FactorsStudied
type: Class
subclass of: ExperimentalFactors
subclass of: Restriction
  on property: units
  some values from: string
subclass of: Class
  union of: Restriction
    on property: isPartOf
    some values from: Data
  union of: Restriction
    on property: isPartOf
    some values from: SOP
subclass of: Restriction
  on property: timepoint
  some values from: integer
disjoint with: MeasuredItem
description: factors studied describe what types of measurements were taken (i.e. what factors were expected to change during the experiment)
comment: also known as ExperimentalConditions when used to set up initial conditions for an experiment/assay

transcripomics
type: Class
subclass of: ExperimentalAssayType
description: The study of the transcriptome, the complete set of RNA transcripts produced by the genome at any one time

Assay
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: hasPart
    some values from: Asset
  intersection of: Restriction
    on property: hasType
    some values from: AssayType
  intersection of: Restriction
    on property: hasType
    some values from: TechnologyType
  intersection of: Restriction
    on property: isPartOf
    some values from: Study
subclass of: ExperimentDescription
subclass of: Restriction
  on property: hasType
  some values from: CultureGrowth
subclass of: Restriction
  on property: investigates
  some values from: organism
disjoint with: Investigation
disjoint with: Study
description: descriptions of individual experiments

mass Spectrometry
type: Class
subclass of: TechnologyType
description: 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

cheminformatics analysis
type: Class
subclass of: informaticsAnalysisType
description: a cheminformatics analysis is an "assay" performed in silico, employing cheminformatics techniques to analyse biological data

ExperimentalFactors
type: Class
disjoint with: Format
disjoint with: Person
disjoint with: Project
description: 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

BioMaterial
type: Class
subclass of: ExperimentalFactors
comment: This part of the ontology is still in development

Model
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: hasFormat
    some values from: ModelExecutionEnvironment
  intersection of: Restriction
    on property: hasFormat
    some values from: ModelFormat
subclass of: Asset
subclass of: Restriction
  on property: termsofDistribution
  some values from: string
subclass of: Restriction
  on property: isDerivedFrom
  some values from: Publication
subclass of: Restriction
  on property: isDerivedFrom
  some values from: Data
description: computational models developed in SysMO

Asset
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: hasContributor
    some values from: Person
  intersection of: Restriction
    on property: isAssociatedWith
    some values from: Project
  intersection of: Restriction
    on property: isPartOf
    some values from: Assay
  intersection of: Restriction
    on property: description
    some values from: string
  intersection of: Restriction
    on property: title
    some values from: string
disjoint with: Equipment
disjoint with: ExperimentDescription
disjoint with: ExperimentalFactors
disjoint with: Format
disjoint with: Project
description: all shareable entities in the SysMO SEEK are kinds of Assets

Data
type: Class
equivalent class: Restriction
  on property: hasFormat
  some values from: DataFileFormat
subclass of: Asset
subclass of: Restriction
  on property: hasPart
  some values from: FactorsStudied
description: SEEK data files

qPCR
type: Class
subclass of: PCR
description: 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
comment: also known as real-time PCR or quantative PCR

Publication
type: Class
subclass of: Asset
description: publication abstracts from SysMO

CultureGrowth
type: Class
subclass of: TechnologyType
description: SysMO studies microorganisms. Each experiment is performed on cell cultures, so it is essential to record the type of culture in use each time

TechnologyType
type: Class
subclass of: ExperimentalFactors
description: describes the technologies and/or techniques used in performing experiments

chromatography
type: Class
subclass of: TechnologyType
description: 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.

amplification
type: Class
subclass of: genomics
description: e.g. RT_PCR to amplify DNA from RNA

binding
type: Class
subclass of: TechnologyType
description: laboratory techniques which involve separation by binding the molecules of interest

ChIP-on-chip
type: Class
subclass of: microarray
comment: Chromatin Immunoprecipitation on Chip

MassSpecAssay
type: Class
description: proteomicsAssay
subclass of: Restriction
  on property: hasPart
  some values from: Instrument
subclass of: Assay
subclass of: Restriction
  on property: hasPart
  some values from: Quantitation
subclass of: Restriction
  on property: hasPart
  some values from: PostSourceComponent
equivalent class: Class
  intersection of: Restriction
    on property: hasType
    some values from: mass Spectrometry
  intersection of: Restriction
    on property: hasType
    some values from: proteomics
subclass of: Restriction
  on property: hasPart
  some values from: software
subclass of: Restriction
  on property: hasType
  some values from: IonizationSource

proteomics
type: Class
subclass of: ExperimentalAssayType
description: Proteomics is the study of the function and structure of proteins in an organism, predominantly using high-throughput techniques

ExperimentDescription
type: Class
subclass of: Restriction
  on property: title
  some values from: string
subclass of: Restriction
  on property: description
  some values from: string
disjoint with: ExperimentalFactors
disjoint with: Format
disjoint with: Person
disjoint with: Project
description: the experimental context for any of the SysMO assets

