BioAssay Ontology
type: Ontology
license: https://creativecommons.org/licenses/by-sa/4.0/
version info: 2.7.2
label: BAO
comment: Created by: Hande Küçük McGinty, Janice Kranz, Joseph Ostrow, Alex Clark, Yu Lin, Saminda Abeyruwan, Uma Vempati, Kunie Sakurai, Vance Lemmon, Ubbo Visser, John Turner, Stephan Schurer*
comment: Contact: Stephan Schurer stephan dot schurer at gmail dot com
date: 8 Jul 2021

endogenous ligand
type: Class
subclass of: biological ligand

synthetic small molecule ligand
type: Class
subclass of: biological ligand

assay provider
type: Class
IAO_0000115: The role of a scientist who has designed an assay and requested it to be run at a screening center.
subclass of: researcher role

assay control
type: Class
IAO_0000115: The role of a compound that is routinely run in the same manner as the test compounds in every run of the assay. This term does not refer to the plate controls used to define the maximum and minimum responses, and they may or may not be a “literature standard” or “reference” compound.

negative control
type: Class
IAO_0000115: It is the role played by the solvent (e.g. DMSO) in which the perturbagen was dissolved. The negative control is used to determine the base-line to compare the effect of the test perturbagen.
subclass of: assay control

positive control
type: Class
IAO_0000115: The role of a chemical compound or reagent used in each plate of an assay to normalize the response of the test perturbagens (by plate). Compounds that can have a positive control role are known from previous experiments or is a previously established standard. It is usually highly active resulting in a strong response of the intended effect. In an inhibition assay the positive control would usually result in the complete inhibition, which is then used for normalization (i.e. set as 100%). In an activation assay it would be activator used to normalize activity. Using controls provides an external reference and reduces the number of false negatives and false positives.
subclass of: assay control

feeder cell
type: Class
IAO_0000115: The role played by a cell line in supporting the growth of another cell line (e.g., stem cell). The feeder cell, e.g., mouse embryonic fibroblasts (MEFs) provides an adhesive surface to which the stem cells can attach and also secrete factors required for their growth.

high signal control
type: Class
IAO_0000115: The role played by the substrate, which is titrated without inhibitor to reflect the maximum enzyme activity at each substrate concentration.
subclass of: assay control

low signal control
type: Class
IAO_0000115: The role played by the substrate, which is titrated without enzyme and without inhibitor. The low controls should reflect the signal expected for no enzyme activity at each substrate concentration. Depending on the composition of the inhibitor stocks, DMSO might be needed in the control wells to assure consistency across all the experiments.
subclass of: assay control

background control
type: Class
IAO_0000115: The role played by the reading obtained from wells to which the sample or one of the reagents was not added. This is subtracted from all the experimental readings prior to further analysis.
subclass of: assay control

assay depositor
type: Class
IAO_0000115: The role of an organization or individual to add an assay to a repository, such as PubChem.
subclass of: researcher role

manufacturer role
type: Class
IAO_0000115: The role of an individual or a company as a creator of an assay kit, compound library, or detection instrument.
subclass of: organization role

biological ligand
type: Class
IAO_0000115: The role played by a soluble molecule, such as a hormone, neurotransmitter, or small molecule that binds to a biomolecular entity, such as a receptor.

measured entity
type: Class
comment: The role of a molecular entity of being the output of a biological reaction or process that is quantitated either directly (by the presence of a tag or probe) or indirectly in a coupled reaction.

cytokine
type: Class
IAO_0000115: The role played by a protein in modulating immune cell function via cell signaling, subsequent to binding to its cognate cell surface receptor.
subclass of: endogenous ligand

growth factor
type: Class
IAO_0000115: The role played by a protein in initiating cell division via cell signaling, subsequent to binding to its cognate cell surface receptor.
subclass of: endogenous ligand

coupled substrate
type: Class
IAO_0000115: The role played by a molecular entity as being the substrate for a coupled enzyme (see definition of coupled enzyme). For e.g., luciferin, which is generated by cytochrome P450 (from modified luciferin) in a coupled enzyme reaction is the coupled substrate for luciferase.

cell culture substrate
type: Class
IAO_0000115: The supportive role of a protein in mediating attachment of cells to a cell culture dish, on which it is coated.

channel blocker
type: Class
IAO_0000115: The role of a chemical entity to bind inside the pore of a specific type of ion channel and block the flow of ions through it, resulting in an alteration of the electrochemical gradient of the cell membrane.

differentiation agent
type: Class
IAO_0000115: The molecular entity that brings about the transformation of less specialized cells to more specialized cell types, which differ morphologically and /or functionally.

activator
type: Class
IAO_0000115: The role of a molecular entity to bring about an increase of a predefined stimulus in an assay.

reference compound
type: Class
IAO_0000115: The role of a small molecule to act as a standard in a particular assay type, e.g., 1,4-Dioxane (for NMR), Cediranib (for Kinomescan).

carrier
type: Class
IAO_0000115: Role of a protein in the transport of ions, small molecules, or macromolecules across a semi-permeable membrane, such as plasma membrane.

