∧ ∃y (CultureMedium(y) ∧ hasSpecifiedOutput(x, y) ∧ ∃z (InputSpecification(z) ∧ satisfiesRequirement(y, z)))”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘media solution process’ then x is a ‘solution preparation process’ that ‘has specified output’ some ‘culture medium’ and ‘satisfies requirement’ some ‘input specification’”

  • example = “dissolving CHO cell culture media powder in water for use in a fed-batch bioreactor; diluting a 10× Dulbecco’s Modified Eagle Medium (DMEM) stock solution with water to prepare a 1× working media solution; preparing Glasgow Minimum Essential Medium (GMEM) by dissolving powdered GMEM in a sodium bicarbonate buffer”

  • firstOrderLogicAxiom = “MediaSolutionPreparation(x) → SolutionPreparationProcess(x) ∧ ∃y(CultureMedium(y) ∧ hasSpecifiedOutput(x,y) ∧ ∃z(InputSpecification(z) ∧ satisfiesRequirement(y,z)))”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘media solution preparation’ then x is a ‘solution preparation process’ that ‘has specified output’ some ‘culture medium’ that ‘satisfies requirement’ some ‘input specification’”

NanofiltrationProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/NanofiltrationProcess

Annotations

  • explanatoryNote = “The stated pore-size values indicate the characteristic scale associated with nanofiltration and are not intended to establish exact lower or upper classification boundaries. A membrane filtration process may still be classified as a nanofiltration process when the nominal pore-size rating lies near or modestly outside this interval, provided that the membrane and its retention performance are recognized as nanofiltration.”

NormalPhaseChromatographyProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/NormalPhaseChromatographyProcess

Annotations

  • example = “A phospholipid extract was separated into distinct lipid classes using a polar silica stationary phase and a mobile phase consisting of hexane and isopropanol; A racemic small molecule API was purified to isolate the active enantiomer using a chiral polar stationary phase and a mobile phase of heptane and ethanol; A glycan mixture derived from enzymatic deglycosylation was separated based on polarity using an amino-functionalized silica stationary phase and an acetonitrile–water mobile phase”

  • example = “Chromatography process in which a phospholipid extract was separated into distinct lipid classes using a polar silica stationary phase and a mobile phase consisting of hexane and isopropanol; Chromatography process in which a racemic small molecule API was purified to isolate the active enantiomer using a chiral polar stationary phase and a mobile phase of heptane and ethanol; Chromatography process in which a glycan mixture derived from enzymatic deglycosylation was separated based on polarity using an amino-functionalized silica stationary phase and an acetonitrile–water mobile phase”

PolishingProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/PolishingProcess

Annotations

  • naturalLanguageDefinition = “purification process in which minute amounts of impurities are removed and that occurs as one of the final processes of drug substance manufacturing process”@en-US

  • naturalLanguageDefinition = “purification process in which minute amounts of impurities are removed and that occurs as one of the final processes of a drug substance manufacturing process”@en-US

PoolingProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/PoolingProcess

Annotations

  • explanatoryNote = “1) This process is typically employed to reduce batch-to-batch variability or to ensure consistent quality attributes before further processing or final release. 2) Pooling can be used to define a lot of material for further processing or release, ensuring a consistent product stream. 3) Not to be confused with Test pooling, which is a testing strategy where individual samples are combined into a single pooled sample for initial testing. If the pooled sample tests negative/correct, all individuals in the pool are considered negative/correct. If the pooled sample tests positive/out of specs, individual samples within the pool are then re-tested to identify the positive/out of specs individual(s). This method is used to reduce testing costs and resources, particularly when dealing with a large number of samples and a low prevalence of the target condition.”

  • firstOrderLogicAxiom = “PoolingProcess(x) → ManufacturingProcess(x)”

  • naturalLanguageDefinition = “manufacturing process in which two or more batches of a product or intermediate are combined to produce a single, larger volume that is more homogenous”@en-US

  • semiFormalNaturalLanguageAxiom = “if x is a ‘pooling process’ then x is a ‘manufacturing process’”

  • explanatoryNote = “1) This process is typically employed to reduce batch-to-batch variability or to ensure consistent quality attributes before further processing or final release. 2) Pooling can be used to define a lot of material for further processing or release, ensuring a consistent product stream. 3) Not to be confused with Test pooling, which is a testing strategy where individual samples are combined into a single pooled sample for initial testing. If the pooled sample tests negative/correct, all individuals in the pool are considered negative/correct. If the pooled sample tests positive/out of specification, individual samples within the pool are then re-tested to identify the positive/out of specification individual(s). This method is used to reduce testing costs and resources, particularly when dealing with a large number of samples and a low prevalence of the target condition.”

