Changes in 🟢 Biopharma Material Ontology

Maturity: 🟢 Released

Added

Classes

Construct	Definition
`AcidifyingAgentRole`	pH adjusting agent role of a material entity when it is used, or planned to be used, to lower pH
`AlkalizingAgentRole`	pH adjusting agent role of a material entity when it is used, or planned to be used, to raise pH
`AmountOfSubstance`	quality of a material entity that is proportional to the number of elementary entities of a particular kind present in that material entity
`AntifoamingAgent`	material entity with an antifoaming agent role
`AntifoamingAgentRole`	role of a material entity when it is used, or planned to be used, to reduce or prevent foam formation in a liquid
`BacteriumCell`	cell that lacks a membrane-bound nucleus and has ribosomes of the bacterial type
`BasalCultureMedium`	culture medium which has the basal culture medium role
`BasalCultureMediumRole`	role held by a culture medium when it is used or planned to be used either directly in a cell culture process to provide essential nutritional and physicochemical support or together with supplements to prepare a complete culture medium for such a process
`Bioburden`	relational quality of a material entity that is the extent to which viable microorganisms are present in or on the surface of the material entity
`BioproductionSupportingFunction`	culture medium specialized function that enables the generation of a target biological product by sustaining cellular activity under production conditions
`BufferSolution`	solution consisting of a mixture of a weak acid and its conjugate base or a weak base and its conjugate acid which is resistant to pH changes upon addition of an acidic or basic component
`BufferingAgentRole`	role of a material entity when it is added or planned to be added to a mixture, typically aqueous, to enable or enhance the mixture’s resistance to changes in pH upon the addition of small amounts of acid or base
`BufferingCapability`	capability of a solution to resist a change in pH when acid or base is added
`BufferingFunction`	function of a solution to resist a change in pH when an acid or base is added
`BulkDensity`	mass density of a particulate material that is the mass per total bulk volume occupied by the material, where the total bulk volume includes particle volume, pore volume within particles, and void volume between particles
`CakingPropensity`	disposition of a particulate material entity to form persistent lumps, agglomerates, or a coherent solid mass
`CarbonSourceRole`	nutrient role held by a material entity that provides carbon used by an organism or cell for biosynthesis, energy generation, or both
`CellBank`	object aggregate consisting of containers whose contents are uniform portions derived from a single pool of cells and that are stored under defined conditions as a referenceable source of cells
`CellCount`	count that is the number of cells that are present as parts of a material entity
`CellCultureDerivedImpurityRole`	manufacturing process related impurity role held by a material entity that originates from an acellular material component of a cell culture
`CellDensity`	number density that is the number of cells per unit size
`CellProliferationSupportingFunction`	specialized culture medium function that supports cell division and maintenance of cell viability during expansion culture by providing appropriate nutrients and culture-supporting physicochemical properties
`CellSubstrateDerivedImpurityRole`	manufacturing process related impurity role held by a material entity that originates from cells used in a manufacturing process
`CellViabilityRatio`	relative abundance that is the number of viable cells in a cell population relative to the total number of cells in that population
`ChemicalSubstanceMaterial`	material entity that is made primarily of one kind of molecular entity, allowing for minor impurities
`ChemicallyDefinedCultureMedium`	serum free culture medium in which each component and its concentration are known and reproducible, and that excludes undefined components such as serum, extracts, or hydrolysates
`CompendialGradeClassifier`	material grade classifier that classifies a material entity as conforming to the requirements stated in an applicable pharmacopeial monograph
`CompleteCultureMedium`	culture medium which has the complete culture medium role
`CompleteCultureMediumRole`	role held by a culture medium when it is used or planned for direct use in a cell culture process to meet the full set of nutritional, biological, and physicochemical requirements specified for that process without requiring prior supplementation
`Concentration`	relational quality of a mixture that is the amount of substance or number or mass or volume of a specified constituent of the mixture per unit volume of that mixture
`ContaminantRole`	material impurity role held by a material entity when it is adventitiously introduced during a manufacturing process
`CryoprotectiveAgentRole`	protective agent role of a material entity when it is used, or planned to be used, to protect one or more other material entities from damage during cooling, freezing, frozen storage, or thawing
`CultureMediumSupplement`	material entity that has a culture medium supplement role
`CultureMediumSupplementRole`	material component role held by a material entity when it is added or planned to be added to culture media to enrich or modify the medium composition or functional properties
