Bioassay ontology
type: Ontology
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,colette Ross, Joan Glenny-Pescov, Jiaming Hu, Caty Chung, Stephan Schurer*
date: May 12, 2023
comment: There is a one-to-one correspondance with rdf:label value and concept descriptions. Concept description starts with the prefix BAO_. contact: Stephan Schurer: stephan dot schurer at gmail dot com
version info: 2.8.2
license: https://creativecommons.org/licenses/by-sa/4.0/
imports: bao metadata.owl

has temperature unit
type: ObjectProperty
sub property of: has unit

has marker
type: ObjectProperty

is substrate of
type: ObjectProperty
inverse of: has substrate

is marker of
type: ObjectProperty
inverse of: has marker

stains
type: ObjectProperty

has orthogonal assay design
type: ObjectProperty
sub property of: has alternate confirmatory assay

has response unit
type: ObjectProperty
sub property of: has unit

has concentration unit
type: ObjectProperty
sub property of: has unit

has perturbagen
type: ObjectProperty
sub property of: topObjectProperty

has mode of action
type: ObjectProperty
sub property of: topObjectProperty

has assay format
type: ObjectProperty
sub property of: topObjectProperty

has detection method
type: ObjectProperty
sub property of: topObjectProperty

has endpoint
type: ObjectProperty
sub property of: topObjectProperty

has measure group
type: ObjectProperty
inverse of: is measure group of
sub property of: topObjectProperty

has assay stage
type: ObjectProperty
sub property of: topObjectProperty

has target
type: ObjectProperty
sub property of: topObjectProperty

has assay method
type: ObjectProperty
sub property of: topObjectProperty

has specification
type: ObjectProperty
sub property of: topObjectProperty

is orthogonal assay design of
type: ObjectProperty
inverse of: has orthogonal assay design
sub property of: is alternate confirmatory assay of

has assay kit
type: ObjectProperty

has curve fit specification
type: ObjectProperty
sub property of: topObjectProperty

has percent response
type: ObjectProperty
sub property of: topObjectProperty

has concentration
type: ObjectProperty
sub property of: topObjectProperty

is perturbagen of
type: ObjectProperty
inverse of: has perturbagen
sub property of: topObjectProperty

is assay method of
type: ObjectProperty
inverse of: has assay method
sub property of: topObjectProperty

has inducer
type: ObjectProperty

is regulated by
type: ObjectProperty
property disjoint with: is regulator of

has transcription factor
type: ObjectProperty

is measure group of
type: ObjectProperty
sub property of: topObjectProperty

is related assay to
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: topObjectProperty

is confirmatory assay of
type: ObjectProperty
comment: Assay performed to confirm activity of compounds identified in the primary screen. It can be performed as replicate measurements at a single screening concentration or as concentration-response assay.
sub property of: is related assay to

is counter assay of
type: ObjectProperty
comment: Counter assays typically follow concentration-response assays to confirm the biological activity of chemical entities identified in the primary assays. Counter assays eliminate active compounds that do not act on the intended target. They are performed using related targets, e.g. a receptor isoform, a homologous gene, etc which are functionally distinct from the intended target. Counter assays are also performed to eliminate cytotoxic compounds. The actives from the primary assay are tested on cultured cells and the cell death is estimated commonly by measuring ATP concentration. Other example for a counter assays a FRET assay when the primary assay used absorption readout; luminescence readout when the primary assay measured fluorescence intensity, etc.
sub property of: is related assay to

is identical assay of
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
comment: Same target, design, technology, format, but not necessarily the same throughput. For example primary, confirmatory, and concentration-response could be related by 'is identical to'
sub property of: is related assay to
equivalent property: has identical assay

is alternate assay format of
type: ObjectProperty
inverse of: has alternate assay format
sub property of: is alternate confirmatory assay of

is assay format of
type: ObjectProperty
inverse of: has assay format
sub property of: topObjectProperty

is endpoint of
type: ObjectProperty
inverse of: has endpoint

is regulator of
type: ObjectProperty
inverse of: is regulated by

is specification of
type: ObjectProperty
inverse of: has specification

has alternate assay format
type: ObjectProperty
sub property of: has alternate confirmatory assay

is target of
type: ObjectProperty
inverse of: has target

is detection method of
type: ObjectProperty
inverse of: has detection method

has manufacturer
type: ObjectProperty

has assay control
type: ObjectProperty

has primary assay
type: ObjectProperty
sub property of: is related assay to

has confirmatory assay
type: ObjectProperty
sub property of: is related assay to
inverse of: is confirmatory assay of

has counter assay
type: ObjectProperty
sub property of: is related assay to
inverse of: is counter assay of

has summary assay
type: ObjectProperty
sub property of: is related assay to

has variant construct assay
type: ObjectProperty
sub property of: has counter assay

is variant construct assay of
type: ObjectProperty
sub property of: is counter assay of
inverse of: has variant construct assay

has parental cell line assay
type: ObjectProperty
sub property of: has counter assay

is parental cell line assay of
type: ObjectProperty
sub property of: is counter assay of
inverse of: has parental cell line assay

has compound toxicity assay
type: ObjectProperty
sub property of: has counter assay

is compound toxicity assay of
type: ObjectProperty
sub property of: is counter assay of
inverse of: has compound toxicity assay

is primary assay of
type: ObjectProperty
sub property of: is related assay to
inverse of: has primary assay

has selectivity assay
type: ObjectProperty
sub property of: is related assay to

is selectivity assay of
type: ObjectProperty
sub property of: is related assay to
inverse of: has selectivity assay

has alternate target assay
type: ObjectProperty
sub property of: has counter assay
sub property of: has selectivity assay

is alternate target assay of
type: ObjectProperty
sub property of: is counter assay of
sub property of: is selectivity assay of
inverse of: has alternate target assay

has alternate cell line assay
type: ObjectProperty
sub property of: has selectivity assay

is alternate cell line assay of
type: ObjectProperty
sub property of: is selectivity assay of
inverse of: has alternate cell line assay

has alternate organism assay
type: ObjectProperty
sub property of: has selectivity assay

is alternate organism assay of
type: ObjectProperty
sub property of: is selectivity assay of
inverse of: has alternate organism assay

has alternate confirmatory assay
type: ObjectProperty
sub property of: is related assay to

is alternate confirmatory assay of
type: ObjectProperty
sub property of: is related assay to
inverse of: has alternate confirmatory assay

has orthogonal assay technology
type: ObjectProperty
sub property of: has alternate confirmatory assay

is orthogonal assay technology of
type: ObjectProperty
sub property of: is alternate confirmatory assay of
inverse of: has orthogonal assay technology

has alternate assay type
type: ObjectProperty
sub property of: has alternate confirmatory assay

is alternate assay type of
type: ObjectProperty
sub property of: is alternate confirmatory assay of
inverse of: has alternate assay type

has alternate assay conditions
type: ObjectProperty
sub property of: has alternate confirmatory assay

is alternate assay conditions of
type: ObjectProperty
sub property of: is alternate confirmatory assay of
inverse of: has alternate assay conditions

has lead optimization assay
type: ObjectProperty
sub property of: is related assay to

is lead optimization assay of
type: ObjectProperty
sub property of: is related assay to
inverse of: has lead optimization assay

has physicochemical profiling assay
type: ObjectProperty
sub property of: has counter assay

is physicochemical profiling assay of
type: ObjectProperty
sub property of: is counter assay of
inverse of: has physicochemical profiling assay

has compound fluorescence assay
type: ObjectProperty
sub property of: has physicochemical profiling assay

is compound fluorescence assay of
type: ObjectProperty
sub property of: is physicochemical profiling assay of
inverse of: has compound fluorescence assay

has compound aggregation assay
type: ObjectProperty
sub property of: has physicochemical profiling assay

is compound aggregation assay of
type: ObjectProperty
sub property of: is physicochemical profiling assay of
inverse of: has compound aggregation assay

has compound redox-activity assay
type: ObjectProperty
sub property of: has physicochemical profiling assay

is compound redox-activity assay of
type: ObjectProperty
sub property of: is physicochemical profiling assay of
inverse of: has compound redox-activity assay

is summary assay of
type: ObjectProperty
sub property of: is related assay to
inverse of: has summary assay

has identical assay
type: ObjectProperty
type: SymmetricProperty
type: TransitiveProperty
sub property of: is related assay to

based on normalization
type: ObjectProperty

has measured entity
type: ObjectProperty

detects
type: ObjectProperty
sub property of: has assay footprint
inverse of: is detected by

catalyzed by
type: ObjectProperty
sub property of: topObjectProperty

has cell line
type: ObjectProperty
inverse of: is cell line of

has form
type: ObjectProperty

involves biological process
type: ObjectProperty

has assay phase characteristic
type: ObjectProperty

is indicator of
type: ObjectProperty

has purity unit
type: ObjectProperty
sub property of: has unit

encodes
type: ObjectProperty

is measured entity of
type: ObjectProperty
inverse of: has measured entity
sub property of: topObjectProperty

