The document discusses the ISA infrastructure, which provides a standardized format (ISA-TAB) for experimental metadata and data exchange. It can be used across various domains like toxicology, systems biology, and nanotechnology. The Risa R package integrates experimental metadata with analysis and allows updating metadata. Nature Scientific Data is a new publication for describing valuable datasets. The ISA framework has been adopted by over 30 public and private resources and is growing in use for facilitating reuse of investigations in various life science domains. Toxicity examples include EU projects on predictive toxicology and a rat study of drug candidates. Questions can be directed to the ISA tools group.

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
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2. 2
The data workflow
Data
Scientist
Visualization
Analysis
Planning
Data
Management
Data CollectionPublication
Use existing
data
Perform new
experiment

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
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
sem
antics
structure

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sem
antics
structure
investigation
study
assay

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infrastructureThe
generic format for experimental
description and data exchange
open source software toolscommunity engagement

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Run Assays4
SAMPLE1
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FILE 1
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Experiment Design Analysis
Arabidopsis thaliana
Treatment groups
70% 90% 100%
Collect Samples1 2 3 5
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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

15. Data Publication with

16. • 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/

17. • 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

18. 1

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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

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Toxicity data
http://xkcd.com/1260/

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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

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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

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26. 26 http://www.ebi.ac.uk/bioinvindex/study.seam?studyId=BII-S-8

27. 27
Data Infrastructure for Chemical Safety
http://www.dixa-fp7.eu/about

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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

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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

30. 30
Data
Scientist
Visualization
Analysis
Planning
Data
Management
Data CollectionPublication

31. 31

32. Questions?
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