Minimal information for Chemosensitivity assays
Following is the glossary for the terms used in MICHA drug screening protocol. Highlighted fields can be automatically extracted by MICHA and users may not need to enter that information.
If data is focusing on cell lines, users have to enter following cell line information. Highlighted fields can be automatically extracted by MICHA and users do not need to enter.
Organism (BAO_0000551): Cell line specie e.g. Homo sapiens.
Cell line modifications (BAO_0000238): Modification to actual cell line.
If data is focusing on patients, users have to enter following patient details information. Patient ID is optional
Comprehensive Information on screened compounds. Most of this information is automatically extracted from public resources such as ChEMBL, DrugComb and ClinicalTrials. Users just need to upload Compound names and standard inchikeys. For example standard inchiKey for imatinib is: XDXDZDZNSLXDNA-TZNDIEGXSA-N. Highlighted fields can be automatically extracted by MICHA and users do not need to enter.
Following is the description about experimental terms used in MICHA.
Medium (BAO_0000596): RPMI1640, 10% FBS, pen/strep, glutamine
Plate type (BAO_0000508): Corning 384-well # 3764
Cell density (cells/well) (BAO_0000572): Number of cells per well e.g 3000.
Assay format (BAO_0000019): An assay format is a conceptualization of assays based on the biological and/or chemical features of the experimental system. For example, assay formats include 1) biochemical, assays with purified protein, 2) cell-based, assays in whole cells, 3) cell-free, assays in cell derivatives, 4) organism-based, assays performed in an organism, 5) physiochemical, assays which measure physical or chemical properties, and 6) tissue-based, assays using tissue derived from a living organism. This information must be selected from drop down list in MICHA excel template.
Biochemical (BAO_0000217): A biochemical assay format is an in vitro format used to measure the activity of a biological macromolecule, e.g. a purified protein or nucleic acid. It is most often a homogeneous assay, but can be heterogeneous if a solid phase, such as beads, is used to immobilize the macromolecule.
Cell-based (BAO_0000219): A cell-based assay format involves the use of living eukaryotic cells and is a heterogeneous assay.
Cell-free (BAO_0000366): A cell-free assay format originates from cells, but does not use intact, live cells. This format is distinct from biochemical assays. It is most often a homogeneous assay, but can be heterogeneous if a solid phase, such as beads, is used to immobilize the components.
Organism-based (BAO_0000218): An organism-based assay format involves the use of a living organism and is a heterogeneous assay.
Physiochemical (BAO_0000684,BAO_0010009): A physiochemical assay format involves the measurement of physical and chemical properties of perturbagens, namely aqueous solubility, octanol/water partition, or cell permeability models e.g. parallel artificial membrane permeability assay (PAMPA).
Tissue based (BAO_0000221): A tissue-based assay format involves the use of a tissue derived from a living organism and is a heterogeneous assay type.
Detection technology (BAO_0000035): A detection technology is the physical method or technique readout used to measure an effect caused by a perturbagen in an assay environment. This information must be selected from drop down list in MICHA excel template.
Fluorescence (BAO_0000046): Fluorescence detection methods use the principles of fluorescence, whereby incident light excites a fluorophore that then emits light at lower energy and higher wavelength, typically in the visible portion of the UV-Visible spectrum.
Fluorescence polarization (FP) (BAO_0000003): Fluorescence polarization (FP) measurements are based on the assessment of size-dependent rotational motions of species and used to measure binding interactions.
Alpha Screen (BAO_0000130): Amplified Luminescent Proximity Homogeneous Assay Screen is a subtype of fluorescence detection technologies.
Time Resolved Fluorescence (TRF) (BAO_0000004): Time Resolved Fluorescence (TRF) is a subtype of fluorescence detection technologies. One commercial name is DELFIA.
Time -Resolved Fluorescence Energy Transfer (TR-FRET) (BAO_0000004): Time-Resolved Fluorescence Energy Transfer (TR-FRET) is a subtype of fluorescence detection technologies. Commercial names are LANCE and HTRF.
Label-free technology (BAO_0000427): Label-free detection technologies measure binding interactions and cell-based reactions in the absence of conventional labels, e.g., fluorescent probes. Advantages include the ability to measure a) functional activity without modifying the binding partners with labels, b) binding interactions independent of functional activity, and c) cell-based assays without the need to engineer cell-lines to over-express given targets, such as GPCRs.
Luminescence (BAO_0000045): Luminescence detection technologies make use of light emission that occurs from an electronically excited state reached by a physical, mechanical, or chemical mechanism.
Microscopy (BAO_0000452): Microscopic detection technologies use microscopes to see objects that cannot be seen with an unaided eye.
Quantitative PCR (qPCR) (BAO_0002089): Quantitative PCR, sometimes referred to as RT-PCR, detection technologies use DNA labeled protein in a binding assay and are detected by quantifying the amount of DNA by PCR. A commercial assay called KINOMEscan was specifically developed for screening purposes.
Radiometry (BAO_0000657): Radiometry detection technologies use radioactive tracers. Examples of assays that use radiometry are filter assays and Scintillation Proximity Assay (SPA).
Spectrophotometry (BAO_0000049): Spectrophotometry detection technologies measure the amount of light that a sample absorbs. A spectrophotometer operates by passing a beam of light through a sample and measuring the intensity of light reaching a detector.
Thermal shift (BAO_0000058): Thermal shift detection technologies detect temperature shifts using a fluorescent dye that is sensitive to a protein environment. Upon heating, a protein unfolds and loses native conformation. Binding of a small molecule can often stabilize the protein conformation, resulting in a higher unfolding temperature. Endpoint mode of action: