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
11. 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
12. 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
13. Why an RDF conversion?
• Interest in federated queries
• Harvard collaborators (S. Das,T.
Clark,W Hide, O Hoffmann)
14. 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.
15. 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)
16. 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
19. 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
20. 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
