The study of the transcriptome, the complete set of RNA transcripts produced by the genome at any one time
a cheminformatics analysis is an "assay" performed in silico, employing cheminformatics techniques to analyse biological data
ExperimentalFactors are descriptors of the properties of the experiment. How the culture was prepared, what organism they are from, and what type of experiment was run
This part of the ontology is still in development
quantitative real time polymerase chain reaction (Q-PCR/qPCR) or kinetic polymerase chain reaction, is based on PCR and is used to amplify and simultaneously quantify a targeted DNA molecule
also known as real-time PCR or quantative PCR
SysMO studies microorganisms. Each experiment is performed on cell cultures, so it is essential to record the type of culture in use each time
Chromatography is the collective term for a set of laboratory techniques for the separation of mixtures. It involves passing a mixture dissolved in a "mobile phase" through a stationary phase, which separates the analyte to be measured from other molecules in the mixture based on differential partitioning between the mobile and stationary phases.
laboratory techniques which involve separation by binding the molecules of interest
all shareable entities in the SysMO SEEK are kinds of Assets
the entity under investigation (e.g. glucose)
Electrophoresis is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field
Standard operating procedures and protocols from SysMO
Mass spectrometry (MS) is an analytical technique for the determination of the elemental composition of a sample or molecule. It is used for elucidating the chemical structures of peptides and sometimes other chemical compounds
Real-time reverse-transcription PCR, qRT-PCR
Reverse transcription polymerase chain reaction (RT-PCR) is a variant of polymerase chain reaction (PCR). In RT-PCR an RNA strand is first reverse transcribed into its DNA complement (complementary DNA, or cDNA) using the enzyme reverse transcriptase, and the resulting cDNA is amplified using traditional or real-time PCR.
describes the technologies and/or techniques used in performing experiments
sodium dodecyl sulfate polyacrylamide gel electrophoresis
factors studied describe what types of measurements were taken (i.e. what factors were expected to change during the experiment)
also known as ExperimentalConditions when used to set up initial conditions for an experiment/assay
a bioinformatics analysis is an "assay" performed in silico, employing bioinformatics techniques to analyse biological data
define what is inside MAGE-TAB from other ontology
fluorescence recovery after photobleaching
An experimental assay is an assay carried out in a laboratory
the study of the network of interactions between proteins, metabolites and other biological objects in the cell, and the consequences of those interactions
the polymerase chain reaction (PCR) is a technique to amplify a single or few copies of a piece of DNA across several orders of magnitude, generating thousands to millions of copies of a particular DNA sequence.
a model analysis type is a model "assay" type to classify the information contained within the model. The categories correspond to the existing categories in JWS Onnline, a tool for model simmulation
Affinity chromatography is based on selective non-covalent interaction between an analyte and specific molecules. It is often used in biochemistry in the purification of proteins bound to tags. These fusion proteins are labeled with compounds such as His-tags, biotin or antigens, which bind to the stationary phase specifically.
techniques for labelling molecules to allow them to be detected in laboratory analyses
a collection of experiments designed to answer a particular biological question
the experimental context for any of the SysMO assets
the study of biochemical reactions in the cell
High Performance Liquid Chromatography. Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid
Two-hybrid screening (also known as yeast two-hybrid system or Y2H) is a molecular biology technique used to discover protein-protein interactions and protein-DNA interactions by testing for physical interactions
Ultra Performance Liquid Chromatography Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid
A high level description of the experimental work undertaken
Proteomics is the study of the function and structure of proteins in an organism, predominantly using high-throughput techniques
an informatics analysis is an "assay" performed in silico, employing informatics techniques to analyse data
analysing the response of single cells to stimuli and perturbations by fluorescence and imaging
Gas chromatography (GC) is a separation technique in which the mobile phase is a gas
need to link to biological objects genes proteins enzyme reactions = GO pathways cells organisms we already have organisms once we can point to the species of reactions, we can model the SBO part more effectively Factors studied and experimental conditions make more sense seperately now we have more examples Can we import the entity part of the SBO? The interaction between models and data is at the heart of SysMO, so the SBO should also be
the dynamic changes of molecules within a cell over time
Size exclusion chromatography (SEC), also known as gel permeation chromatography or gel filtration chromatography, separates particles on the basis of size. It is generally a low resolution chromatography and thus it is often reserved for the final, "polishing" step of a purification. It is also useful for determining the tertiary structure and quaternary structure of purified proteins.
The assay_type hierarchy allows scientists to categorise their experimental assays, informatics analyses and computational models within SysMO
An assay type describes the type of experiment being performed