has quality
type: ObjectProperty

uses assay kit
type: ObjectProperty

has assay kit component
type: ObjectProperty

uses as substrate
type: ObjectProperty

has time unit
type: ObjectProperty
sub property of: has unit

has substrate
type: ObjectProperty

is binding site of
type: ObjectProperty
inverse of: has binding site

tagged with
type: ObjectProperty

has detected entity
type: ObjectProperty

is cell line of
type: ObjectProperty

has assay protocol
type: ObjectProperty

is assay protocol of
type: ObjectProperty
inverse of: has assay protocol

has associated disease
type: ObjectProperty

is associated disease of
type: ObjectProperty

has assay readout content
type: ObjectProperty

has assay readout content parametricity
type: ObjectProperty

has assay source
type: ObjectProperty

has assay title
type: ObjectProperty

has bioassay type
type: ObjectProperty

is bioassay type of
type: ObjectProperty
inverse of: has bioassay type

has assay readout type
type: ObjectProperty

has signal direction
type: ObjectProperty

has endpoint modifier
type: ObjectProperty

has phenotype
type: ObjectProperty

is phenotype of
type: ObjectProperty
inverse of: has phenotype

is localized in
type: ObjectProperty

has concentration throughput
type: ObjectProperty

has repetition throughput
type: ObjectProperty

uses detection instrument
type: ObjectProperty

has assay footprint
type: ObjectProperty

silences
type: ObjectProperty

has gene symbol
type: ObjectProperty

is role of
type: ObjectProperty
inverse of: has role

is unit of
type: ObjectProperty

has unit
type: ObjectProperty
inverse of: is unit of

is detected by
type: ObjectProperty

has antibody source
type: ObjectProperty

recombinantly expressed in
type: ObjectProperty

has preparation method
type: ObjectProperty

has organism
type: ObjectProperty

has assay medium
type: ObjectProperty

has assay serum
type: ObjectProperty

is grown in
type: ObjectProperty

is transfected into
type: ObjectProperty

has role
type: ObjectProperty

reports
type: ObjectProperty

has binding site
type: ObjectProperty

has function
type: ObjectProperty

involves molecular function
type: ObjectProperty

is derived from
type: ObjectProperty

detects phenotype
type: ObjectProperty

has indicator
type: ObjectProperty

is described by
type: ObjectProperty

quantifies
type: ObjectProperty

has molecular phenotype
type: ObjectProperty
sub property of: has phenotype

has morphological phenotype
type: ObjectProperty
sub property of: has phenotype

has positive control
type: ObjectProperty
sub property of: has assay control

has negative control
type: ObjectProperty
sub property of: has assay control

has experimental setting
type: ObjectProperty

has response value
type: DatatypeProperty

has temperature value
type: DatatypeProperty

has percent response value
type: DatatypeProperty
type: FunctionalProperty
range: float
sub property of: topDataProperty

has id value
type: DatatypeProperty
type: FunctionalProperty
sub property of: topDataProperty
range: Datatype
  union of: integer
  union of: string

has DNA sequence
type: DatatypeProperty
type: FunctionalProperty
sub property of: has nucleic acid sequence
range: string

has display info
type: DatatypeProperty
type: FunctionalProperty
range: string
sub property of: topDataProperty

has date
type: DatatypeProperty
range: dateTime

has purity value
type: DatatypeProperty

has concentration value
type: DatatypeProperty

has time value
type: DatatypeProperty

has concentration-point number
type: DatatypeProperty

has passage number
type: DatatypeProperty
range: int

has cell count
type: DatatypeProperty

has copy number
type: DatatypeProperty
IAO_0000115: This describes the number of repeats of an entity (e.g., artificial regulatory element, cDNA, etc.) present in a DNA construct.

has gene copy number
type: DatatypeProperty
IAO_0000115: This describes the number of repeats of a gene of interest cloned in a DNA construct.
sub property of: has copy number

has cDNA copy number
type: DatatypeProperty
IAO_0000115: This describes the number of repeats of a cDNA of interest cloned in a DNA construct.
sub property of: has copy number

has artificial regulatory region copy number
type: DatatypeProperty
IAO_0000115: This describes the number of repeats of an artificial regulatory element present in a DNA construct.
sub property of: has copy number

has sequence
type: DatatypeProperty

has protein sequence
type: DatatypeProperty
sub property of: has sequence

has nucleic acid sequence
type: DatatypeProperty
sub property of: has sequence

has RNA sequence
type: DatatypeProperty
sub property of: has nucleic acid sequence

has shRNA sense sequence
type: DatatypeProperty
sub property of: has RNA sequence

has enzyme reaction temperature value
type: DatatypeProperty
sub property of: has assay temperature value
range: int

has sense strand sequence
type: DatatypeProperty
sub property of: has DNA sequence

has anti-sense strand sequence
type: DatatypeProperty
sub property of: has DNA sequence

has assay deposition date
type: DatatypeProperty
sub property of: has date
range: dateTime