`CulturePreservationFunction`	culture medium specialized function that maintains cell viability and structural integrity during storage and transport by providing physicochemical conditions and protective components that minimize cellular stress under refrigerated or cryogenic conditions
`Dead`	viability status of a biological material entity that has irreversibly ceased to maintain the biological processes characteristic of life
`DeadCellCount`	cell count that is the number of dead cells that are present as parts of a material entity
`DeadCellDensity`	cell density that is the number of dead cells per unit size
`DeadCellPopulation`	cell population consisting of only dead cells
`DissolutionRole`	role held by a material entity that is realized in a dissolution process in which it participates in forming a solution
`DissolvedOxygenSaturationRatio`	solution saturation ratio that is the dissolved oxygen concentration in a liquid solution relative to the dissolved oxygen saturation concentration in that liquid solution
`DownstreamDerivedImpurityRole`	manufacturing process related impurity role held by a material entity that originates from a raw material, production consumable, or equipment used in a downstream manufacturing process
`DustingPropensity`	disposition of a particulate material entity to generate airborne particulate matter during handling or processing
`EmulsionPropensity`	disposition of a material entity to form an emulsion
`EnergySubstrateRole`	nutrient role held by a material entity that is metabolized in cellular pathways to generate adenosine triphosphate, reducing equivalents, or other forms of metabolic energy required for growth, maintenance, or biosynthesis
`EquilibriumSaturationConcentration`	solution saturation concentration of a particular solute at thermodynamic equilibrium
`ExpansionCultureMedium`	specialized culture medium that has a cell proliferation supporting function
`ExtractableAndLeachableImpurityRole`	material impurity role held by a material entity in virtue of that material entity being present in a target material as a result of transfer from an artifact that contacts the target material
`Filterability`	capability of a fluid to pass through a filtration medium without undue blockage or loss of permeability
`Flowability`	capability of a material entity to move by flow
`Foamability`	capability of a liquid to form foam during a particular process
`Hygroscopicity`	capability of a material entity to attract and hold moisture from the surrounding environment
`ImpurityFraction`	fraction of a material entity that is determined by the proportion of material considered an impurity relative to the material entity as a whole
`InfectedHostCell`	cell that is infected by a virus or another type of microorganism
`InoculumRole`	role held by a material entity containing biological material when it is being added, or is planned to be added, to initiate or establish biological growth, culture, infection, propagation or biological response
`IntactMolecularMass`	molecular mass of a molecular entity or molecular entity population considered in its whole, intact form, without fragmentation, cleavage, or removal of any covalently bound parts
`IntermediateStockSolutionRole`	stock solution role held by a solution when the solution is prepared by diluting another stock solution and is used, or planned to be used, to prepare further dilutions
`IsoelectricPoint`	electrical quality of a molecular entity that corresponds to the pH of a homogeneous aqueous mixture at which that molecular entity has zero net electric charge and does not migrate in an electric field
`ManufacturingProcessRelatedImpurityRole`	material impurity role held by a material entity that is present in a process intermediate material or material product and whose presence is attributable to planned or inherent aspects of manufacturing execution
`MassConcentration`	concentration that is the mass of a specified constituent of a mixture per unit volume of that mixture
`MasterCellBank`	cell bank produced in a single preparation event from a well-characterized cell line or clone, stored under validated cryogenic conditions, and established as the authoritative reference lot for direct use or the generation of further banks
`MaterialDifferentiationInducer`	material entity with a material differentiation inducer role
`MaterialDifferentiationInducerRole`	role held by a material entity when it is used, or planned to be used to activate signaling pathways that drive cell fate decisions, lineage commitment, or functional specialization within a cell culture
`MaterialFunctionalInducer`	material entity with a material functional inducer role
`MaterialFunctionalInducerRole`	role held by a material entity when it is used, or planned to be used, to trigger, enhance, or repress a specified cellular activity or pathway in a cell culture, organism, or microbial community beyond baseline nutrient support
`MaterialGradeClassifier`	classifier that classifies a material entity into an organization- or authority-defined material grade based on the material entity’s conformance to a documented set of acceptance requirements and associated controls
`MaterialMetabolicInducer`	material entity with a material metabolic inducer role
`MaterialMetabolicInducerRole`	role held by a material entity when it is used, or planned to be used to activate expression of enzymes or pathways involved in the utilization or regulation of metabolites within a cell culture, organism, or microbial community
