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Hcls sci disc-isa2rdf



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  • Funding agencies will be interested in slide 14: show experiments by where they're done, who funds them, etc.
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  • 1. ISA project , ISA tools and RDF conversion efforts Philippe Rocca-Serra Oxford University, Oxford, UKHCLS Scientific Discourse call, November, 29th 2010 proccaserra@gmail.com
  • 2. ISA infrastructure overview mage-tab | pride-ml | sra-xml | others
  • 3. A focus on standards... comply to common standards
  • 4. Not just microarray data....
  • 5. Telling more about experimental design
  • 6. repeated measurements, sample sizes....
  • 7. IISAcreator: a tool for reporting studies
  • 8. structured reports...declaring variables
  • 9. Making sense: ontology term tagging
  • 10. MIAPE MIGS XML XML MIMS MIAME XML XML MIENS XMLISAcreator Configurator provides configurations to ISAcreator...These configurations tell ISAcreator what is the minimum amount of information needed to describe experiments.ISAcreator is packaged with a default set of configurations, however you can create your own...
  • 11. ISA Converter: parsing ISA-TAB documents ->Conversion to Objectsconvert to different formats for submission to public repositories,e.g. MAGE-TAB (for ArrayExpress), PRIDE-ML (for PRIDE) or SRA-XML (for ENA/NCBI)
  • 12. Why an RDF conversion?• Interest in federated queries• Harvard collaborators (S. Das, T. Clark, W Hide, O Hoffmann)
  • 13. Why are we doing this?• Experiments where transcription profiling and metaboliting profiling  and liver injury in rodent• Experiments funded by UK BBSRC• Experiments performed by an organization located in the Netherlands• Experiments performed on rodent where there are at least 3 biological replicates per treatment groups• Experiments performed by persons belonging to John smith group.
  • 14. RDF conversion: the plan • Initial focus on representation of experimental design • treatment, perturbation • response variable • Later on, focus on molecular dimension • rely on biordf preliminary work on gene expression (generilized solution)
  • 15. RDF conversion: resources• Identifying Existing Ontological Resources • dc, skos for document metadata • foaf, foafCorp, vcard for Person/Contact • bibo, cito, fabio for Publication references. • swan experiment, obi for material processing, data production & analysis
  • 16. RDF conversion: snippet
  • 17. RDF conversion:Experimental graphCredit: Sudeshna Das, Tim Clark, HCLS Sci-Disc,November 2010
  • 18. has_specific_input Rattus norvegicus organism planned process is_about has_specific_input planning protocol chemical mixture treated role ? has_specific_output has_specific_output bearer_of has_part intraperitoneal is_a administration treated subject* treated organism* study design waiting has_specific_input is_a collecting specimen from organism has_specific_output realizes/ factorial design orotic acid* concretizes blood specimen some is_a liver specimen specification derives_from DMSO has_part is_about specimen role bearer_of skeletal muscle specimen* anatomical entityhas_part chemical compound is_about is_duration_of gonadal adipose tissue specimen* independent is_about is_a variable strain Wistar rat*; Kyoto rat* specification has_specific_input has_specific_ is_about 1 day post injection* total RNA extraction extraction is_a output duration of exposure 3 days post injection* derives_from has_specific_output phenol phase supernatant* 14 days post injection* is_about total RNA biotin bearer_of oligonucleotide sequence has_specific_input RNA realizes bearer_of concretizes labeling complementary nucleotide probe role has_part label role is_a has_specific_output transcription measurement function MOE430_2 design* dependent variable specification labeled cRNA realizes realizes inheres_in manufacturing is_about is_about transcript Transcript has_specific_input has_specific_input transcription profiling utilises instrument DNA microarray abundance* utilises instrument nucleic acid hybridization NMR assay is manufacturer of has_specific_output is_about hybridized microarray slide* metabolite concentration* Affymetrix has_specific_output has_specific_input is_about is_proxy_for image acquisition /scanning metabolite has_specific_output free induction image decay normalized data has_specific_output spectrum* set has_specific_input measured GCRMA feature extraction is_proxy_for expression level normalization* transformed data has_specific_input set has_specific_output data transformation measurement datum has_specific_output has_specific_input has_specific_output measuring function inheres_in realizes is_a utilises instrument utilises instrument Instrument Bruker BEST NMR system metabolite profiling intensity of magnetic field has_part isatab.sf.net number of acquisition proccaserra@gmail.com 5 mm inverse geometry 1H/broadband probe
  • 19. AcknowledgementsSusanna Sansone, Un. of OxfordEamonn Maguire, Un. of OxfordSWAN-Data-Experiments working groupSudeshna DasTim ClarkStephane CorlosquetHCLS working groups