  • firstOrderLogicAxiom = “PoolingProcess(x) → ∃m1∃m2(((MaterialProduct(m1) ∨ ProcessIntermediateMaterial(m1)) ∧ (MaterialProduct(m2) ∨ ProcessIntermediateMaterial(m2))) ∧ hasInput(x,m1) ∧ hasInput(x,m2) ∧ m1 ≠ m2)”

  • naturalLanguageDefinition = “manufacturing process in which two or more batches of a product or intermediate are combined to produce a single, larger volume that is more homogeneous”@en-US

  • semiFormalNaturalLanguageAxiom = “if x is a ‘pooling process’ then x ‘has input’ at least two distinct entities that are each a ‘material product’ or ‘process intermediate material’”

Axioms

  • SubClassOf: constr:hasInput some (constr:MaterialProduct or constr:ProcessIntermediateMaterial)

ReversePhaseChromatographyProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/ReversePhaseChromatographyProcess

Annotations

  • example = “A synthetic peptide was purified to remove synthesis byproducts using a C18-bonded silica stationary phase and a mobile phase composed of water and acetonitrile with 0.1% TFA;A monoclonal antibody digest was resolved to quantify fragment abundance using a hydrophobic C18 stationary phase and a mobile phase gradient of water and methanol with 0.1% formic acid”

  • adaptedFrom = “http://wolfson.huji.ac.il/purification/PDF/affinity/GE_Affinity_Chromatography_Handbook-Antibodies.pdf and CHMO:0002302 and https://www.sigmaaldrich.com/RS/en/technical-documents/protocol/analytical-chemistry/purification/reverse-phased-chromatography-in-practice?srsltid=AfmBOorOQim54doE5guL_YoH41EUR9xT6oikpa5rJhbNFAYeFTiIxs0I”

  • example = “Chromatography process in which a synthetic peptide was purified to remove synthesis byproducts using a C18-bonded silica stationary phase and a mobile phase composed of water and acetonitrile with 0.1% trifluoroacetic acid (TFA); Chromatography process in which a monoclonal antibody digest was resolved to quantify fragment abundance using a hydrophobic C18 stationary phase and a mobile phase gradient of water and methanol with 0.1% formic acid”

  • adaptedFrom = “http://wolfson.huji.ac.il/purification/PDF/affinity/GE_Affinity_Chromatography_Handbook-Antibodies.pdf and http://purl.obolibrary.org/obo/CHMO_0002302 and https://www.sigmaaldrich.com/RS/en/technical-documents/protocol/analytical-chemistry/purification/reverse-phased-chromatography-in-practice?srsltid=AfmBOorOQim54doE5guL_YoH41EUR9xT6oikpa5rJhbNFAYeFTiIxs0I”

SeedTrain

  • IRI: https://spec.industrialontologies.org/ontology/construct/SeedTrain

Annotations

  • example = “a monoclonal antibody seed train expanded CHO cells through sequential steps in shake flasks, a 10 L bioreactor, and a 200 L seed bioreactor based on target inoculation density;CHO suspension cells were expanded through a seed train process involving shake flasks, benchtop bioreactors, and a 5,000 L production bioreactor;”

  • explanatoryNote = “1) The seed train is a series of steps used to generate the sufficient amount of viable cells for large-scale production of vaccines, viral vectors, monoclonal antibodies and other biologics. The purpose of the seed train is to progressively grow and expand the initial small-scale cell culture to inoculate the large-scale bioreactor for higher capacity production. 2) A single cell culture expansion process within the seed train is also called as a “passage” 3)>the following terms are commonly used when discussing a seed train or inoculum expansion with multiple steps: “N” refers to the production vessel; “N-1” refers to the final expansion used to inoculate the production vessel; “N-2” refers to the expansion before that, used to inoculate the N-1, and so on”

  • firstOrderLogicDefinition = “SeedTrain(x) ↔ ManufacturingProcess(x) ∧ ∃a (CellCulture(a) ∧ hasInput(x, a)) ∧ ∃b (CellCultureExpansionProcess(b) ∧ hasOccurrentPart(x, b)) ∧ ∃c (CellCulture(c) ∧ hasSpecifiedOutput(x, c) ∧ ∃i ∃p ∃s (InputSpecification(i) ∧ PlanSpecification(p) ∧ RecipeProcessStage(s) ∧ satisfiesRequirement(c, i) ∧ continuantPartOfAtAllTimes(i, p) ∧ prescribes(p, s) ∧ ProductionCultureProcess(y) ∧ prescribes(s, y)))”

