JERM:00079
JERM:110002
JERM:00122
JERM:00031
JERM:00078
JERM:40005
JERM:87160
JERM:40008
JERM:00081
JERM:00035
JERM:85192
JERM:00086
JERM:00069
JERM:00029
JERM:00020
JERM:00120
JERM:00085
The study of the transcriptome, the complete set of RNA transcripts produced by the genome at any one time
JERM:20946
JERM:00047
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
JERM:00017
This part of the ontology is still in development
JERM:67650
JERM:00012
computational models developed in SysMO
JERM:00011
SEEK data files
JERM:97016
JERM:00082
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
JERM:00104
publication abstracts from SysMO
JERM:00014
SysMO studies microorganisms. Each experiment is performed on cell cultures, so it is essential to record the type of culture in use each time
JERM:00026
JERM:50003
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.
JERM:00095
e.g. RT_PCR to amplify DNA from RNA
JERM:000007
JERM:50016
JERM:75160
JERM:69863
JERM:22481
JERM:40002
laboratory techniques which involve separation by binding the molecules of interest
JERM:00094
JERM:24776
JERM:00103
JERM:40011
JERM:00091
JERM:00041
Chromatin Immunoprecipitation on Chip
JERM:00130
proteomicsAssay
JERM:0007
JERM:40001
JERM:00042
all shareable entities in the SysMO SEEK are kinds of Assets
JERM:00010
the entity under investigation (e.g. glucose)
JERM:00028
This part of the ontology is still in development
JERM:00133
JERM:00062
Electrophoresis is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field
JERM:00096
JERM:110000
JERM:00064
JERM:00037
JERM:00061
JERM:40012
JERM:00049
JERM:40017
JERM:00033
Standard operating procedures and protocols from SysMO
JERM:00015
JERM:00065
JERM:90004
JERM:50017
JERM:00123
JERM:82270
JERM:00032
JERM:00141
JERM:40017
JERM:00068
JERM:00090
JERM:50015
JERM:00137
JERM:00076
JERM:00092
JERM:00019
JERM:50009
JERM:40018
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
JERM:00099
JERM:40019
JERM:50006
JERM:000001
JERM:50925
Real-time reverse-transcription PCR, qRT-PCR
JERM:00105
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.
JERM:40021
JERM:40016
JERM:00038
JERM:00100
JERM:90003
JERM:00129
JERM:00025
describes the technologies and/or techniques used in performing experiments
JERM:00116
sodium dodecyl sulfate polyacrylamide gel electrophoresis
JERM:40014
JERM:00142
JERM:00077
JERM:50008
JERM:00098
activity
JERM:110001
also called cDNA Microarray
JERM:00089
JERM:00074
factors studied describe what types of measurements were taken (i.e. what factors were expected to change during the experiment)
JERM:00027
also known as ExperimentalConditions when used to set up initial conditions for an experiment/assay
JERM:00140
JERM:00113
JERM:00139
JERM:00055
JERM:00115
a bioinformatics analysis is an "assay" performed in silico, employing bioinformatics techniques to analyse biological data
JERM:00046
define what is inside MAGE-TAB from other ontology
JERM:91021
enzymeActivity
JERM:00097
JERM:00118
JERM:50001
JERM:38539
JERM:50020
JERM:00119
fluorescence recovery after photobleaching
JERM:00052
JERM:40013
JERM:44538
JERM:26754
JERM:40006
JERM:00043
An experimental assay is an assay carried out in a laboratory
JERM:00063
the study of the network of interactions between proteins, metabolites and other biological objects in the cell, and the consequences of those interactions
JERM:00053
JERM:00093
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.
JERM:00136
JERM:50000
JERM:00092
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
JERM:00044
JERM:58493
JERM:40009
JERM:00110
affinity_purification
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.
JERM:00075
JERM:00059
JERM:00051
JERM:00134
JERM:00101
techniques for labelling molecules to allow them to be detected in laboratory analyses
JERM:00034
JERM:40003
JERM:00054
JERM:00125
JERM:00132
JERM:00121
JERM:00135
a collection of experiments designed to answer a particular biological question
JERM:00023
JERM:00114
JERM:00126
JERM:00018
JERM:00067
JERM:00138
JERM:50012
JERM:501000
JERM:00016
the experimental context for any of the SysMO assets
JERM:40004
JERM:50002
JERM:00127
JERM:15506
the study of biochemical reactions in the cell
JERM:00080
JERM:00108
High Performance Liquid Chromatography
High Performance Liquid Chromatography.
Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid
JERM:00102
yeast 2 hybrid
JERM:00106
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
JERM:00128
JERM:00131
JERM:00039
JERM:00021
descriptions of individual experiments
JERM:00060
JERM:00050
JERM:00107
Ultra Performance Liquid Chromatography
Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid
Ultra Performance Liquid Chromatography
JERM:00109
JERM:00066
JERM:50004
JERM:00058
JERM:00022
A high level description of the experimental work undertaken
JERM:00030
JERM:00072
Proteomics is the study of the function and structure of proteins in an organism, predominantly using high-throughput techniques
JERM:00045
an informatics analysis is an "assay" performed in silico, employing informatics techniques to analyse data
JERM:00084
analysing the response of single cells to stimuli and perturbations by fluorescence and imaging
JERM:00124
JERM:37735
Gas chromatography (GC) is a separation technique in which the mobile phase is a gas
JERM:00111
JERM:00057
the study of the genome of an organism
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
pressure
JERM:90001
JERM:00036
the dynamic changes of molecules within a cell over time
JERM:00056
JERM:00088
JERM:30184
JERM:40010
JERM:40020
JERM:000002
quantitative metabolomics
JERM:00071
JERM:90002
Fluorescence Activated Cell Sorting
JERM:00117
JERM:00073
not sure about this one
cellAssay
JERM:40007
JERM:00048
JERM:50005
JERM:00070
JERM:50007
JERM:00040
JERM:40015
JERM:00083
JERM:00087
JERM:62033
size_exclusion_chromatography
JERM:00112
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
JERM:00024
An assay type describes the type of experiment being performed
timepoint
version
manufacturer
instrument_model
termsofDistribution
units
sequence_accession
Streptococcus_pneumoniae
SilicoTryp
Trypanosoma_brucei
Noisy-Strep