`MaterialProductionInducer`	material entity with a material production inducer role
`MaterialProductionInducerRole`	role held by a material entity when it is added, or planned to be added, to a cell culture to trigger the synthesis of a target product
`Miscibility`	capability of two or more material entities to form a single homogeneous phase when combined as a mixture
`MixedMaterial`	material entity composed of at least two material constituents that are distinct in chemical identity or material composition, excluding constituents present only as minor impurities
`MoistureContent`	ratio that is the mass of water contained in a material entity relative to a defined reference mass of that material entity
`MolarConcentration`	concentration that is the amount of substance of a specified constituent of a mixture per unit volume of that mixture
`MolecularCarrierRole`	role of a material entity when it supports the transport, or delivery of one or more molecular entities in a physical, chemical, or biological system without serving primarily as a reactant in their chemical transformation
`MolecularMass`	mass that is either the mass of a molecular entity or an average of the masses of the molecular entities in a molecular entity population
`MycoplasmaCell`	bacterium cell that lacks a rigid cell wall and is capable of infecting mammalian cells
`NitrogenSourceRole`	nutrient role held by a material entity that provides nitrogen for synthesis of amino acids, nucleotides, and other nitrogen-containing cellular material
`NonGlycosylatedMolecularMass`	molecular mass of a glycoprotein or population of glycoproteins that characterizes the mass contribution of its non-glycan molecular structure
`NutrientFeed`	material entity with a nutrient feed role
`NutrientFeedRole`	role held by a material entity when it is added, or planned to be added, to a cell culture during cultivation or production to supply or replenish nutrients
`NutrientRole`	role held by a material entity that is made available to an organism or cell to support metabolism, growth, maintenance, or biomass formation by providing energy for cellular activities or to build or maintain cellular material
`Osmolality`	relational quality of a solution that is the amount of osmotically active solute entities in that solution per unit mass of solvent
`Osmolarity`	relational quality of a solution that is the amount of osmotically active solute entities in that solution per unit volume of that solution
`PH`	quality of a material entity that is quantified as the negative decimal logarithm of the relative activity of hydrogen ions in that material entity
`PHAdjustingAgentRole`	role of a material entity when it is used, or planned to be used to adjust pH
`PartialPressure`	pressure that is the contribution of a particular gaseous constituent of a gas mixture to the total pressure of that mixture
`PharmaceuticalDegradationProductImpurityRole`	pharmaceutical product related impurity role held by a material entity that differs from the targeted drug substance or drug product as a result of chemical change occurring during manufacture or storage
`PharmaceuticalProductRelatedImpurityRole`	material impurity role held by a material entity that is related to the targeted drug substance or drug product but is not part of the desired product composition or accepted product heterogeneity at the relevant stage and does not have properties comparable to the desired product with respect to safety, efficacy or activity
`PortionOfWater`	chemical substance material composed primarily of water molecules, allowing for minor impurities arising from production, handling, or environmental exchange
`PortionOfWaterForInjection`	portion of water that is classified by a water for injection classifier
`PrecipitationPropensity`	disposition of a liquid mixed material to form an insoluble solid phase from dissolved constituents
`PreservationCultureMedium`	specialized culture medium that has a culture preservation function
`ProductionCultureMedium`	specialized culture medium that has a bioproduction supporting function
`ProtectiveAgentRole`	role of a material entity when it is used or planned to be used to protect one or more other material entities from stress or damage
`ProteinFreeCultureMedium`	serum free culture medium that does not include any proteins
`ProteinHydrolysate`	mixed material produced by partial or extensive hydrolysis of protein-containing material and composed primarily of oligopeptides, peptides, and free amino acids
`Reconstitutability`	capability of a dried or concentrated material entity to form a liquid mixture that satisfies specified usage requirements when combined with an appropriate solvent or diluent
`RelativeAbundance`	ratio that is determined by the magnitude of a specified member or subset of a defined group of material entities relative to the total magnitude of that group
`RelativeHumidity`	saturation ratio of a gas mixture whose magnitude is the partial pressure of water vapor in that gas mixture relative to the saturation vapor pressure of water under the same temperature conditions
`SaturatedState`	material state of a solution in which the dissolved solute concentration stays at the solute’s equilibrium saturation concentration in that solution under prevailing conditions
`SaturationRatio`	ratio of a material entity whose magnitude is the magnitude of a quality of that material entity relative to the magnitude at the saturation limit for that quality under defined conditions
