EBI Expression Atlas RDF Schema vocabulary
type: Ontology
creator: Simon Jupp
version info: 1
comment: This resource defines a vocabulary used to create a schema for the RDF transformation of the EMBL-EBI Expression Atlas database. The vocabulary defined in here is mapped where possible to external reference ontologies such as EFO, SIO and OBI. See http://rdf.ebi.ac.uk/resource/gxa/mapping
creator: James Malone
rights: This Ontology is distributed under a Creative Commons Attribution License - http://creativecommons.org/licenses/by/3.0/
version IRI: expressionatlas

depiction
type: AnnotationProperty
comment: An image depiction of some thing
type: ObjectProperty

dbXref
type: ObjectProperty
comment: a releationship between some information entity and a reference database entry

geneXref
type: ObjectProperty
description: A relationship to a gene database reference
range: Gene database reference
sub property of: dbXref

hasAnalysis
type: ObjectProperty
description: A relationship to a resource that represents some analysis e.g. The analysis of data from a micro-array experiment to generate a gene list

hasAssay
type: ObjectProperty
description: A relation from an Experiment to an Assay
range: Assay
domain: Experiment

hasAssociatedArrayDesign
type: ObjectProperty
description: A relation between an differential gene expression analysis and the associated type of array design
range: design platform

has factor value
type: ObjectProperty
description: A relationship between an information entity and an independent experimental factor variable
range: Experimental Factor

hasOutput
type: ObjectProperty
description: A relation between a differentional gene expression analysis and an individual gene expression value
domain: Differential expression analysis
range: Differential expression ratio
inverse of: isOutputOf

hasReferenceAssay
type: ObjectProperty

hasSampleCharacteristic
type: ObjectProperty
description: A characteristic born in a biological sample e.g. human sample
domain: Sample

hasSpecifiedInput
type: ObjectProperty
description: A relation from an assay to the related samples
domain: Assay
range: Sample

hasTestAssay
type: ObjectProperty

implementedBy
type: ObjectProperty
description: A relation from a software analysis process and the softwrare that performed the analysis

is about
type: ObjectProperty
equivalent to: IAO_0000136
equivalent to: SIO_000332

isOutputOf
type: ObjectProperty

refersTo
type: ObjectProperty
description: A relation between a measurement value and the probe design element being measured
range: Probe design element

taxon
type: ObjectProperty
description: An assoiative relationship between some entity or resource and an organism
sub property of: dbXref

fpkm
type: DatatypeProperty
description: Fragments Per Kilobase of transcript per Million mapped reads

organism
type: Class
subclass of: Restriction
  on property: depiction
  has value: organism image
description: A material entity that is an individual living system, such as animal, plant, bacteria or virus, that is capable of replicating or reproducing, growth and maintenance in the right environment. An organism may be unicellular or made up, like humans, of many billions of cells divided into specialized tissues and organs.
type: NamedIndividual

Analysis
type: Class
description: A planned process that produces output data from input data.

Assay
type: Class
subclass of: Restriction
  on property: has factor value
  some values from: Experimental Factor
subclass of: Restriction
  on property: hasSpecifiedInput
  some values from: Sample
description: An assay is an investigative (analytic) procedure in laboratory medicine, pharmacology, environmental biology, and molecular biology for qualitatively assessing or quantitatively measuring the presence or amount or the functional activity of a target entity (the analyte) which can be a drug or biochemical substance or a cell in an organism or organic sample.
equivalent to: OBI_0000070
equivalent to: SIO_001007
type: NamedIndividual

BaselineExpressionAnalysis
type: Class
subclass of: Analysis
subclass of: Restriction
  on property: hasReferenceAssay
  some values from: Assay
description: A basline expression analysis is a data transformation that has an objective to detremine which gene products are present (and at what abundance) in normal conditions (e.g. tissue, cell type). FASTQ files are mapped to the reference genome from Ensembl using TopHat. FPKMs are generated by cufflinks. Raw counts are generated using htseq-count.

