Susanna-Assunta Sansone's talk at the DataCite Summer meeting in Copenhagen on "The ISA-Commons - experiences from the field", 14th June 2012

1. bioscience
The ISA Commons: experiences from! field
the
Susanna-Assunta Sansone, PhD
Principal Investigator, Team Leader,
University of Oxford e-Research Centre,
Oxford, UK
http://uk.linkedin.com/in/sasansone
#biosharing
DataCite Summer Meeting
DIGITAL RESEARCH DATA IN PRACTICE: solutions for improving discovery, access and use
June 14, 2012 Copenhagen

2. • Reproducible research
• annotated research data and methods offer new
discovery opportunities and prevent unnecessary
repetition of work;
• improved data sharing underpins science of the future;
• but !.. shared data have little or no value if they are
not interpretable and, consequently, reusable
Image from datacite.org

3. Reproducibility
Ioannidis et al., Repeatability of published microarray
gene expression analyses. Nature Genetics 41(2),
3!
149-55 (2009) doi:10.1038/ng.295

4. Reproducibility
Ioannidis et al., Repeatability of published microarray
gene expression analyses. Nature Genetics 41(2),
4!
149-55 (2009) doi:10.1038/ng.295

5. Reproducibility
Ioannidis et al., Repeatability of published microarray
gene expression analyses. Nature Genetics 41(2),
5!
149-55 (2009) doi:10.1038/ng.295

6. Reproducibility
6!
6!

7. Across studies
and groups
7!
7!

8. Reproducibility
8!
8!

9. NO to ‘data blobs’
YES to verifiable, complete
and structured information
Image from datacite.org

10. Structured description of datasets
! Capture all salient features
of the experimental workflow
! Make annotation explicit and
discoverable
! Structure the descriptions
for consistency, tracking
! independent variables
! dependent variables
using
! cross reference and
resolvable identifiers

11. Not too much, not too little, just ‘right’
! We must strike a balance
between
• depth and breadth of
information; and
• sufficient information
required to reuse the data

12. Example of experiments by
InnoMed PredTox
12 The International Conference on Systems Biology (ICSB), 22-28 August, 2008 a FP6 public-private consortium
Susanna-Assunta Sansone
www.ebi.ac.uk/net-project

13. Different community, different norms and standards, e.g.:
use the same word and
allow data to flow from report the same core,
refer to the same ‘thing’
one system to another essential information
Challenges: lack of coordination, fragmentation and uneven coverage

14. Growing number of reporting standards
+ 303
+ 150
+ 130
Source: MIBBI,
Source: BioPortal
EQUATOR
Estimated
MAGE-Tab! AAO! MIAME!
GCDML! MIAPA!
CHEBI!
SRAxml! OBI! MIRIAM!
VO!
SOFT! MIQAS!
FASTA! PATO! MIX!
CML! ENVO! REMARK!
DICOM! MIGEN!
GELML! MOD!
SBRML! MIAPE! MIQE!
TEDDY!
MITAB! MzML! XAO! CIMR! CONSORT!
BTO!
ISA-Tab! SEDML…! DO PRO! IDO…! MIASE! MISFISHIE….!

15. A catalogue to map the
landscape of standards and the
systems implementing them:
Over 400 bio-standards
(public and in curation)
Field*, Sansone* et al., Omics data sharing. Science
15 The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
326, 234-36 (2009) doi:0.1126/science.1180598
www.ebi.ac.uk/net-project

16. A catalogue to map the
landscape of standards and the
systems implementing them:
Over 400 bio-standards
(public and in curation)
Field*, Sansone* et al., Omics data sharing. Science
16 The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
326, 234-36 (2009) doi:0.1126/science.1180598
www.ebi.ac.uk/net-project

17. Bioscience is not one domain!
&+'.!&*
+,-* '/("*
!"#$%&'()'*
! Bioscience is interdisciplinary and integrative in character
• need to deal with new and existing datasets
• deal with a variety of data types
Source of the figure: EBI website

18. Is it possible to achieve a common, structured
representation of diverse bioscience experiments that:
• transcends individual bioscience domains, but also
• follows the appropriate community norms and
standards?

