BioAssay Ontology
type: Ontology
license: https://creativecommons.org/licenses/by-sa/4.0/
version info: 2.8.17
label: BAO
comment: Created by: Caty Chung, Nicolette Ross, Joan Glenny-Pescov, Jiaming Hu, Stephan Schurer*
comment: Contact: Stephan Schurer stephan dot schurer at med dot miami dot edu

nucleosome format
type: Class
IAO_0000115: They are the basic repeating units of the eukaryotic chromatin consisting of DNA wound around a histone protein core.
subclass of: subcellular format

assay format
type: Class
IAO_0000115: Assay format is a conceptualization of assays based on the biological and / or chemical features of the experimental system. For example assay formats include biochemical assays - referring to assays with purified protein, cell-based - referring to assays in whole cells, or organism-based - referring to assays performed in an organism.
subclass of: assay format component

small-molecule physicochemical format
type: Class
IAO_0000115: Assays in which the physical and chemical properties of perturbagens are measured, namely, aqueous solubility, octanol water partition, cell permeability models, for e.g. Caco2 cells, parallel artificial membrane permeability assay (PAMPA), etc.
subclass of: assay format

biochemical format
type: Class
IAO_0000115: It is an in vitro format used to measure the activity of a biological macromolecule, either a purified protein or a nucleic acid. It is most often a homogeneous assay type, but can be heterogeneous if a solid phase such as beads is used to immobilize the macromolecule.
subclass of: assay format

organism-based format
type: Class
IAO_0000115: Involves the use of a living organism, either single or multi-celled, and is a heterogeneous assay type.
subclass of: assay format

cell based format
type: Class
label: cell-based format
IAO_0000115: Involves the use of living cells of eukaryotic origin, derived from a multicellular organism, and is a heterogeneous assay type. Typically, this refers to permanent (immortal) cell lines, or primary cells, or some form of stem cells. This is distinct from a single-celled organism-based format (classically bacteria or yeast).
subclass of: assay format

subcellular format
type: Class
IAO_0000115: subcellular organelles / component (not individual proteins) obtained via cell lysis and differential centrifugation (or potentially other method of purification / extraction of the organelles)
subclass of: cell-free format

tissue-based format
type: Class
IAO_0000115: Involves the use of a tissue derived from a living organism and is a heterogeneous assay type.
subclass of: assay format

protein complex format
type: Class
IAO_0000115: Two or more proteins interact to form a stable complex. Each of the members of this complex has a distinct role in mediating the overall function of the complex, which can be as a chaperone (DnaK, DnaJ and grpE), an enzyme (mitochondrial respiratory complexes), a signaling complex (G-proteins), etc. It can be viewed as a quaternary structure of the proteins.
subclass of: protein format

protein format
type: Class
IAO_0000115: In this format, the perturbagen targets a protein to regulate its function.
subclass of: biochemical format

nucleic acid format
type: Class
IAO_0000115: In this format, the perturbagen targets a nucleic acid (DNA or RNA) to regulate its function.
subclass of: biochemical format

cell membrane format
type: Class
IAO_0000115: The thin outer covering of a cell consisting of lipid-bilayer embedded with proteins. It is semi-permeable and is also called "plasma membrane"
subclass of: subcellular format

cytosol format
type: Class
IAO_0000115: The fluid component of cytoplasm, without the organelles and the insoluble cytoplasmic components.
subclass of: subcellular format

microsome format
type: Class
IAO_0000115: Microsomes are vesicle-like structures formed as an artifact from the endoplasmic reticulum after the cell has been ruptured by homogenization.
subclass of: subcellular format

mitochondrion format
type: Class
IAO_0000115: An organelle found in the cytoplasm of eukaryotic cells that metabolizes glucose and other sugars to produce usable energy in the form of ATP. It contains its own genome which encodes proteins, tRNA and rRNA.
subclass of: subcellular format

nuclear extract format
type: Class
IAO_0000115: It is a soluble extract prepared from the cellular nuclei, which are obtained by differential centrifugation of the cell lysate.
subclass of: subcellular format

whole cell lysate format
type: Class
IAO_0000115: A cell whose membrane has been ruptured, either mechanically or by freeze-thawing. The entire cell lysate is used in the assay without extensive purification (or separation).
subclass of: cell-free format

rabbit reticulocyte lysate format
type: Class
IAO_0000115: The lysate contains the cellular components necessary for in vitro protein synthesis (tRNA, ribosomes, amino acids, initiation, elongation and termination factors). It is prepared from rabbit reticulocytes by lysis, followed by treatment with micrococcal nuclease to destroy endogenous mRNA for background reduction.
subclass of: whole cell lysate format

single protein format
type: Class
IAO_0000115: one protein sequence
subclass of: protein format

cell-free format
type: Class
IAO_0000115: This originates from a cell, but does not use intact (live) cells; does not include biochemical assays, which is one of the major formats that is categorized separately. It is most often a homogeneous assay type, but can be heterogeneous if a solid phase such as beads are used to immobilize the components.
subclass of: assay format

assay phase characteristic
type: Class
IAO_0000115: It refers to whether all the assay components are in solution or some are in solid phase, which determines their ability to scatter light.
subclass of: assay format component

homogeneous phase
type: Class
IAO_0000115: All assay components exist in solution phase at the time of detection (e.g. none of the components are in beads or cells). Technically no component scatters light.
subclass of: assay phase characteristic

heterogeneous phase
type: Class
IAO_0000115: One or more assay components are present in solid phase at time of detection. (e.g.: cells, beads).
subclass of: assay phase characteristic

solid phase
type: Class
subclass of: homogeneous phase

liquid phase
type: Class
subclass of: homogeneous phase

assay format component
type: Class

liposome format
type: Class
IAO_0000119: PubChem AID: 602155
IAO_0000116: Date from BAE: 7/19/2016
subclass of: subcellular format

plasma format
type: Class
IAO_0000119: PubChem AID: 623907
IAO_0000116: Date from BAE: 7/6/2016
IAO_0000115: Plasma is the liquid part of the blood and lymphatic fluid, which makes up about half of the volume of blood. Plasma is devoid of cells and, unlike serum, has not clotted.
subclass of: cell-free format

serum format
type: Class
IAO_0000119: PubChem AID:
IAO_0000116: Date from BAE: 7/6/2016
IAO_0000115: Serum is the clear cell-free liquid that is separated from clotted blood. Serum differs from plasma in that the blood is first allowed to clot before centrifugation (separating from cells) while plasma preparations entail preventing blood clotting. Both are cell-free and contain antibodies.
subclass of: cell-free format

experimental setting
type: Class
subclass of: assay format component

ex vivo
type: Class
subclass of: experimental setting

in silico
type: Class
subclass of: experimental setting

in vitro
type: Class
subclass of: experimental setting

in vivo
type: Class
subclass of: experimental setting

S9 fraction format
type: Class
subclass of: subcellular format
IAO_0000115: Obtained by disrupting and centrifuging human liver or intestine cells, resulting in a combination of cell cytosol and microsomes. It encompasses a diverse array of drug-metabolizing enzymes and serves as a commonly utilized medium for conducting in vitro DMPK studies.
has xref: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5405623/
submitted by: https://github.com/BioAssayOntology/BAO/issues/84
IAO_0000118: S9 format

blood format
type: Class
subclass of: cell-free format
IAO_0000115: The liquid component of blood devoid of cellular elements (such as red blood cells, white blood cells, and platelets) and insoluble components, typically obtained through processes like centrifugation or filtration.
has xref: http://purl.org/net/OCRe/OCRe.owl#OCRE400034
submitted by: SEED Project - Pistoia Alliance

tissue membrane format
type: Class
IAO_0000115: Tissue membrane format (often using morter and pestal to homogenize tissue) is considered a cell-free subcellular format that contains issues and broken down components of cells.
subclass of: subcellular format
submitted by: Opioid Drug Ontology (ODO) (https://opioiddrugontology.github.io/) - Nicolette Ross (https://orcid.org/0000-0002-4677-2140)
IAO_0000119: https://doi.org/10.1016/B978-0-12-411604-7.00009-X
IAO_0000116: [DefinitionUpdate: BAO v 2.8.15 (May 2025)] [NodeCreation: BAO v 2.8.13 (March 2025)]

synaptosomal fraction format
type: Class
IAO_0000115: The synaptosomal fraction represents neuronal components, specifically crude synaptosomes, which are obtained by breaking open neural tissue and centrifuging it to separate synaptic structures (from neurons) from the soluble cytosolic material. This fraction contains synaptosomes but may also include other cellular contaminants until further purification steps are applied.
subclass of: subcellular format
submitted by: Opioid Drug Ontology (ODO) (https://opioiddrugontology.github.io/) - Nicolette Ross (https://orcid.org/0000-0002-4677-2140)
IAO_0000119: https://doi.org/10.1016/j.xpro.2023.102061
IAO_0000116: [DefinitionUpdate: BAO v 2.8.15 (May 2025)] [NodeCreation: BAO v 2.8.13 (March 2025)]

synaptosomal P2 fraction format
type: Class
IAO_0000115: The P2 synaptosomal fraction is a crude neuronal sub-cellular fraction enriched in synaptosomes, obtained by centrifuging lysate at 10,000 × g to separate the cytosol (S2) from the pellet, which is resuspended in Buffer B.
subclass of: synaptosomal fraction format
submitted by: Opioid Drug Ontology (ODO) (https://opioiddrugontology.github.io/) - Nicolette Ross (https://orcid.org/0000-0002-4677-2140)
IAO_0000119: https://doi.org/10.1016/j.xpro.2023.102061
IAO_0000116: [DefinitionUpdate: BAO v 2.8.15 (May 2025)] [NodeCreation: BAO v 2.8.13 (March 2025)]

Transwell chamber format
type: Class
subclass of: cell based format
IAO_0000115: Assay format using a permeable support insert (Transwell) to form a polarized cell monolayer separating apical and basolateral compartments for permeability measurements.
IAO_0000119: dx.doi.org/10.17504/protocols.io.5qpvo3wn9v4o/v1
submitted by: Joan Glenny Pescov (https://orcid.org/0009-0008-8186-7058)
IAO_0000116: [BAO v 2.8.17 (Oct 2025)]