has biosafety level
type: DatatypeProperty
IAO_0000115: A biosafety level is the level of biocontainment required to isolate hazardous biological agents in an enclosed facility. The levels of containment range from the lowest biosafety level of 1 to the highest at level 4. The levels are as follows: BSL1: Suitable for work involving well-characterized agents not known to consistently cause disease in immunocompetent adult humans, and present minimal potential hazard to laboratory personnel and the environment (definition from CDC). BSL2: Suitable for work involving agents that pose moderate hazards to personnel and the environment. It differs from BSL-1 in that 1) laboratory personnel have specific training in handling pathogenic agents and are supervised by scientists competent in handling infectious agents and associated procedures; 2) access to the laboratory is restricted when work is being conducted; and 3) all procedures in which infectious aerosols or splashes may be created are conducted in BSCs or other physical containment equipment (definition from CDC). BSL3: Suitable for clinical, diagnostic, teaching, research, or production facilities where work is performed with indigenous or exotic agents that may cause serious or potentially lethal disease through inhalation route exposure. Laboratory personnel must receive specific training in handling pathogenic and potentially lethal agents, and must be supervised by scientists competent in handling infectious agents and associated procedures. All procedures involving the manipulation of infectious materials must be conducted within BSCs, other physical containment devices, or by personnel wearing appropriate personal protective equipment (definition from CDC). BSL4:
range: string

has assay pH value
type: DatatypeProperty
IAO_0000115: pH approximates the negative logarithm (base 10) of the molar concentration of dissolved hydronium ions in a solution.
range: float

has assay pressure value
type: DatatypeProperty
IAO_0000115: It is the force per unit area applied in a direction perpendicular to the surface of an object in an assay.
range: float

has cell modification temperature value
type: DatatypeProperty
sub property of: has assay temperature value
range: int

has perturbagen incubation temperature value
type: DatatypeProperty
sub property of: has assay temperature value
range: int

has substrate incubation temperature value
type: DatatypeProperty
sub property of: has assay temperature value
range: int

has assay temperature value
type: DatatypeProperty
IAO_0000115: It is the temperature at which the biological experiment was conducted.
range: int
sub property of: topDataProperty

has incubation time value
type: DatatypeProperty
IAO_0000115: It is the interval of time between the addition of a perturbagen, substrate or cell modification and the measurement of change, as observed by a detection method in the bioassay.
range: int
sub property of: topDataProperty

has cell modification time value
type: DatatypeProperty
IAO_0000115: It is the interval of time between the cell modification, namely transient transfection of plasmid DNA/ siRNA, viral transduction, etc and the measurement of change, as observed by a detection method in the bioassay.
sub property of: has incubation time value
range: int

has coupled substrate incubation time value
type: DatatypeProperty
sub property of: has incubation time value
range: int

has enzyme reaction time value
type: DatatypeProperty
IAO_0000115: It is the interval of time between the enzyme activity measurement in a kinetic assay.
sub property of: has incubation time value
range: int

has perturbagen incubation time value
type: DatatypeProperty
IAO_0000115: It is the interval of time between the addition of a perturbagen and the measurement of change, as observed by a detection method in the bioassay.
sub property of: has incubation time value
range: int

has substrate incubation time value
type: DatatypeProperty
IAO_0000115: It is the interval of time between the addition of an enzyme substrate and the measurement of change, as observed by a detection/ readout in a bioassay.
sub property of: has incubation time value
range: int

has coupled substrate incubation temperature value
type: DatatypeProperty
sub property of: has assay temperature value
range: int

has repetition point-number
type: DatatypeProperty
IAO_0000115: The number of replicate measurements (repetitions) per concentration value used.
range: int

has wavelength value
type: DatatypeProperty
range: int

is input data value of
type: DatatypeProperty
range: float

has sequence position
type: DatatypeProperty

has shRNA probe sense sequence position
type: DatatypeProperty
IAO_0000115: The nucleotide number in the sense strand of a gene that marks the beginning and end of the shRNA probe.
sub property of: has sequence position

has siRNA probe sense sequence position
type: DatatypeProperty
IAO_0000115: The nucleotide number in the sense strand of a gene that marks the beginning and end of the siRNA probe.
sub property of: has sequence position

has ligand incubation time value
type: DatatypeProperty
sub property of: has incubation time value

has activity threshold value
type: DatatypeProperty
IAO_0000115: The value (in conjunction with the signal direction) used to determine perturbagens of interest (hits.) Perturbagens with a readout value beyond the threshold in the direction of interest are considered active in the assay.

has excitation wavelength value
type: DatatypeProperty
sub property of: has wavelength value

has emission wavelength value
type: DatatypeProperty
sub property of: has wavelength value

has absorbance wavelength value
type: DatatypeProperty
sub property of: has wavelength value

has recommended name
type: DatatypeProperty

has value
type: DatatypeProperty

reports assay measurment value
type: DatatypeProperty

has assay design method
type: DatatypeProperty

has assay supporting method
type: DatatypeProperty