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*
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
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.
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.
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'
is binding site of
tagged with
has detected entity
is cell line of
has assay protocol
is assay protocol of
has associated disease
is associated disease of
has assay readout content
has assay readout content parametricity
has assay source
has assay title
has bioassay type
is bioassay type of
has assay readout type
has signal direction
has endpoint modifier
has phenotype
is phenotype of
is localized in
has concentration throughput
has repetition throughput
uses detection instrument
has assay footprint
silences
has gene symbol
is role of
is unit of
has unit
is detected by
has antibody source
recombinantly expressed in
has preparation method
has organism
has assay medium
has assay serum
is grown in
is transfected into
is derived from
detects phenotype
has indicator
is described by
quantifies
has molecular phenotype
has morphological phenotype
has positive control
has negative control
has experimental setting
has DNA sequence
has concentration-point number
has passage number
has cell count
has copy number
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
This describes the number of repeats of a gene of interest cloned in a DNA construct.
has cDNA copy number
This describes the number of repeats of a cDNA of interest cloned in a DNA construct.
has artificial regulatory region copy number
This describes the number of repeats of an artificial regulatory element present in a DNA construct.
has sequence
has protein sequence
has nucleic acid sequence
has RNA sequence
has shRNA sense sequence
has enzyme reaction temperature value
has sense strand sequence
has anti-sense strand sequence
has assay deposition date
has biosafety level
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:
has assay pH value
pH approximates the negative logarithm (base 10) of the molar concentration of dissolved hydronium ions in a solution.
has assay pressure value
It is the force per unit area applied in a direction perpendicular to the surface of an object in an assay.
has cell modification temperature value
has perturbagen incubation temperature value
has substrate incubation temperature value
has assay temperature value
It is the temperature at which the biological experiment was conducted.
has incubation time value
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.
has cell modification time value
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.
has coupled substrate incubation time value
has enzyme reaction time value
It is the interval of time between the enzyme activity measurement in a kinetic assay.
has perturbagen incubation time value
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.
has substrate incubation time value
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.
has coupled substrate incubation temperature value
has repetition point-number
The number of replicate measurements (repetitions) per concentration value used.
has wavelength value
is input data value of
has sequence position
has shRNA probe sense sequence position
The nucleotide number in the sense strand of a gene that marks the beginning and end of the shRNA probe.
has siRNA probe sense sequence position
The nucleotide number in the sense strand of a gene that marks the beginning and end of the siRNA probe.
has ligand incubation time value
has activity threshold value
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
has emission wavelength value
has absorbance wavelength value
has recommended name
has value
reports assay measurment value
has assay design method
has assay supporting method