coupled enzyme
type: Class
IAO_0000115: The role played by an enzyme in reporting the activity of a different enzyme by being able to use the substrate or product of the latter in its own reaction (either as a substrate or cofactor). E.g., luciferase acts as a coupled enzyme for cytochrome P450, as the luciferin generated (from modified luciferin) by the latter acts as its substrate.

depolarizer
type: Class
IAO_0000115: The role of a molecular entity (e.g., barium chloride, acetylcholine) to change a cell's membrane potential, making it more positive.

media component
type: Class
IAO_0000115: The role played by a molecular entity that is added as an ingredient to a broth that is used to culture cells.

transfection agent
type: Class
IAO_0000115: The role of a molecular entity of mediating the introduction of a foreign nucleic acid into cells, e.g., Lipofectamine 2000, Fugene 6, etc.

protein tag
type: Class
IAO_0000115: The role of the peptide that is appended at the N- or C-terminal of a protein (e.g., GST, His, HA, Myc, etc) which allows for easy identification and/or separation of that protein.

organization role
type: Class
IAO_0000115: The role of an organization or individual in the various stages of implementation of an assay, such as manufacturing an assay kit or depositing an assay in a repository.
subclass of: role

commercial vendor
type: Class
IAO_0000115: The role of a company as a creator of an assay kit, compound library, or detection instrument.
subclass of: organization role

academic chemist
type: Class
IAO_0000115: The role of an individual, who works at an academic institution as a creator of a chemical compound.
subclass of: researcher role

biologics and screening manufacturer
type: Class
IAO_0000115: The role of a company as a creator of reagents and assay kits.
subclass of: manufacturer role

compound library manufacturer
type: Class
IAO_0000115: The role of a company as a creator of a compound library.
subclass of: manufacturer role

instrumentation manufacturer
type: Class
comment: The role of a company as a creator of detection instrumentation.
subclass of: manufacturer role

antibody role
type: Class
IAO_0000115: This categorizes the distinct roles played by antibodies in recognizing either the antigen or an antibody itself.

primary antibody
type: Class
IAO_0000115: The role of an antibody to detect and bind a specific antigen in a sample (cell, tissue, protein blot).
subclass of: antibody role

secondary antibody
type: Class
IAO_0000115: The role of an antibody to detect and bind a primary antibody in a sample (cell, tissue, protein blot).
subclass of: antibody role

reporter gene
type: Class
IAO_0000115: A gene that performs the role of encoding a reporter protein, which can easily be detected in an assay, e.g., luciferase gene that encodes the luciferase protein. DNA constructs that contain reporter genes are excellent tools to understand regulation of gene expression.

assay component
type: Class
IAO_0000115: The role played by a molecular entity that is added as an ingredient to an assay.

second messenger
type: Class

DNA tag
type: Class

detected entity
type: Class

on plate control
type: Class
subclass of: assay control

off plate control
type: Class
subclass of: assay control

screening lab investigator
type: Class
subclass of: researcher role

screening principal investigator
type: Class
subclass of: researcher role

researcher role
type: Class
subclass of: role

role
type: Class

screened entity role
type: Class

inducer
type: Class
IAO_0000115: The role of a molecular entity to initiate a biological process. E.g., interferon-gamma has an inducer role in STAT-1 mediated transcriptional activation of cells.

perturbagen
type: Class
IAO_0000115: The role of a molecular entity (small molecule, siRNA/shRNA, etc.) in altering the activity of proteins that serve as targets in a bioassay.

potentiator
type: Class
IAO_0000115: The role of a molecular entity as a known activator of a target/pathway, added prior to screening the compounds for selective inhibitor indications (e.g., forskolin is a potentiator for Gi/o pathway of G-proteins).

reporter protein
type: Class
IAO_0000115: The role of a protein to be easily detected in an assay by virtue of its innate properties (fluorescence) or catalyzing a reaction that result in easily measurable products, such as luminescence, colored product, etc. Examples include luciferase, GFP, beta-galactosidase, etc.

sensitizer
type: Class
IAO_0000115: The role of a compound to increase or decrease the ability of a cell to respond to its signaling molecule.

substrate
type: Class
IAO_0000115: The role of a molecular entity to serve as the input for an enzymatic reaction that generates a product, e.g. ATP has the role of a substrate for ATPase, which hydrolyzes it to produce ADP and Pi.

target
type: Class
IAO_0000115: The role of a molecular entity (protein or nucleic acid) that is the presumed subject of an assay and whose activity is being regulated by an entity with a perturbagen role in that assay.

viability indicator
type: Class
IAO_0000115: The role of a molecular entity of specifying the cell's status of being alive, e.g., ATP.

depolarization blocker
type: Class
IAO_0000115: A chemical entity that has the role of depolarization, which is to make the cell's membrane potential more negative.
subclass of: channel blocker

product
type: Class

selectable marker
type: Class
IAO_0000115: The role of a chemical entity to distinguish two populations of cells, e.g., ampicillin is added to culture medium to identify ampicillin resistant bacteria.

chemical role
type: Class
deprecated: true
subclass of: role

application
type: Class
deprecated: true
subclass of: role

biological role
type: Class
deprecated: true
subclass of: role

quencher
type: Class

detection agent
type: Class

rescue treatment
type: Class

protein binding ligand
type: Class