BaselineExpressionValue
type: Class
subclass of: Thing
description: A gene expression value representing normalized expression levels (FPKMs) across the analyzed experimental factor values

DatabaseReference
type: Class
description: Reference to a database entry. This is usually some database accession that uniquely identifes an entry

Decreased differential expression ratio
type: Class
subclass of: Differential expression ratio
description: A descreased ratio of gene expression values from a test sample compared to a control sample.
equivalent to: SIO_001082
type: NamedIndividual

design platform
type: Class
subclass of: Restriction
  on property: taxon
  some values from: organism
description: An instrument design which specifes a platform for doing gene expression detection
equivalent to: EFO_0001451

Differential expression analysis
type: Class
subclass of: Analysis
subclass of: Restriction
  on property: hasTestAssay
  some values from: Assay
subclass of: Restriction
  on property: depiction
  has value: differential expression analysis image
subclass of: Restriction
  on property: hasReferenceAssay
  some values from: Assay
subclass of: Restriction
  on property: implementedBy
  some values from: expressionatlas R statistics package
subclass of: Restriction
  on property: hasOutput
  some values from: Differential expression ratio
description: A differential expression analysis is a data transformation that has objective differential expression analysis
equivalent to: OBI_0000650
equivalent to: SIO_000594
type: NamedIndividual

Differential expression ratio
type: Class
subclass of: Restriction
  on property: refersTo
  some values from: Probe design element
subclass of: Restriction
  on property: pValue
  some values from: double
subclass of: Restriction
  on property: tStatistic
  all values from: double
subclass of: Restriction
  on property: has factor value
  some values from: Experimental Factor
description: The ratio of gene expression values from a test sample compared to a control sample.
equivalent to: SIO_001078
equivalent to: EFO_0004034

EnsemblDatabaseReference
type: Class
subclass of: Gene database reference
description: Reference to an ensembl gene entry
equivalent to: data 1033
type: NamedIndividual

EntrezGeneDatabaseReference
type: Class
subclass of: Gene database reference
description: Reference to an NCBI entrez gene entry
equivalent to: data 1027
type: NamedIndividual

Experiment
type: Class
subclass of: Restriction
  on property: bibliographicCitation
  some values from: string
subclass of: Restriction
  on property: depiction
  has value: experiment image
subclass of: Restriction
  on property: hasAssay
  some values from: Assay
subclass of: Restriction
  on property: identifier
  some values from: string
subclass of: Restriction
  on property: description
  some values from: string
subclass of: Restriction
  on property: dateSubmitted
  some values from: dateTime
subclass of: Restriction
  on property: pubmedid
  some values from: string
description: An experiment is an investigation that has the goal of verifying, falsifying, or establishing the validity of a hypothesis.
equivalent to: SIO_000994
comment: experiment image
type: NamedIndividual

Experimental Factor
type: Class
description: An experimental factor is a variable that may change within the scope of a given experiment.
equivalent to: SIO_000367

FlybaseDatabaseReference
type: Class
subclass of: Gene database reference
description: Reference to a flybase gene entry
equivalent to: data 1089
type: NamedIndividual

Gene
type: Class
subclass of: Restriction
  on property: depiction
  has value: gene image
description: A region (or regions) that includes all of the sequence elements necessary to encode a functional transcript. A gene may include regulatory regions, transcribed regions and/or other functional sequence regions.
equivalent to: SO_0000704
equivalent to: SIO_010035
type: NamedIndividual

Gene database reference
type: Class
subclass of: DatabaseReference
subclass of: Restriction
  on property: isIdentifierFor
  some values from: Gene
subclass of: Restriction
  on property: taxon
  some values from: organism
description: Reference to a gene entry. This is usually some database accession that uniquely identifes that entry

Increased differential expression ratio
type: Class
subclass of: Differential expression ratio
description: A increased ratio of gene expression values from a test sample compared to a control sample.
equivalent to: SIO_001081
type: NamedIndividual

MgiGeneDatabaseReference
type: Class
subclass of: Gene database reference
description: Reference to a MGI gene database entry
type: NamedIndividual

MicroarrayDifferentialExpressionAnalysis
type: Class
subclass of: Differential expression analysis
subclass of: Restriction
  on property: depiction
  has value: differential expression analysis image
description: A microarray differential expression analysis is a data transformation that has objective differential expression analysis of microarray data. Raw single-channel microarray intensities are normalized using RMA via the oligo package from Bioconductor (Affymetrix data) or using quantile normalization via the limma package (Agilent data). Two-channel Agilent data is normalized using LOESS via the limma package. Pairwise contrasts are performed using a moderated t-test for each gene using limma.

