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...
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)
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