`Serum`	mixed material that is obtained from blood following coagulation and removal of cells and clotting factors
`SerumContainingCultureMedium`	culture medium that contains serum
`SerumFreeCultureMedium`	culture medium that contains no serum
`ShearProtectiveAgentRole`	protective agent role of a material entity when it is used, or planned to be used, to protect one or more other material entities from mechanical damage caused by shear stress
`SolubilityCapability`	capability of a material entity to dissolve in a particular solvent
`Solute`	material entity with a solute role
`SoluteRole`	dissolution role held by a material entity that is realized in a process where it is dissolved within another substance (the solvent) to form a solution
`Solution`	mixed material composed of one homogeneous phase in which constituent particles are not visible to the naked eye and that does not exhibit visible light scattering characteristic of a colloidal dispersion
`SolutionSaturationConcentration`	concentration of a dissolved solute in a solution at the solubility limit of that solute under stated conditions
`SolutionSaturationRatio`	saturation ratio of a solution whose magnitude is the concentration of a dissolved solute in that solution relative to the saturation concentration of that solute for the solution under the same conditions
`SolutionSaturationState`	material state of a solution in which the dissolved solute concentration stays below, at, or above the solute’s equilibrium saturation concentration in that solution under prevailing conditions
`Solvent`	material entity with a solvent role
`SolventRole`	dissolution role held by a material entity that is realized in a process where it dissolves another substance (the solute) to form a solution
`SpecializedCultureMedium`	culture medium that has a specialized culture medium function
`SpecializedCultureMediumFunction`	designed function that inheres in a culture medium and is specified to satisfy the culture requirements of a particular cell type, tissue, microorganism, or cultivation application, often through selective supplements or tailored nutrient formulations
`SpentCultureMediumState`	material state of culture medium that has participated in a cell cultivation process and is characterized by compositional changes caused by cellular activity, process additions, or accumulation of extracellular material
`StockSolutionRole`	role held by a solution that is prepared with an accurately known solute concentration so that measured portions can be diluted to the concentration needed for a particular use
`SupersaturatedState`	solution saturation state in which the dissolved solute concentration stays above the solute’s equilibrium saturation concentration in that solution under prevailing conditions
`SurfaceTension`	quality of a liquid material entity that is the resistance of the liquid surface to an increase in surface area, arising from unbalanced cohesive forces between molecules at the liquid surface
`Surfactant`	material entity with a surfactant role
`SurfactantRole`	role of a material entity when it is used, or planned to be used, to lower the surface tension of a medium or the interfacial tension between phases by preferentially adsorbing at liquid-vapor or other phase interfaces
`TappedDensity`	mass density of a particulate material that is the mass per tapped volume occupied by the material after tapping until little or no further volume change is observed
`TotalCellCount`	cell count that is the number of all cells present as parts of a material entity
`TotalCellDensity`	cell density that is the total number of cells per unit size
`UnsaturatedState`	material state of a solution in which the dissolved solute concentration stays below the solute’s equilibrium saturation concentration in that solution under prevailing conditions
`ViabilityStatus`	quality of a biological material entity by virtue of whether that entity is alive and capable of maintaining or recovering relevant physiological activity
`Viable`	viability status of a biological material entity that is alive and capable of maintaining or recovering relevant physiological activity
`ViableCellCount`	cell count that is the number of viable cells that are present as parts of a material entity
`ViableCellDensity`	cell density that is the number of viable cells per unit size
`ViableCellPopulation`	cell population consisting of only viable cells
`Virus`	minute infectious agent that has a DNA or RNA genome, lacks independent metabolism, and replicates only through use of a living host cell
`VirusSeed`	object aggregate consisting of containers whose contents are portions of a virus preparation derived from a single defined virus source and maintained as a referenceable lot
`WaterForInjectionClassifier`	compendial grade classifier that classifies a portion of water that conforms to the requirements stated in a Water for Injection pharmacopeial monograph and thus has very high purity
`Wettability`	capability of a solid material to be wetted by a liquid
`WorkingCellBank`	cell bank prepared from cells recovered from one or more containers of a master cell bank and stored under validated cryogenic conditions as a source of cryopreserved cells for routine use in research, development, or manufacturing
`WorkingSolutionRole`	role held by a solution when the solution is prepared from a stock solution or intermediate stock solution at the concentration required for use in a planned process that is not itself a dilution process

