Overview of the landscape of standards in life sciences for the NIH BD2K "Frameworks for Community-Based Standards Efforts" workshop September 25, 2013 - September 26, 2013 Co-Chairs: Susanna Sansone, PhD and David Kennedy PhD. The overall goal of this workshop is to learn what has worked and what has not worked in community-based standards efforts. Participants will have experience in leading specific community based standards initiatives. Prior to the workshop, participants will be asked to address in writing answers to specific questions regarding formulating, conducting, and maintaining such efforts. This information will be used to facilitate focused and actionable discussion at the workshop. Issuance of a Request for Information soliciting comment from the broader community on some of the key issues addressed in the workshop is currently envisioned. Contact: BD2Kworkshops@mail.nih.gov Agenda: Frameworks for Community-Based Standards Efforts (PDF 40.7KB) Participant List: Roster of Invited Participants (PDF 32KB) Forum (Join the discussion): http://frameworks.prophpbb.com Watch Live: http://videocast.nih.gov/summary.asp?live=13088 - See more at: http://bd2k.nih.gov/workshops.html#cbse

1. Data Consultant,
Honorary Academic Editor
Susanna-Assunta Sansone, PhD
Associate Director,
Principal Investigator
NIH BD2K Workshop: Frameworks for Community-Based Standards Efforts, Sept 25-26, 2013
Mapping the Landscape of Community Standards
Challenges and Opportunities
www.slideshare.net/SusannaSansone

2. § Researchers and bioinformaticians in both
academic and commercial arenas, along with
funding agencies and publishers, embrace
the concept that community-developed,
standards are pivotal to structure, enrich
the description and share
• entities of interest
e.g., genes, metabolites,
phenotypes, models
• experimental steps
e.g., provenance of study materials,
technology and measurement types
Growing movement for reproducible research

3. A community mobilization to develop standards, e.g.:
§ Structural and operational differences
• organization types (open, close to members, society, WG etc.)
• standards development (how to formulate, conduct and maintain)
• adoption, uptake, outreach (link to journals, funders and commercial sector)
• funds (sponsors, memberships, grants, volunteering)
de jure de facto
grass-roots
groups
standard
organizations
Nanotechnology Working Group

4. Types of reporting standards
Nanotechnology Working Group
Including minimum
information reporting
requirements, or
checklists to report the
same core, essential
information
Including controlled
vocabularies, taxonomies,
thesauri, ontologies etc. to
use the same word and
refer to the same ‘thing’
Including conceptual
model, conceptual
schema from which an
exchange format is derived
to allow data to flow from
one system to another

5. Technologically-delineated
views of the world
Biologically-delineated
views of the world
Generic features ( common core )
- description of source biomaterial
- experimental design components
Arrays
Scanning Arrays &
Scanning
Columns
Gels
MS MS
FTIR
NMR
Columns
transcriptomics
proteomics
metabolomics
plant biology
epidemiology
microbiology
Fragmentation, duplications and gaps
To compare and integrate data we need interoperable standards

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

7. But how much do we know about these standards

9. • A coherent, curated and searchable registry of standards for describing
and reporting experiments in life science, environmental, biomedical and
biotechnological domains

10. • A coherent, curated and searchable registry of standards for describing
and reporting experiments in life science, environmental, biomedical and
biotechnological domains
• Progressively associate standards to data policies and databases
• Develop assessment criteria for usability and popularity of standards
• Help stakeholders to make informed decisions on e.g. what standards or
databases to use or recommend; identify efforts they have funded

11. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-project
11

12. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-project
12
Users can claim
records and
maintain them

13. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-project
13
Criteria to be used in evaluating standards for adoption

14. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-project
14
Help prospective users to select and use appropriate one

15. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-project
15
Classify, links standards and visualize relations

16. Example
The relationship among popular standard formats for pathway information
BioPAX and PSI-MI are designed for data exchange to and from databases and pathway and
network data integration. SBML and CellML are designed to support mathematical simulations
of biological systems and SBGN represents pathway diagrams.
CREDIT:
Demir, et al., The BioPAX
community standard for
pathway data sharing, 2010.

17. Drug Discovery Today Volume 16, Numbers 21/22 November 2011
research with
The information landscape in the industrial sector
Big Life
Science
Company
Yesterday Today Tomorrow
Big Life
Science
Company
Proprietary
content
provider
Public
content
provider
Academic
group
Software vendor
CRO
Service provider
Regulatory
authorities
…evolving…
Credit: Pistoia Alliance
Michael Braxenthaler, Roche

18. Not just technological but also social challenges
§ Ownership of open standards can be problematic in broad,
grass-root collaborations
• legal framework is still embryonic
• it requires improved models, to encourage maintenance of and
contributions to these efforts, supporting their evolutions
• Extensive community liaison needs to be
• managed and funded
• rewards and incentives need to be identified for all contributors

19. Acknowledgements
• Jessica Tenenbaum
• Michael Braxenthaler
• Lee Harland
• Bryn Williams-Jones
• Ian Dix
• Trish Whetzel
• Mark Musen
• Collaborators in
• OBO Foundry
• COSMOS
• ISA Commons (especially ISA-Tab-Nano team)
• GSC
• Metabolomics Society
• Data Dryad
• Pistoia Alliance
• Elixir UK
• and many more….