19. A growing ecosystem of over 30 public and internal resources
using the ISA metadata tracking framework to facilitate standards-
compliant collection, curation, management and reuse of
investigations in an increasingly diverse set of life science domains,
including:
• environmental health • stem cell discovery
• environmental genomics • system biology
• metabolomics • transcriptomics
• metagenomics • toxicogenomics
• nanotechnology • also by communities working to build
• proteomics, a library of cellular signatures
We aim to achieve a common
representation of experimental content that
transcends individual bioscience domains
Sansone et al., Towards interoperable
bioscience data. Nature Genetics 44,
121-126 (2012) doi:10.1038/ng.1054

20. A growing ecosystem of over 30 public and internal resources
using the ISA metadata tracking framework to facilitate standards-
compliant collection, curation, management and reuse of
investigations in an increasingly diverse set of life science domains,
including:
• environmental health • stem cell discovery
• environmental genomics • system biology
• metabolomics • transcriptomics
• metagenomics • toxicogenomics
• nanotechnology • also by communities working to build
• proteomics a library of cellular signatures
Some of the public groups/resources: Some of the internal projects:
Stem Cell Commons
Nanotechnology
Informatics Working
Group

21. A growing ecosystem of over 30 public and internal resources
using the ISA metadata tracking framework to facilitate standards-
compliant collection, curation, management and reuse of
investigations in an increasingly diverse set of life science domains,
including:
• environmental health • stem cell discovery
• environmental genomics • system biology
• metabolomics • transcriptomics
• metagenomics • toxicogenomics
• nanotechnology • also by communities working to build
• proteomics a library of cellular signatures
Some of the public groups/resources: Some of the internal projects:
Stem Cell Commons
Nanotechnology
Informatics Working
Group

22. Metadata tracking framework, designed to
support the use us several standards
checklists, terminologies conversions to
(a growing number of) other metadata
formats, used by public repositories, e.g.
MAGE-Tab Pride-xml
SRA-xml SOFT
Currently finalizing conversion to RDF to
explore the growing Linked Data universe,
in collaboration with the W3C HCLSIG)

23. empowering researchers to use standards
To mint DOIs
23 The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-project

24. TOWARDS INTEROPERABLE BIOSCIENCE DATA doi:10.1038/ng.1054
Sansone SA, Rocca-Serra P, Field D, Maguire E, Taylor C, Hofmann O, Fang H, Neumann
S, Tong W, Amaral-Zettler L, Begley K, Booth T, Bougueleret L, Burns G, Chapman B,
Clark T, Coleman LA, Copeland J, Das S, de Daruvar A, de Matos P, Dix I, Edmunds S,
Evelo C, Forster M, Gaudet P, Gilbert J, Goble C, Griffin J, Jacob D, Kleinjans J, Harland
L, Haug K, Hermjakob H, Sui S, Laederach A, Liang S, Marshall S, Merrill E, McGrath A,
Feb 2012
Reilly D, Roux M, Shamu C, Shang C, Steinbeck C, Trefethen A, Williams-Jones B,
www.biosharing.org www.isacommons.org
Wolstencroft K, Xenarios J, Hide W. www.isacommons.org
Community involvement and uptake!
1st ISA-Tab workshop! 3rd ISA-Tab workshop! User workshops/visits - start! 1st public instance: ! !
2nd ISA-Tab workshop! Other tools implement ! Harvard Stem Cell ! Growing number of
ISA-Tab! Discovery Engine! systems starts to adopt
ISA-Tab!
Core developments!
Conversions to ! Links to
Pride-XML/SRA-XML/! analysis tools
Strawman ISA-Tab spec! ISA software v1! MAGE-Tab and more! starts!
Final ISA-Tab spec! Database instance !
at EBI! RDF format starts!
Publications!
Stem Cell !
ISA-Tab and ! Discovery ! ISA Commons!
Omics data sharing!
Workshop reports! ISA software suite! Engine!
(Science)! (Nature Genetics)!
(Bioinformatics)! (NAR)!
2007 2008 2009 2010 2011 2012
Development timeline!