Data Consultant,
Honorary Academic Editor
Susanna-Assunta Sansone, PhD
Associate Director,
Principal Investigator
NIH BD2K...
§  Researchers and bioinformaticians in both
academic and commercial arenas, along with
funding agencies and publishers, ...
A community mobilization to develop standards, e.g.:
§  Structural and operational differences
•  organization types (ope...
Types of reporting standards
Nanotechnology Working Group
Including minimum
information reporting
requirements, or
checkli...
Technologically-delineated
views of the world
Biologically-delineated
views of the world
Generic features ( common core )
...
Growing number of reporting standards
+ 130
+ 150
+ 303
Source:BioPortal
Databases,
annotation,
curation
tools
implementin...
But how much do we know about these standards
•  A coherent, curated and searchable registry of standards for describing
and reporting experiments in life science, envi...
•  A coherent, curated and searchable registry of standards for describing
and reporting experiments in life science, envi...
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-proje...
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-proje...
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-proje...
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-proje...
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone
www.ebi.ac.uk/net-proje...
Example
The relationship among popular standard formats for pathway information
BioPAX and PSI-MI are designed for data ex...
Drug Discovery Today Volume 16, Numbers 21/22  November 2011
research with
The information landscape in the industrial sec...
Not just technological but also social challenges
§  Ownership of open standards can be problematic in broad,
grass-root ...
Acknowledgements
•  Jessica Tenenbaum
•  Michael Braxenthaler
•  Lee Harland
•  Bryn Williams-Jones
•  Ian Dix
•  Trish Wh...
"Standards landscape" NIF Big Data 2 Knowledge (BD2K) Initiative, Sep, 2013
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"Standards landscape" NIF Big Data 2 Knowledge (BD2K) Initiative, Sep, 2013

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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

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"Standards landscape" NIF Big Data 2 Knowledge (BD2K) Initiative, Sep, 2013

  1. 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. 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. 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. 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. 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. 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. 7. But how much do we know about these standards
  8. 8. •  A coherent, curated and searchable registry of standards for describing and reporting experiments in life science, environmental, biomedical and biotechnological domains
  9. 9. •  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
  10. 10. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 11
  11. 11. 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
  12. 12. 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
  13. 13. 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
  14. 14. 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
  15. 15. 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.
  16. 16. 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
  17. 17. 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
  18. 18. 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….

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