Biopharma Material Ontology
This module contains terms and relations enabling representation of material types and their associated properties. Terms for characterizing material usages in internal operation systems are also included (e.g., consumable, process intermediate, final product…).
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
cell
CHO-K1 cell; HeLa cell; T cell isolated from peripheral blood;Freshly isolated hepatocyte; Hematopoietic stem cell isolated from bone marrow
1) From CL term: The definition of cell is intended to represent all cells, and thus a cell is defined as a material entity and not an anatomical structure, which implies that it is part of an organism (or the entirety of one). 2) In the cell line ontology the term is directly under material entity. However, given the definitional criteria of a plasma membrane and maximal connectedness of cell compartments, the cell has been put under object within the ontology.
object of anatomical origin (part of or deriving from an organism) that has as its parts a maximally connected cell compartment surrounded by a plasma membrane
There are currently insufficient constructs to represent cellular components or cell derivation
cell culture
culture broth
CHO Suspension Culture in CD-CHO Medium; HEK293 Monolayer in DMEM + 10% FBS;
In situ cells are observed and studied within their natural tissue context without being cultured or removed, e.g., neurons, alveolar epithelial cells; Post-centrifugation cell pellet; Uninoculated Culture Medium; Glass Slide with Fixed Cells (No Live Media); Tissue Biopsy in PBS Buffer
A cell culture includes the cells in culture, as well as the media and all additives in which the cells are being grown or in which they are stored.
CellCulture(x) → MaterialEntity(x) ∧ ∃y (CultureMedium(y) ∧ hasContinuantPartAtAllTimes(x, y)) ∧ ∃z (CulturedCellPopulation(z) ∧ hasContinuantPartAtAllTimes(x, z))
material entity that has cultured cells and the media in which they are being propagated or stored as parts
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
if x is a 'cell culture' then x is a 'material entity' and x 'has continuant part at all times' some 'culture medium' and x 'has continuant part at all times' some 'cultured cell population'
cell line
CLO:0000031 and https://www.fda.gov/media/78428/download
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.
cultured cell population that is derived from a primary cell source and that has been propagated through repeated subculture under defined conditions, resulting in a genetically stable and homogeneous population of cells with a shared propagation history
There are insufficient constructs to define necessary and sufficient conditions.
if x is a 'cell line' then x is a 'cultured cell population'
cell line lineage
HEK293 history: derived from human embryonic kidney cells transfected with adenovirus 5 DNA; selected for stable growth in culture;
The cell line lineage may include the original cell type from a tissue and organism that derives the cell line cell. It may also include the cell line passage and cell culturing information.
CellLineLineage(x) ↔ History(x) ∧ ∃y(CellLine(y) ∧ historyOf(x, y))
history of the development of a cell line
every instance of 'cell line lineage' is defined as exactly an instance of 'history' that 'is history of' some 'cell line'
cell population
CHO Cell Line; FACS-isolated CD4+ T cell population; Red blood cell pellet; freshly isolated hepatocytes from mouse liver
CellPopulation(x) ↔ ObjectAggregate(x) ∧ ∃y(Cell(y) ∧ hasMemberPartAtSomeTime(x, y)) ∧ ∀z(hasMemberPartAtSomeTime(x, z) → Cell(z))
object aggregate which only has cells as its member parts
every instance of 'cell population' is defined as exactly an instance of 'object aggregate' that 'has member part at some time' some 'cell' and 'has member part at some time' only 'cell'
cloned cell line
CHO DG44 clone 5F7 – a clonal derivative of CHO DG44 cells selected for high monoclonal antibody productivity; Jurkat E6-1 – a cloned subline of Jurkat cells used in T cell signaling research
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
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.)
cell line that originates from a single ancestral cell
if x is a 'cloned cell line' then x is a 'cell line'
culture medium
https://pmc.ncbi.nlm.nih.gov/articles/PMC7417654/pdf/fbioe-08-00911.pdf and https://www.sigmaaldrich.com/US/en/technical-documents/technical-article/microbiological-testing/microbial-culture-media-preparation/types-of-media-in-microbiology?srsltid=AfmBOopAW7ApixpJ8J-96cmEfgfSiT8dX8wszs06BrclD3tYImJkEcYV
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.
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
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.
if x is a 'culture medium' then x is a 'material entity'
cultured cell
https://www.thermofisher.com/rs/en/home/references/gibco-cell-culture-basics/introduction-to-cell-culture.html and http://purl.obolibrary.org/obo/CL_0000010
Freshly isolated hepatocyte; Hematopoietic stem cell isolated from bone marrow
1)Cultured cells are typically immortalized, meaning they retain the capacity to proliferate indefinitely under suitable growth conditions; in contrast, primary cells such as those directly isolated from a patient without genetic or oncogenic modification undergo a limited number of mitotic divisions before entering senescence or undergoing cell death 2) A blurred line would be the case of the CAR-T cell therapy situation where the cells are often taken directly from the patient, modified (not immortalized), expanded in a bioreactor and then infused back into the patient. In this case, CAR-T cells are still considered cultured cells because they are subjected to ex vivo cultivation under controlled, artificial conditions. After being isolated from a patient (typically as primary T cells), they are genetically modified and then expanded in bioreactors or culture vessels using defined media, gas control, and temperature regulation. Although they are not immortalized, they undergo proliferation outside their native environment. This fulfills the defining criteria of a cultured cell as one that grows in an artificial, controlled setting. Their classification as cultured reflects the environmental and procedural context, not the permanence or origin of the cell line.
cell that is grown, maintained, or adapted to grow in a controlled artificial environment that supports its survival and proliferation
There are currently inssuficient constructs to adequately represent adapt to grow in artificial environment.
if x is a 'cultured cell' then x is a 'cell'
cultured cell population
population of CHO-K1 cell; population of HeLa cell;
CulturedCellPopulation(x) ↔ CellPopulation(x) ∧ ∃y(CulturedCell(y) ∧ hasMemberPartAtSomeTime(x, y)) ∧ ∀z(hasMemberPartAtSomeTime(x, z) → CulturedCell(z))
cell population which only has cultured cells as its member parts
every instance of 'cultured cell population' is defined as exactly an instance of 'cell population' that 'has member part at some time' some 'cultured cell' and 'has member part at some time' only 'cultured cell'
molar mass
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
https://spec.pistoiaalliance.org/idmp/ontology/ISO/ISO11238-Substances/MolecularWeight and PATO:0001681
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)
quality that is the quality of a molecular entity or population of molecular entities, and is either the mass of one mole of that single entity, or the average mass of one mole of molecules in the population
if x is a 'molar mass' then x is a 'quality'