Changed

Classes

`CellCulture`

IRI: https://spec.industrialontologies.org/ontology/construct/CellCulture

Annotations

example = “CHO Suspension Culture in CD-CHO Medium; HEK293 Monolayer in DMEM + 10% FBS;”
primitiveRationale = “There is currently a lack of a constituency relation (is made of) in this release. It is expected that that relation will be available in the next release of IOF Core”

example = “CHO Suspension Culture in CD-CHO Medium; HEK293 cells growing as an adherent monolayer when cultured in DMEM (Dulbecco’s Modified Eagle’s Medium) + 10% FBS (Fetal Bovine Serum)”
primitiveRationale = “There are insufficient constructs to create a set of necessary and sufficient conditions.”

`CellLine`

IRI: https://spec.industrialontologies.org/ontology/construct/CellLine

Annotations

adaptedFrom = “CLO:0000031 and https://www.fda.gov/media/78428/download”
explanatoryNote = “1) A cell line is typically stored in a cell bank and used to ensure consistent and reproducible performance across experimental or manufacturing contexts. 2) The term excludes freshly isolated or short-lived primary cultures.”

adaptedFrom = “http://purl.obolibrary.org/obo/CLO_0000031 and https://www.fda.gov/media/78428/download”
explanatoryNote = “1) A cell line is typically stored in a cell bank and used to support consistent and reproducible performance across experimental or manufacturing contexts. 2) The term excludes freshly isolated or short-lived primary cultures. 3) Genetic stability and homogeneity are relative to the characteristics by which the cell line is established and maintained and do not imply complete genetic identity among all cells or the absence of genetic or phenotypic change during continued propagation.”

`CellPopulation`

IRI: https://spec.industrialontologies.org/ontology/construct/CellPopulation

Annotations

example = “CHO Cell Line; FACS-isolated CD4+ T cell population; Red blood cell pellet; freshly isolated hepatocytes from mouse liver”

example = “CHO Cell Line; CD4+ T cell population that have been obtained from a mixed cell suspension using fluorescence-activated cell sorting (FACS); Red blood cell pellet; freshly isolated hepatocytes from mouse liver”

`ClonedCellLine`

IRI: https://spec.industrialontologies.org/ontology/construct/ClonedCellLine

Annotations

adaptedFrom = “https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cell-clone#:~:text=Clone%20of%20cells%20is%20a,ignored%20that%20may%20be%20different and CLO:0000177”
explanatoryNote = “1) A cloned cell line consists of cells that are genetically identical with respect to antigen recognition, gene sequence, and key phenotypic traits. It represents a uniform lineage of cells with shared ancestry and consistent functional characteristics. 2) 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. 3) FDA considers monoclonality essential: production cell lines must originate from a single progenitor cell to ensure consistent and safe product characteristics. Each clone selected after transfection or genetic manipulation is treated as a distinct cell line, subject to full characterization (identity, purity, adventitious agent testing, etc.)”

adaptedFrom = “https://www.sciencedirect.com/topics/biochemistry-genetics-and-molecular-biology/cell-clone#:~:text=Clone%20of%20cells%20is%20a,ignored%20that%20may%20be%20different and http://purl.obolibrary.org/obo/CLO_0000177”
explanatoryNote = “1) A cloned cell line consists of cells that are expected to be genetically identical with respect to antigen recognition, gene sequence, and key phenotypic traits. It represents a uniform lineage of cells with shared ancestry and consistent functional characteristics. 2) 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. 3) FDA considers monoclonality essential: production cell lines must originate from a single progenitor cell to ensure consistent and safe product characteristics. Each clone selected after transfection or genetic manipulation is treated as a distinct cell line, subject to full characterization (identity, purity, adventitious agent testing, etc.)”

`CultureMedium`

IRI: https://spec.industrialontologies.org/ontology/construct/CultureMedium

Annotations

example = “DMEM;LB agar;HEK293”
explanatoryNote = “1) “Specific metabolic activity” refers to those metabolic processes that are intentionally supported or induced by the medium in a manufacturing or experimental context. This includes the synthesis and secretion of desired biomolecules (e.g., recombinant proteins, metabolites) or the replication and viability of cells when the cells themselves are the intended product. It excludes background or non-targeted metabolic processes such as basal energy maintenance or stress responses not relevant to the production goal. 2) In the context of biomanufacturing, “specific metabolic activity” typically refers to the set of biochemical processes carried out by microorganisms or cells that result in the synthesis, modification, and/or secretion of desired biological products. This includes processes such as the expression of recombinant proteins (e.g., monoclonal antibodies, enzymes), production of metabolites (e.g., amino acids, organic acids, antibiotics), or replication of the cells themselves when they are the product. These activities require the uptake and transformation of nutrients and are influenced by the composition and physicochemical properties of the culture medium. 4)Some types of culture media also include selection agents or antibiotics to suppress the growth of unwanted or contaminating organisms.”
firstOrderLogicAxiom = “CultureMedium(x) → MaterialEntity(x)”
naturalLanguageDefinition = “material entity that is a liquid or solid aqueous formulation that provides essential nutrients (such as carbon, nitrogen, vitamins, and minerals) and controlled physicochemical conditions (such as pH and osmotic balance) required for the growth, maintenance, or specific metabolic activity of microorganisms or cells”@en-US
primitiveRationale = “There are insufficient constructs to accurately represent the structure and the capabilities that the media has in this release. They will be treated in great detail for a subsequent release orienting around upstream.”
semiFormalNaturalLanguageAxiom = “if x is a ‘culture medium’ then x is a ‘material entity’”

example = “DMEM (Dulbecco’s Modified Eagle’s Medium); LB (Lysogeny Broth) agar; AMBIC (Advanced Mammalian Biomanufacturing Innovation Center) medium”
explanatoryNote = “1) “Specific metabolic activity” refers to those metabolic processes that are intentionally supported or induced by the medium in a manufacturing or experimental context. This includes the synthesis and secretion of desired biomolecules (e.g., recombinant proteins, metabolites) or the replication and viability of cells when the cells themselves are the intended product. It excludes background or non-targeted metabolic processes such as basal energy maintenance or stress responses not relevant to the production goal. 2) In the context of biomanufacturing, “specific metabolic activity” typically refers to the set of biochemical processes carried out by microorganisms or cells that result in the synthesis, modification, and/or secretion of desired biological products. This includes processes such as the expression of recombinant proteins (e.g., monoclonal antibodies, enzymes), production of metabolites (e.g., amino acids, organic acids, antibiotics), or replication of the cells themselves when they are the product. These activities require the uptake and transformation of nutrients and are influenced by the composition and physicochemical properties of the culture medium. 3) Some types of culture media also include selection agents or antibiotics to suppress the growth of unwanted or contaminating organisms.”
firstOrderLogicAxiom = “CultureMedium(x) → MixedMaterial(x)”
naturalLanguageDefinition = “mixed material that is a liquid, semi-solid or solid formulation that provides essential nutrients (such as carbon, nitrogen, vitamins, and minerals) and controlled physicochemical conditions (such as pH and osmotic balance) required for the growth, maintenance, or specific metabolic activity of microorganisms or cells”@en-US
primitiveRationale = “This term is expected to remain primitive because it encompasses a broad set of media that are used for different purposes and have different compositions”
semiFormalNaturalLanguageAxiom = “if x is a ‘culture medium’ then x is a ‘mixed material’”