  • semiFormalNaturalLanguageDefinition = “every instance of ‘seed train’ is defined as exactly an instance of ‘manufacturing process’ that ‘has input’ some ‘cell culture’, ‘has occurrent part’ some ‘cell culture expansion process’, and ‘has specified output’ some ‘cell culture’ that ‘satisfies requirement’ some ‘input specification’ that is ‘continuant part of at all times’ some ‘plan specification’ that ‘prescribes’ some ‘recipe process stage’ that ‘prescribes’ some ‘production culture process’”

  • example = “a monoclonal antibody seed train expanded CHO cells through sequential steps in shake flasks, a 10 L bioreactor, and a 200 L seed bioreactor based on target inoculation density; a seed train progressing through shake flasks and seed bioreactors to generate inoculum for a 5,000 L production bioreactor”

  • explanatoryNote = “1) The seed train is a series of steps used to generate the sufficient amount of viable cells for large-scale production of vaccines, viral vectors, monoclonal antibodies and other biologics. The purpose of the seed train is to progressively grow and expand the initial small-scale cell culture to inoculate the large-scale bioreactor for higher capacity production. 2) A single cell culture expansion process within the seed train is also called a “passage” 3) The following terms are commonly used when discussing a seed train or inoculum expansion with multiple steps: “N” refers to the production vessel; “N-1” refers to the final expansion used to inoculate the production vessel; “N-2” refers to the expansion before that, used to inoculate the N-1, and so on”

  • firstOrderLogicDefinition = “SeedTrain(x) ↔ ManufacturingProcess(x) ∧ ∃a (CellCulture(a) ∧ hasInput(x, a)) ∧ ∃b (CellCultureExpansionProcess(b) ∧ hasOccurrentPart(x, b)) ∧ ∃c (CellCulture(c) ∧ hasSpecifiedOutput(x, c) ∧ ∃i ∃p ∃y (InputSpecification(i) ∧ PlanSpecification(p) ∧ satisfiesRequirement(c, i) ∧ continuantPartOfAtAllTimes(i, p) ∧ ProductionCultureProcess(y) ∧ prescribes(p, y)))”

  • semiFormalNaturalLanguageDefinition = “every instance of ‘seed train’ is defined as exactly an instance of ‘manufacturing process’ that ‘has input’ some ‘cell culture’, ‘has occurrent part’ some ‘cell culture expansion process’, and ‘has specified output’ some ‘cell culture’ that ‘satisfies requirement’ some ‘input specification’ that is ‘continuant part of at all times’ some ‘plan specification’ that ‘prescribes’ some ‘production culture process’”

SolutionPreparationProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/SolutionPreparationProcess

Annotations

  • firstOrderLogicAxiom = “SolutionPreparationProcess(x) → PlannedProcess(x)”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘solution preparation process’ then x is a ‘planned process’”

  • firstOrderLogicAxiom = “SolutionPreparationProcess(x) → PlannedProcess(x) ∧ ∃s(Solution(s) ∧ hasSpecifiedOutput(x,s))”

  • semiFormalNaturalLanguageAxiom = “if x is a ‘solution preparation process’ then x is a ‘planned process’ that ‘has specified output’ some ‘solution’”

Axioms

  • SubClassOf: constr:hasSpecifiedOutput some constr:Solution

TangentialFlowFiltration

  • IRI: https://spec.industrialontologies.org/ontology/construct/TangentialFlowFiltration

Annotations

  • firstOrderLogicDefinition = “TangentialFlowFiltrationProcess(x) ↔ FiltrationProcess(x) ∧ ∃y (TangentialFlowOrientation(y) ∧ hasProperOccurrentPart(x, y))”

  • semiFormalNaturalLanguageDefinition = “every instance of ‘tangential flow filtration process’ is defined as exactly an instance of ‘filtration process’ that ‘has proper occurrent part’ some ‘tangential flow orientation’”

  • firstOrderLogicDefinition = “TangentialFlowFiltration(x) ↔ FiltrationProcess(x) ∧ ∃y (TangentialFlowOrientation(y) ∧ hasProcessProfile(x, y))”

  • semiFormalNaturalLanguageDefinition = “every instance of ‘tangential flow filtration’ is defined as exactly an instance of ‘filtration process’ that ‘has process profile’ some ‘tangential flow orientation’”

Disjoint With

  • DirectFlowFiltration (https://spec.industrialontologies.org/ontology/construct/DirectFlowFiltration)

