An overview of the ISA tools (http://isa-tools.org) presented at the COPO kick-off meeting in Norwich, UK, September 2014.

1. ISA tools overview
Alejandra González-Beltrán, PhD
Oxford e-Research Centre, University of Oxford
alejandra.gonzalezbeltran@oerc.ox.ac.uk @alegonbel
COPO kick-off meeting September 16, 2014 Norwich, UK

2. • Nature Publishing Group‘s Scientific Data
• BioMedCentral and BGI‘s GigaScience
• F1000 Research
• Oxford University Press
Ontology and sematic web knowledge
representations
Ontology for Biomedical Investigation (OBI) for the
description of the experimental steps
Statistical ontology (STATO) for the description of
statistical results
Applying the linked data and the nanopublication
approaches to ISA-Tab
eTRIKS – EUTranslational Information and
Knowledge management Services
Consortium of academic (Imperial College, CNRS, Un
of Luxemburg) and pharmas (Janssen, Merck, AZ,
Lilly, Lundbeck, Pfizer, Roche, Sanofi, Bayer, GSK)
building a sustainable, open translational research
informatics platform
WG in involving PloS, NPG, BMC, BMJ, OUP, etc.
Centre for Extended Data Annotation
and Retrieval (pending notification of
award)
Centre will explore a variety of technique to ease the
work of creating and using standards-driven templates
for describing and reporting biomedical datasets
A community-driven platform for plant
science
Coordinated by TGAC and in collaboration with
EMBL-European Bioinformatics Institute and Warwick
University, COPO will provide platform- and software-as-
a-service

3. Related Funded Project:
Continued Development and Curation
of the MetaboLights database
• Large metabolomics lab submission interfaces/
integration (API)
• Analysis tools (online)
• Tools for visualisation of metabolomics data
• Enrichment and extension to the reference layer
• A curation tool for MetaboLights submissions
• Metabolite identification assistant
http://www.bbsrc.ac.uk/pa/grants/AwardDetails.aspx?FundingReference=BB/L024152/1

4. Experimental Metadata
4
Notes in lab notebooks
(information for humans)

5. Experimental Metadata
Notes in lab notebooks
(information for humans) Spreadsheets & tables
ISA-Tab
5

6. Experimental Metadata
Notes in lab notebooks
(information for humans) Spreadsheets & tables
ISA-Tab
6
RDF statements
(information for machines)

7. Experimental Metadata
Notes in lab notebooks
(information for humans) Spreadsheets & tables
ISA-Tab
RDF statements
(information for machines)
It is all about structuring experimental information to make it available to
computers and software agents to enable:
7
!
provenance tracking
assessment and evaluation
accountability, reliability, trust, evidence
conservation, preservation, storage, archiving and mining

8. 8

9. http://www.ama-rochester.org/WP/wp-content/uploads/2013/01/three-pillars.png
Rocca-Serra et al, 2010!
Bioinformatics!
ISA software suite

10. The format

11. Why ISA format and Tools?
investigation
assay(s) assay(s)
pointers to data file
names/location
external files in
native or other for-mats
data data
investigation
high level concept to link
related studies
study
the central unit, containing
information on the subject
under study, its characteristics
and any treatments applied.
a study has associated assays
assay
test performed either on
material taken from the sub-ject
or on the whole initial
subject, which produce quali-tative
or quantitative meas-urements
(data)
H. Sapiens
H. Sapiens
H. Sapiens
H. Sapiens
33 Years
H1
H1
H2
35
35
33
Years
Years
Years
ISA metadata specifications:
!
• workflow and process
orientated
• compatible with checklist
enforcement
• compatible with external
vocabulary resources
• compatible by design with
existing schemas
!
H1.sample1
H1.sample2
H2.sample1
Labeling
Labeling
H1.sample1.labeled
H2.sample1.labeled
h1-s1.cel
h1-s2.cel
h2-s1.cel
H1
H2
H1.sample1
H1.sample2
H2.sample1
Labeling
Labeling
H1.sample1.labeled
H2.sample1.labeled
h1-s1.cel
h1-s2.cel
h2-s1.cel
H. Sapiens
35 Years
MAGE-Tab
Pride-xml SRA-xml

12. The software suite

14. 1

15. 2

16. Personalized NSAID Therapeutics Consortium [PENTACON]
https://pentacon-bii.princeton.edu/

17. investigation studies assays
measurement technology

19. https://github.ISA-Tab Viewer com/ISA-tools/ISATab-Viewer

20. 3

21. 4

22. 22
ISA-Tab
validation
ISA-Tab
to
SRA
conversion
Submission
to ENA
ISA-Tab
creation
(SRA-xml schema)

23. 5

24. 6

25. The community

26. 26
A growing ecosystem of over 30 public and internal resources using
the ISA metadata tracking framework (ISA-Tab and/or tools) 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

27. funders
27

28. Thanks for your attention!
Questions?
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