hcls sci disc-isa2rdf
TRANSCRIPT
ISA project , ISA tools and RDF conversion efforts
Philippe Rocca-SerraOxford University, Oxford, UK
HCLS Scientific Discourse call, November, 29th 2010
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 amount of information needed to describe experiments.
ISAcreator is packaged with a default set of configurations, however you can create your own...
MIAPEXML
MIAMEXML
MIMSXML
MIENSXML
MIGSXML
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
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
• 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.
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)
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
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 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 mixturetreated 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*
DMSOis_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
realizesinheres_in
3 days post injection*
AcknowledgementsSusanna Sansone, Un. of OxfordEamonn Maguire, Un. of Oxford
SWAN-Data-Experiments working groupSudeshna DasTim ClarkStephane Corlosquet
HCLS working groups