OpenTox Europe 2013

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OpenTox Europe 2013

  1. 1. Alejandra González-Beltrán, Ph.D University of Oxford e-Research Centre, UK From experimental planning to data publication: the ISA infrastructure and case studies in toxicology alejandra.gonzalezbeltran@oerc.ox.ac.uk OpenTox Europe - Mainz, Germany - 30th September, 2013 1
  2. 2. 2 The data workflow Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment
  3. 3. 3 The data workflow Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment metadata metadata metadata metadata metadata metadata metadata tracking infrastructure
  4. 4. 4 Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication Use existing data Perform new experiment metadata metadata metadata metadata metadata metadata Traceability Assessment Accountability Evidence Reusability Reproducibility Storage Mining Provenance
  5. 5. 5 sem antics structure
  6. 6. 6 sem antics structure investigation study assay
  7. 7. 7
  8. 8. 8 infrastructureThe generic format for experimental description and data exchange open source software toolscommunity engagement
  9. 9. 11 Run Assays4 SAMPLE1 SAMPLE2 SAMPLE3 SAMPLE4 SAMPLE5 SAMPLE6 SAMPLE7 SAMPLE8 SAMPLE9 SAMPLE10 SAMPLE11 SAMPLE 1 SAMPLE 2 SAMPLE 3 SAMPLE 4 SAMPLE 5 SAMPLE 6 SAMPLE 7 SAMPLE 8 SAMPLE 9 SAMPLE 10 SAMPLE 11 FILE 1 FILE 2 FILE 3 FILE 4 FILE 5 FILE 6 FILE 7 FILE 8 FIL FIL FIL Experiment Design Analysis Arabidopsis thaliana Treatment groups 70% 90% 100% Collect Samples1 2 3 5 6 Parses ISA-Tab datasets into R objects, allowing to update them and save them after analysis. Bridges the ISA-Tab metadata to analysis pipelines of specific assay types, by building objects for use in other R packages downstream: currently considering mass spectrometry (xmcs package, xcmsSet) and DNA microarray (Biobase package, ExpressionSet) Suggests packages in BioConductor that might be relevant for an assay type, according to the BioCViews annotations. Gonzalez-Beltran et al. The Risa R/Bioconductor package: integrative data analysis from experimental metadata and back again. In press
  10. 10. Data Publication with
  11. 11. • New open-access, online-only publication for descriptions of scientifically valuable datasets • Only content type: Data Descriptor, narrative + structured parts • Initially focused on the life, environmental and biomedical sciences • Data Descriptor will be complementary to traditional research journals and data repositories • Designed to foster data sharing and reuse, and ultimately to accelerate scientific discoverywww.nature.com/scientificdata Data Publication with http://www.nature.com/scientificdata/
  12. 12. • New open-access, online-only publication for descriptions of scientifically valuable datasets • Only content type: Data Descriptor, narrative + structured parts • Initially focused on the life, environmental and biomedical sciences • Data Descriptor will be complementary to traditional research journals and data repositories • Designed to foster data sharing and reuse, and ultimately to accelerate scientific discoverywww.nature.com/scientificdata Data Publication with http://www.nature.com/scientificdata/ http://gigasciencejournal.com
  13. 13. 1
  14. 14. 20 A growing ecosystem of over 30 public and internal resources using the ISA metadata tracking framework (ISA-Tab and/or format) to facilitate standards-compliant collection, curation, management and reuse of investigations in an increasingly diverse set of life science domains, including: • stem cell discovery • system biology • transcriptomics • toxicogenomics • also by communities working to build a library of cellular signatures • environmental health • environmental genomics • metabolomics • metagenomics • nanotechnology • proteomics
  15. 15. 21 Toxicity data http://xkcd.com/1260/
  16. 16. 22 Suter et al 2011. EU Framework 6 Project: Predictive Toxicology (PredTox)—overview and outcome. Boitier et al 2011.A comparative integrated transcript analysis and functional characterization of differential mechanisms for induction of liver hypertrophy in the rat InnoMed PredTox Project Goal: earlier pre-clinical safety evaluation by combining results from ‘omics technologies and conventional toxicology methods
  17. 17. 23 2-week systemic rat study using male Wistar rats (N=15 per dose group) 14 proprietary drug candidates from participating companies and 2 reference toxic compounds
  18. 18. 24
  19. 19. 25
  20. 20. 26 http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-8
  21. 21. 27 Data Infrastructure for Chemical Safety http://www.dixa-fp7.eu/about
  22. 22. 28 Kohonen et al. 2013 The ToxBank Data Warehouse: a research cluster of 7 EU FP7 Health systems toxicology and toxicogenomics projects. Safety Evaluation Ultimately Replacing Animal Testing-1 (SEURAT-1): looking at improving safety assessment without the need for animal experiments ToxBank: cross-cluster infrastructure project http://toxbank.net
  23. 23. 29 https://wiki.nci.nih.gov/display/ICR/ISA-TAB-Nano Nanotechnology Informatics Working Group Thomas et al. 2013 ISA-TAB-Nano: A specification for sharing nanomaterial research data in spreadsheet-based format Baker et al. 2013 Standardizing data ISA-TAB-Nano Extension of ISA-TAB format to represent nano-materials, small molecules and biological specimens along with their assay characterisation data
  24. 24. 30 Data Scientist Visualization Analysis Planning Data Management Data CollectionPublication
  25. 25. 31
  26. 26. Questions? You can email us... isatools@googlegroups.com View our blog http://isatools.wordpress.com Follow us onTwitter @isatools View our website http://www.isa-tools.org View our Git repo & contribute http://github.com/ISA-tools

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