ISA Project update CaNano November 12 th,2012 Philippe Rocca-Serra

Roadmap collaborative annotation facilitated data manipulation consistency in result/finding report bridge with linked data cloud

Collaborative annotation Hallmark of large projects multicentric studies cross border/institution collaboration coordinating with in-life study sample collection and data acquisition The need of collaborative editing version tracking (possibility of going in time) ontology lookups security and real time sharing

Collaborative annotation integration with Google documents creation of ISA compatible Google Templates development of ontomaton annotation widget (collaboration with NCBO)

Collaborative annotation Lookup Markup / Tagging Restriction Templating No circulating spreadsheet

OntoMaton workflow

Facilitate data manipulation for analysis RISA R-package

Facilitate data manipulation for analysis RISA R-package being augmented to recommend analysis packages depending on type of assays found in ISA archive recommended with XCMS R-package for MS data Expand to NMR data: link to BATMAN R- package (Imperial College) [

Integration with other data dimension: Transcriptomics / Epigenomics: MAGE2ISA converter SRA/ENA Metagenomics (gut microbiome) SRA ->MIMARKS/MIXS annotations Facilitate data manipulation for analysis

Streamline reporting of results OSGI plugin for reporting identification events in ISAcreator by Metabolights Team agreeing on quantitation type for data matrices facilitate queries on conclusion

-supporting transition to networks of interconnected data ISA2OWL: a full OWL BFO based (compatible with Gene Ontology, Cell Ontology, CHEBI) semantic representation current bottlenecks: gaps in coverage in the ontologies e.g. unstable structure for representing evidence supporting a claim. sparql endpoint for exposing and linking data

We need input from you collecting (hunting) data collecting use cases and queries: what do you want to ask to the system? how to speed up data formatting process how to promote uptake how to improve data access (slicing)

ISA tools

Work completed during investigation of new approach for creation of glyphs with use of taxonomy for guidance. See Maguire et al, Taxonomy-Based Glyph Design – with a Case Study on Visualizing Workflows of Biological Experiments, IEEE Transactions on Visualization and Computer Graphics, 2012 Visualization work: visualizing experimental workflows

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