HCLSIG BioRDF Subgroup/MicroarrayExperimentContext

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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