Microarray experiment
type: Class
subclass of: Experiment

Probe design element
type: Class
subclass of: Restriction
  on property: dbXref
  some values from: DatabaseReference
description: The probe which is used in an assay such as an array for detecting sequence or gene expression levels.
equivalent to: EFO_0004903

Protein database reference
type: Class
subclass of: DatabaseReference
subclass of: Restriction
  on property: taxon
  some values from: organism
description: Reference to a protein database entry. This is usually some database accession that uniquely identifes that entry

RNASeqDifferentialAnalysis
type: Class
subclass of: Differential expression analysis
subclass of: Restriction
  on property: depiction
  has value: differential expression analysis image
description: A RNS-Seq differential expression analysis is a data transformation that has objective differential expression analysis of RNS-Seq data. FASTQ files are mapped to the reference genome from Ensembl using TopHat. FPKMs are generated by cufflinks. Raw counts are generated using htseq-count. Pairwise contrasts are performed using a conditioned test based on the negative binomial distribution, using DESeq.

RicegapDatabaseReference
type: Class
subclass of: Gene database reference
description: Reference to the Rice genome annotation project database
type: NamedIndividual

Sample
type: Class
subclass of: Restriction
  on property: hasSampleCharacteristic
  some values from: Experimental Factor
description: a sample is a limited quantity of something (e.g. an individual or set of individuals from a population, or a portion of a substance) to be used for testing, analysis, inspection, investigation, demonstration, or trial use.
equivalent to: OBI_0100051
equivalent to: SIO_001050
type: NamedIndividual

TairDatabaseReference
type: Class
subclass of: Gene database reference
description: Reference to a TAIR gene database entry. The Arabidiopsis Information Resource
equivalent to: data 1037
type: NamedIndividual

UniprotDatabaseReference
type: Class
subclass of: Protein database reference
description: Reference to a uniprot protein databse entry
equivalent to: data 2291

Microarray 1 colour microRNA differential
type: Class
subclass of: Microarray experiment
description: A differential experiment dtermines which microRNA is up– or down–regulated in different experimental conditions. They are based on a set of highly curated differential expression Microarray 1 colour experiments from ArrayExpress that have been re-processed using our in–house differential expression statistical analysis pipeline.

Microarray 1 colour mRNA differential
type: Class
subclass of: Microarray experiment
description: A differential experiment dtermines which mRNA ise up– or down–regulated in different experimental conditions. They are based on a set of highly curated differential expression Microarray 1 colour experiments from ArrayExpress that have been re-processed using our in–house differential expression statistical analysis pipeline.

Microarray 2 colour mRNA differential
type: Class
subclass of: Microarray experiment
description: A differential experiment dtermines which mRNAs is up– or down–regulated in different experimental conditions. They are based on a set of highly curated differential expression Microarray 2 colour experiments from ArrayExpress that have been re-processed using our in–house differential expression statistical analysis pipeline.

RNA-Seq mRNA baseline
type: Class
subclass of: Experiment
description: A Baseline experiment represents information about which gene products are present (and at what abundance) in which norma" condition (e.g., tissue, cell type). These experiments consists of highly curated RNA–seq experiments from ArrayExpress. The above experiments have been re–analyzed using an in–house RNA–seq processing pipeline. The resulting data matrix stores gene expression profiles across the analyzed experimental factor values as a set of normalized expression levels (FPKMs)

RNA-Seq mRNA differential
type: Class
subclass of: Experiment
description: A differential experiment dtermines which genes are up– or down–regulated in different experimental conditions. They are based on a set of highly curated differential expression RNA-Seq experiments from ArrayExpress that have been re-processed using our in–house differential expression statistical analysis pipeline.

expressionatlas R statistics package
type: Class

image
type: Class

assay image
type: image
type: NamedIndividual

differential expression analysis image
type: image
type: NamedIndividual

experiment image
type: image
type: NamedIndividual

gene image
type: image
type: NamedIndividual

organism image
type: image
type: NamedIndividual

sample image
type: image
type: NamedIndividual