This Ontology is distributed under a Creative Commons Attribution License - http://creativecommons.org/licenses/by/3.0/
EBI Gene Expression Atlas RDF Schema vocabulary
This resource defines a vocabulary used to create a schema for the RDF transformation of the EMBL-EBI Gene 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
a releationship between some information entity and a reference database entry
A relationship to a gene database reference
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
A relation from an Experiment to an Assay
A relation between an differential gene expression analysis and the associated type of array design
A relationship between an information entity and an independent experimental factor variable
A relation between a differentional gene expression analysis and an individual gene expression value
hasReferenceAssay
A characteristic born in a biological sample e.g. human sample
A relation from an assay to the related samples
hasTestAssay
A relation from a software analysis process and the softwrare that performed the analysis
is about
isOutputOf
A relation between a measurement value and the probe design element being measured
An assoiative relationship between some entity or resource and an organism
fpkm
Fragments Per Kilobase of transcript per Million mapped reads
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.
Analysis
A planned process that produces output data from input data.
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.
BaselineExpressionAnalysis
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
A gene expression value representing normalized expression levels (FPKMs) across the analyzed experimental factor values
Reference to a database entry. This is usually some database accession that uniquely identifes an entry
A descreased ratio of gene expression values from a test sample compared to a control sample.
An instrument design which specifes a platform for doing gene expression detection
A differential expression analysis is a data transformation that has objective differential expression analysis
The ratio of gene expression values from a test sample compared to a control sample.
An experiment is an investigation that has the goal of verifying, falsifying, or establishing the validity of a hypothesis.
An experimental factor is a variable that may change within the scope of a given experiment.
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.
Reference to a gene entry. This is usually some database accession that uniquely identifes that entry
A increased ratio of gene expression values from a test sample compared to a control sample.
MicroarrayDifferentialExpressionAnalysis
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
The probe which is used in an assay such as an array for detecting sequence or gene expression levels.
Reference to a protein database entry. This is usually some database accession that uniquely identifes that entry
RNASeqDifferentialAnalysis
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.
Reference to the Rice genome annotation project database
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.
Reference to a TAIR gene database entry. The Arabidiopsis Information Resource
Reference to a uniprot protein databse entry
Microarray 1 colour microRNA differential
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.
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.
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.
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)
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.
assay image