HCLSIG BioRDF Subgroup/MicroarrayExperimentContext
Microarray Experiment Context
This document has been created to collect provenance-specific terms to (re)create the experiment context of microarray data being used by the HCLS BioRDF group.
Contact for this page: SatyaSahoo, JunZhao, KeiCheung, MScottMarshall
Sample scenarios of using the Microarray experiment context information
- Integration of gene expression data created under different experiment conditions and/or using different samples
- Possibly regenerate/recreate a list of genes in published literature from raw experiment data (includes re-running scientific workflow for data processing and statistical analysis)
- Evaluate microarray data quality using provenance information describing experiment conditions
- Influence federated query planning/execution using provenance of the microarray gene expression datasets
Sample queries using the Microarray experiment context information
- Find out the tissue type and the organism from which the genes were sampled
- Find out the expression of those genes that were sampled from Alzheimer's Disease patients with NFT, of those from non-NFT AD patients, and of those from non-demented controls
- Find out the age of the population
- Find out the statistic analysis method used to analyze the difference between gene expression profiles of AD NFT neurons and AD non-NFT neurons
In the near term, we can start with the following example queries:
- Find experiments involving the same disease/phenotype, brain region, and species
- Find experiments that involve AD patients of certain disease states (e.g., mild vs severe AD patients)
- Find particular types of genes (e.g., energy metabolism) that are expressed in a given brain region
List of Provenance Terms
1. Organization identifier: ontology term-http://purl.obofoundry.org/obo/OBI_0000245, http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Organization, Biomedical Resource ontology, GeoSpecies ontology
Examples:NINDS-NIMH Microarray Consortium, TGen
2. BioSource: ontology term-http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSource
Examples: entorhinal cortex (EC control 1, EC_affected_4), hippocampus (HIP control 13), medial temporal gyrus (MTG control 11), posterior cingulate (PC control 1, PC control 4), primary visual cortex (VCX control 6), posterior cingulate cortex (PC_affected_7)
3. Organism: ontology term-http://mged.sourceforge.net/ontologies/MGEDontology.php#Organism
Examples: Human
4. OrganismPartRegion: ontology term-http://purl.org/biotop/dev#OrganismPart, http://www.ebi.ac.uk/efo/EFO_0000635 (Experiment Factor ontology), Microarray experiment conditions ontology
Examples: Entorhinal Cortex, Medial Temporal Gyrus, Posterior Singulate, hippocampus, Superior Frontal Gyrus
5. CellType: ontology term-http://mged.sourceforge.net/ontologies/MGEDontology.php#CellType
Examples: layer III neurons, pyramidal neuron
6. Ethnicity: ontology term-http://bioontology.org/projects/ontologies/birnlex#birnlex_3016, NCI Thesaurus, NIFSTD
Examples: Caucasian
7. BioSampleType: ontology term-http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSampleType, NCI Thesaurus (BioSample)
Examples: not_extract(http://mged.sourceforge.net/ontologies/MGEDontology.php#not_extract), extract (http://mged.sourceforge.net/ontologies/MGEDontology.php#extract)
8. MaterialType: ontology term-http://mged.sourceforge.net/ontologies/MGEDOntology.owl#MaterialType, NCI Thesaurus (Material), Galen (Material)
Examples: total_RNA(http://mged.sourceforge.net/ontologies/MGEDontology.php#total_RNA), cell(http://mged.sourceforge.net/ontologies/MGEDontology.php#cell), whole_organism (http://mged.sourceforge.net/ontologies/MGEDontology.php#whole_organism)
9. Age: ontology terms-http://mged.sourceforge.net/ontologies/MGEDontology.php#Age
Examples: 80 years, 83 years (http://mged.sourceforge.net/ontologies/MGEDontology.php#years)
10. DevelopmentalStage: ontology term-http://mged.sourceforge.net/ontologies/MGEDontology.php#DevelopmentalStage
Examples: Adult, Adult (Postmortem)
11. DiseaseState: ontology term-http://mged.sourceforge.net/ontologies/MGEDontology.php#DiseaseState
Examples: normal, Alzheimer's Disease, Mild Cognitive Impairment
12. Treatment: ontology term-http://mged.sourceforge.net/ontologies/MGEDOntology.owl#Treatment, NCI Thesaurus, Ontology for clinical research
Examples: Laser capture microdissection
13. Statistical tools used in analysis of gene expression data, http://www.ebi.ac.uk/efo/swo/SWO_0000001 found in Software Ontology http://www.ebi.ac.uk/efo/swo
Example: Bioconductor Software, http://www.ebi.ac.uk/efo/swo/SWO_0000072
14. Parameters used by these tools, the versions and providers of these tools, found in Software Ontology http://www.ebi.ac.uk/efo/swo, and Information Artifact Ontology
Software version: http://purl.obolibrary.org/obo/IAO_0000129
15. Tissue details
Below are the terms that are automatically identified using NCBO Annotator with NIFSTD being the input ontology and the 4 abstracts listed in the microarray use case.
- Area
- Associated with
- Brain
- CA1
- Cingulate cortex
- Complex
- Damage
- Disease
- Dopamine
- Energy
- Entorhinal cortex
- Gene
- Genome
- Hippocampus
- Human
- Tissue
- Functional
- Interleukin-1
- In Vivo
- Laser capture
- Middle temporal gyrus
- Neurofibrilliary tangle
- Neuron
- Neuritic plague
- Normal
- Plague
- Posterior cingulate cortex
- Protein
- Rat
- Rate
- Reference
- Substantial Nigra
- Superior frontal gyrus
- Transcription Factor
- Visual
Provenance ontologies modeling experiment conditions
1. Provenir ontology - An upper-level ontology for provenance modeling based on OBO Foundry principles. Can be extended to create interoperable domain-specific provenance ontologies (for example, the Parasite Experiment ontology)
2. MGED
3. EFO
4. OBI
See also MIAME