Axioms

  • EquivalentTo: constr:FiltrationProcess and bfo:has_proper_occurrent_part some constr:TangentialFlowOrientation

  • constr:TangentialFlowFiltration DisjointWith: constr:DirectFlowFiltration

  • EquivalentTo: constr:FiltrationProcess and constr:hasProcessProfile some constr:TangentialFlowOrientation

TangentialFlowOrientation

  • IRI: https://spec.industrialontologies.org/ontology/construct/TangentialFlowOrientation

Disjoint With

  • PerpendicularlFlowOrientation (https://spec.industrialontologies.org/ontology/construct/PerpendicularlFlowOrientation)

  • PerpendicularFlowOrientation (https://spec.industrialontologies.org/ontology/construct/PerpendicularFlowOrientation)

Axioms

  • constr:TangentialFlowOrientation DisjointWith: constr:PerpendicularlFlowOrientation

  • constr:TangentialFlowOrientation DisjointWith: constr:PerpendicularFlowOrientation

ThawingProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/ThawingProcess

Annotations

  • naturalLanguageDefinition = “planned process in which the temperature of a material entity is raised in a controlled manner to specified setpoint, typically to transition it from a solid or frozen state to a soft or liquid state”@en-US

  • naturalLanguageDefinition = “planned process in which the temperature of a material entity is raised in a controlled manner to a specified setpoint, typically to transition it from a solid or frozen state to a soft or liquid state”@en-US

UltrafiltrationProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/UltrafiltrationProcess

Annotations

  • example = “Ultrafiltration is used in cheese making to concentrate casein and whey proteins while removing water, lactose, and soluble components; In mAb production, ultrafiltration concentrates antibody solutions before formulation;Ultrafiltration is applied to remove host cell proteins and buffer exchange before viral filtration”

  • explanatoryNote = “Ultrafiltration (UF) is a variety of membrane filtration in which forces such as pressure or concentration gradients lead to a separation through a semipermeable membrane. Suspended solids and solutes of high molecular weight are retained in the so-called retentate, while water and low molecular weight solutes pass through the membrane in the permeate (filtrate).”

  • example = “Ultrafiltration is used in cheese making to concentrate casein and whey proteins while removing water, lactose, and soluble components; In mAb production, ultrafiltration concentrates antibody solutions before formulation; Ultrafiltration is applied to remove host cell proteins and as part of buffer exchange before viral filtration”

  • explanatoryNote = “1) Ultrafiltration (UF) is a variety of membrane filtration in which forces such as pressure or concentration gradients lead to a separation through a semipermeable membrane. Suspended solids and solutes of high molecular weight are retained in the so-called retentate, while water and low molecular weight solutes pass through the membrane in the permeate (filtrate). 2) The stated pore-size values indicate the characteristic scale associated with ultrafiltration and are not intended to establish exact lower or upper classification boundaries. A membrane filtration process may still be classified as an ultrafiltration process when the nominal pore-size rating lies near or modestly outside this interval, provided that the membrane and its retention performance are recognized as ultrafiltration.”

ViralInactivation

  • IRI: https://spec.industrialontologies.org/ontology/construct/ViralInactivation

Annotations

  • explanatoryNote = “1) In viral inactivation the viral particles are not necessairly removed from the input 2) Common inactivation methods include heat (e.g., pasteurization), acidic pH, solvent-detergent treatment, or UV exposure. Effectiveness is validated through spiking studies: known amounts of virus are added to the process and their infectivity is monitored over time.”

  • explanatoryNote = “1) In viral inactivation the viral particles are not necessarily removed from the input 2) Common inactivation methods include heat (e.g., pasteurization), acidic pH, solvent-detergent treatment, or UV exposure. Effectiveness is validated through spiking studies: known amounts of virus are added to the process and their infectivity is monitored over time.”

ViralRemovalProcess

  • IRI: https://spec.industrialontologies.org/ontology/construct/ViralRemovalProcess

Annotations

  • example = “anion exchange chromatography operated in flow-through mode to remove retrovirus-like particles from CHO cell harvest;nanofiltration of plasma-derived products to remove non-enveloped viruses; use of tangential flow filtration to separate viral particles from cell lysate during vaccine production”

  • example = “anion exchange chromatography operated in flow-through mode to remove retrovirus-like particles from CHO cell harvest; nanofiltration of plasma-derived products to remove non-enveloped viruses; tangential flow filtration used to remove contaminating virus particles from a process intermediate during manufacture of a nonviral biological product”

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