MeasuredItem
type: Class
subclass of: ExperimentalFactors
description: the entity under investigation (e.g. glucose)
comment: This part of the ontology is still in development

genomics
type: Class
subclass of: ExperimentalAssayType
description: the study of the genome of an organism

electrophoresis
type: Class
subclass of: TechnologyType
description: Electrophoresis is the motion of dispersed particles relative to a fluid under the influence of a spatially uniform electric field

SOP
type: Class
equivalent class: Restriction
  on property: hasFormat
  some values from: SOPFileFormat
subclass of: Asset
subclass of: Restriction
  on property: hasPart
  some values from: FactorsStudied
description: Standard operating procedures and protocols from SysMO

ExperimentalAssayType
type: Class
subclass of: AssayType
is defined by: An experimental assay is an assay carried out in a laboratory

Thing
type: Class
description: 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

qRT-PCR
type: Class
subclass of: PCR
comment: Real-time reverse-transcription PCR, qRT-PCR
description: 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.

PCR
type: Class
subclass of: TechnologyType
description: 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.

SDS PAGE
type: Class
subclass of: gel electrophoresis
comment: sodium dodecyl sulfate polyacrylamide gel electrophoresis

activity
type: Class
subclass of: FactorsStudied

transcriptional profiling
type: Class
subclass of: gene expression profiling
description: also called cDNA Microarray

ModelAnalysisType
type: Class
subclass of: AssayType
description: 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

bioinformatics analysis
type: Class
subclass of: informaticsAnalysisType
description: a bioinformatics analysis is an "assay" performed in silico, employing bioinformatics techniques to analyse biological data

informaticsAnalysisType
type: Class
subclass of: AssayType
description: an informatics analysis is an "assay" performed in silico, employing informatics techniques to analyse data

MAGE-TAB
type: Class
subclass of: MicroarrayFileFormat
description: define what is inside MAGE-TAB from other ontology

enzymeActivity
type: Class
subclass of: activity

FRAP
type: Class
subclass of: imaging
comment: fluorescence recovery after photobleaching

interactomics
type: Class
subclass of: ExperimentalAssayType
description: the study of the network of interactions between proteins, metabolites and other biological objects in the cell, and the consequences of those interactions

AssayType
type: Class
subclass of: ExperimentalFactors
disjoint with: TechnologyType
comment: The assay_type hierarchy allows scientists to categorise their experimental assays, informatics analyses and computational models within SysMO
description: An assay type describes the type of experiment being performed

affinity chromatography
type: Class
subclass of: chromatography
comment: affinity_purification
description: 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.

molecule labelling
type: Class
subclass of: TechnologyType
description: techniques for labelling molecules to allow them to be detected in laboratory analyses

Study
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: hasPart
    some values from: Assay
  intersection of: Restriction
    on property: isPartOf
    some values from: Investigation
subclass of: ExperimentDescription
description: a collection of experiments designed to answer a particular biological question

reactomics
type: Class
subclass of: ExperimentalAssayType
description: the study of biochemical reactions in the cell

HPLC
type: Class
subclass of: chromatography
comment: High Performance Liquid Chromatography
description: High Performance Liquid Chromatography. Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid

2-hybrid system
type: Class
subclass of: binding
comment: yeast 2 hybrid
description: 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

Investigation
type: Class
equivalent class: Class
  intersection of: Restriction
    on property: hasPart
    some values from: Study
  intersection of: Restriction
    on property: isAssociatedWith
    some values from: Project
subclass of: ExperimentDescription
disjoint with: Study
description: A high level description of the experimental work undertaken

UPLC
type: Class
subclass of: chromatography
description: Ultra Performance Liquid Chromatography Liquid chromatography (LC) is a separation technique in which the mobile phase is a liquid
comment: Ultra Performance Liquid Chromatography

single cell
type: Class
subclass of: ExperimentalAssayType
description: analysing the response of single cells to stimuli and perturbations by fluorescence and imaging

gas chromatography
type: Class
subclass of: chromatography
description: Gas chromatography (GC) is a separation technique in which the mobile phase is a gas

pressure
type: Class
subclass of: FactorsStudied

fluxomics
type: Class
subclass of: ExperimentalAssayType
description: the dynamic changes of molecules within a cell over time

metabonomics
type: Class
subclass of: metabolomics
comment: quantitative metabolomics

FACS
type: Class
subclass of: flow cytometry
description: Fluorescence Activated Cell Sorting

immune precipitation
type: Class
subclass of: proteomics
comment: not sure about this one

cellAssay
type: Class
subclass of: Assay
description: cellAssay

gel filtration
type: Class
subclass of: chromatography
comment: size_exclusion_chromatography
description: 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.

timepoint
type: DatatypeProperty

version
type: DatatypeProperty

manufacturer
type: DatatypeProperty
domain: Instrument

instrument_model
type: DatatypeProperty

termsofDistribution
type: DatatypeProperty

units
type: DatatypeProperty

sequence_accession
type: DatatypeProperty

Streptococcus_pneumoniae
type: Thing
type: organism
is investigated by: SilicoTryp

SilicoTryp
type: Thing
type: Project

Trypanosoma_brucei
type: organism
type: Thing
is investigated by: Noisy-Strep

Noisy-Strep
type: Project
type: Thing