ISA project , ISA tools and
RDF conversion efforts
Philippe Rocca-Serra
Oxford University, Oxford, UK
HCLS Scientific Disco...
mage-tab | pride-ml | sra-xml | others
	

	

 	

 	

 ISA infrastructure overview
A focus on standards...
comply to
common
standards
Not just microarray data....
Telling more about experimental design
repeated measurements, sample sizes....
IISAcreator: a tool for reporting studies
structured reports...declaring variables
Making sense: ontology term tagging
ISAcreator Configurator provides configurations to ISAcreator...
These configurations tell ISAcreator what is the minimum
amo...
convert to different formats for submission to public repositories,
e.g. MAGE-TAB (for ArrayExpress), PRIDE-ML (for PRIDE)...
Why an RDF conversion?
• Interest in federated queries
• Harvard collaborators (S. Das,T.
Clark,W Hide, O Hoffmann)
Why are we doing this?
• Experiments where transcription profiling and
metaboliting profiling  and liver injury in rodent
• ...
RDF conversion: the plan
• Initial focus on representation of
experimental design
• treatment, perturbation
• response var...
RDF conversion: resources
• Identifying Existing Ontological Resources
• dc, skos for document metadata
• foaf, foafCorp, ...
RDF conversion: snippet
RDF
conversion:
Experimental
graph
Credit: Sudeshna Das,Tim Clark, HCLS Sci-Disc,
November 2010
protocol
planned process
transcription profiling
measurement datum
transcript
abundance*
MOE430_2 design*
planning
labeled ...
Acknowledgements
Susanna Sansone, Un. of Oxford
Eamonn Maguire, Un. of Oxford
SWAN-Data-Experiments working group
Sudeshna...
Hcls sci disc-isa2rdf
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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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Hcls sci disc-isa2rdf

  1. 1. ISA project , ISA tools and RDF conversion efforts Philippe Rocca-Serra Oxford University, Oxford, UK HCLS Scientific Discourse call, November, 29th 2010 proccaserra@gmail.com
  2. 2. mage-tab | pride-ml | sra-xml | others ISA infrastructure overview
  3. 3. A focus on standards... comply to common standards
  4. 4. Not just microarray data....
  5. 5. Telling more about experimental design
  6. 6. repeated measurements, sample sizes....
  7. 7. IISAcreator: a tool for reporting studies
  8. 8. structured reports...declaring variables
  9. 9. Making sense: ontology term tagging
  10. 10. ISAcreator 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... MIAPE XML MIAME XML MIMS XML MIENS XML MIGS XML
  11. 11. convert to different formats for submission to public repositories, e.g. MAGE-TAB (for ArrayExpress), PRIDE-ML (for PRIDE) or SRA-XML (for ENA/NCBI) ISA Converter: parsing ISA-TAB documents ->Conversion to Objects
  12. 12. Why an RDF conversion? • Interest in federated queries • Harvard collaborators (S. Das,T. Clark,W Hide, O Hoffmann)
  13. 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. 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. 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. 16. RDF conversion: snippet
  17. 17. RDF conversion: Experimental graph Credit: Sudeshna Das,Tim Clark, HCLS Sci-Disc, November 2010
  18. 18. protocol planned process transcription profiling measurement datum transcript abundance* MOE430_2 design* planning labeled cRNA image Affymetrix has_specific_output has_specific_input is_about utilises instrument is manufacturer of total RNA collecting specimen from organism blood specimen liver specimen skeletal muscle specimen* gonadal adipose tissue specimen* total RNA extraction intraperitoneal administration Rattus norvegicus treated subject* labeling has_specific_output has_specific_input has_specific_output nucleic acid hybridization has_specific_input strain chemical compound has_specific_output has_specific_input has_specific_output has_specific_input independent variable specification dependent variable specification biotin label role duration of exposure DNA microarray feature extraction data transformation specimen role anatomical entity factorial design treated organism* metabolite concentration* metabolite profiling utilises instrument Instrument 5 mm inverse geometry 1H/broadband probe NMR assay bearer_of derives_from is_a has_specific_input realizes has_part has_specific_output utilises instrument image acquisition /scanning free induction decay spectrum* utilises instrument has_specific_input has_specific_output organism bearer_of hybridized microarray slide* transcription measurement function inheres_inrealizes concretizes is_about is_about is_about is_about is_about chemical mixture treated role ? bearer_of has_part study design has_part is_about measuring function intensity of magnetic field number of acquisition extraction phenol phase supernatant* GCRMA normalization* has_specific_input has_specific_output is_a orotic acid* DMSO is_a Wistar rat*; Kyoto rat* is_a 1 day post injection* 14 days post injection* is_a normalized data set has_specific_output has_specific_input has_specific_output is_duration_of waiting realizes/ concretizes some specification Bruker BEST NMR system has_part has_specific_input has_specific_ output is_a has_specific_input has_specific_output measured expression level Transcript metabolite is_about oligonucleotide sequence has_part derives_from is_proxy_for manufacturing RNA is_a is_about transformed data set is_proxy_for has_specific_output realizes complementary nucleotide probe role bearer_of is_about realizes inheres_in 3 days post injection* isatab.sf.net proccaserra@gmail.com
  19. 19. Acknowledgements Susanna Sansone, Un. of Oxford Eamonn Maguire, Un. of Oxford SWAN-Data-Experiments working group Sudeshna Das Tim Clark Stephane Corlosquet HCLS working groups

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