Parents

BFO_0000040 (http://purl.obolibrary.org/obo/BFO_0000040)

MixedMaterial (https://spec.industrialontologies.org/ontology/construct/MixedMaterial)

Axioms

SubClassOf: bfo:material_entity
constr:CultureMedium DisjointWith: (constr:CellCulture, constr:Cell, constr:CulturedCellPopulation)

SubClassOf: constr:MixedMaterial
constr:CultureMedium DisjointWith: (constr:Cell, constr:CellCulture, constr:CulturedCellPopulation)

`CulturedCell`

IRI: https://spec.industrialontologies.org/ontology/construct/CulturedCell

Annotations

primitiveRationale = “There are currently inssuficient constructs to adequately represent adapt to grow in artificial environment.”

primitiveRationale = “There are insufficient constructs to create a set of necessary and sufficient conditions.”

`CulturedCellPopulation`

IRI: https://spec.industrialontologies.org/ontology/construct/CulturedCellPopulation

Annotations

example = “population of CHO-K1 cell; population of HeLa cell;”

example = “population of CHO-K1 cells; population of HeLa cells”

Axioms

constr:CulturedCellPopulation DisjointWith: (constr:CellCulture, constr:Cell, constr:CultureMedium)

constr:CulturedCellPopulation DisjointWith: (constr:Cell, constr:CellCulture, constr:CultureMedium)

`MolarMass`

IRI: https://spec.industrialontologies.org/ontology/construct/MolarMass

Annotations

altLabel = “molecular weight”
example = “The molar mass of albumin is 66.5 kDa; The molar mass of a particular antibody mixture that contains a percentage of mAb dimers is 175 kDa while a population without dimers would have a molar mass of 150 kDa; The molar mass for a population of high density polyethylene polymer is 300 000 g/mol; molar mass of glucose is 180 g/mol; molar mass of sodium chloride is 58.44 g/mol”
adaptedFrom = “https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/MolecularWeight and PATO:0001681”
explanatoryNote = “1) The value of molecular weight is typically expressed in daltons (Da) or grams per mole (g/mol) 2) In case of a heterogenous population of molecular entities it can be a regular average or a weighted awerage whereby the weigthing depends on the application 3) Molar mass includes small molecules, charged species, ionic compounds (treated as a defined unit), and macromolecular complexes such as proteins with tertiary or quaternary structure. It excludes isolated atoms and unspecified atomic groups (e.g. R-groups)”
firstOrderLogicAxiom = “MolarMass(x) → Quality(x)”
semiFormalNaturalLanguageAxiom = “if x is a ‘molar mass’ then x is a ‘quality’”

example = “The molar mass for a population of high density polyethylene polymer is 300 000 g/mol; molar mass of glucose is 180 g/mol; molar mass of sodium chloride is 58.44 g/mol”
adaptedFrom = “https://goldbook.iupac.org/terms/view/12214 and https://goldbook.iupac.org/terms/view/12215”
explanatoryNote = “1) Molar mass is mass divided by amount of substance and is expressed in units such as grams per mole or kilograms per mole. 2) When molar mass is the quality of a molecular entity, it represents the mass per mole of molecular entities of the same kind as that entity. For a non-uniform molecular entity population, it may be a specified molar-mass average, and the averaging method should be recorded with the measurement result. 3) The numerical value of a molecular mass expressed in daltons and the corresponding molar mass expressed in grams per mole are conventionally equal, but they are different quantities with different dimensions.”
firstOrderLogicAxiom = “MolarMass(x) → Quality(x) ∧ ∃m ((MolecularEntity(m) ∨ MolecularEntityPopulation(m)) ∧ qualityOf(x, m))”
semiFormalNaturalLanguageAxiom = “if x is a ‘molar mass’ then x is a ‘quality’ that is the ‘quality of’ some ‘molecular entity’ or some ‘molecular entity population’”

Axioms

SubClassOf: constr:qualityOf some (constr:MolecularEntity or constr:MolecularEntityPopulation)