Sansone mibbi-intro

Innovative technology accelerating research

Susanna-Assunta Sansone, PhD

Team Leader,

University of Oxford, UK

Biocuration, 11th-14th October 2010, Tokyo, Japan

Omics Data Sharing

BioSharing: on Data Policies’s Plans

and Reporting Standards 

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

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Modern studies often run source material through several kinds of assay in parallel

• E.g. genomic sequencing, protein-protein interaction assays, or the measurement of metabolite concentrations and fluxes

Information intensive research investigationsInformation intensive research investigations

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

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Data (descriptions of biological entities of interest, e.g., genes, targets and their measurements, e.g., intensity, location) must be shared accompanied by enough, well annotated experimental information (i.e. - ‘metadata’- provenance of study materials, technology and measurement types, etc.)

Comprehensible, reusable, reproducible research Comprehensible, reusable, reproducible research

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

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Three types of standards enable unambiguous representation, description and communication of the experimental information

• Minimum core information specifications: checklists

• Semantics: nomenclatures and terminologies

• Syntax: exchange formats

Reporting standards as enablersReporting standards as enablers

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

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Journals, biocurators and the research community continue to participate in the development of standards, tools and databases

• to support sharing of sufficiently well annotated datasets

• to enable comprehensible, reusable, reproducible research

Strong advocatorsStrong advocators

Several data preservation, management and sharing policies have emerged in response to increased funding for genomics and functional genomics (omics) bioscience domains

...funders are developing data policies......funders are developing data policies...

“… lack of standardized data affects CDER’s review processes by curtailing a reviewer’s ability to perform integral tasks such as rapid acquisition, storage, analysis......efficient management of a portfolio of standards projects will require coordinated efforts and clear roles for multiple participants within/outside FDA”

....similar trend in the regulatory arena....similar trend in the regulatory arena

R&D has invested heavily in procedures and tools that integrate external information with their own data to enhance the decision-making process

• Now joining forces to streamline non-competitive elements of the life science workflow by the specification of common standards, business terms, relationships and processes

....and commercial sector....and commercial sector

Increased efficiency• Metadata remains associated with the results generated

• Avoids the risk of loss of information through staff turnover

• Enables time-efficient handover of projects

Enhanced confidence in data• Enables fully-informed assessment of results (methods used etc.)

• Supports the discovery of sources of systematic or random errors

• Facilitates better-informed comparisons or cross analysis of data sets

Defined requirements for submission, exchange and/or publication• Within multi-sites organization or between collaborators

• To journals or repositories

• To regulatory bodies

Reporting standards as a means to an endReporting standards as a means to an end

Escalating number of efforts (omics domain), Escalating number of efforts (omics domain), e.g. e.g.

Wide variety of ‘authorities’• Standard organizations• International projects• Working groups• Grass-root movements

Multi-stakeholders and multi-disciplinary• Researchers, biocurators, software/database developers , modellers

• Academics, industries, governmental and regulatory bodies

• Manufacturers, software vendors, journal editors and funders

Heterogeneous focus - beyond reporting requirements- e.g.• Broader understanding of the use of omics’ data• Agreed world-wide recommendations• Measurements and methods validation

Heterogeneity of the efforts Heterogeneity of the efforts

Navigating a sea of ‘standards’Navigating a sea of ‘standards’

I work on plants, are these just for

biomedical applications?

Which one are mature enough for me to use or recommend?

How can I get involved to propose

extensions or modifications?

Which tools and databases implement which one?

Which one are widely accepted and recognized?

What are the criteria to evaluate status

and value? ...?.... ...?....

....?... ...?....

....?... ...?....

I use HT sequencing technologies, which one are applicable to

me?

Navigating a sea of ‘standards’Navigating a sea of ‘standards’

Which tools and databases implement which one?

I use HT sequencing technologies, which one are applicable to

me?

EBI NCBI

ENA SRA

HT sequencing: public databases and ‘standards’HT sequencing: public databases and ‘standards’

EBI NCBI

ENA SRA

• checklists: MIAME, MINSEQ• formats: MAGE-ML, MAGE-Tab• ontologies: MGED Ontology...

• checklists: MIGS, MIENS• format: GCDML• ontologies: EnVO light...

INSDC feature table

HT sequencing: public databases and ‘standards’HT sequencing: public databases and ‘standards’

(2008) Vol 26 No 8

http://mibbi.org

Serves researchers, biocurators, journal editors and reviewers, and funders to

discover checklists for a particular domain monitor progress of extant efforts facilitate collaborations

Link a sister effort in health research EQUATOR (www.equator-network.org) Funds for coordination activities and meetings

• Our next meeting is in Germany, Dec 2010

Linking checklists to terminologiesLinking checklists to terminologies

http://www.ebi.ac.uk/ontology-lookup/

http://bioportal.bioontology.org/

http://www.obofoundry.org/

Science(2009), Vol 326, 234-236

http://biosharing.org

Aim to protect cumulative data outputs, recognizing • data sharing as a way to accelerate subsequent exploitation

• the right of first use for data provides and right to appropriate accreditation

• the importance of ‘standards’ in annotation and reporting process, but...

Often inconsistent and/or unclear on the standards and methods to be used for preserving, managing and sharing data

• “..recommend use of appropriate standards..”, “..where these exists..”, “...mature, stable efforts..”, “..MIAME format..”, “..accredited standards organizations..”, “..deposition to public repositories..”, “..release on websites..”...etc

Urgent need for fostering communications between policy makers, the ‘standards’ groups

• including researchers, biocurators and developers

http://biosharing.org

‘‘Social Social engineering’engineering’

http://biosharing.org

It is NOT

• a top down initiative to harmonize the standards

• another society to develop another standard

• a data or tool resource

Started as a blog (supplementary materials for the article in Science).......

http://biosharing.org

Call for participation

• We need more..........

• Suggestions on how to best create and populate the website, list the ‘standards’, allow updates, link to other portals etc...

Close engagement with the Biocuration Society and the new BioDBcore effort

Part of our software development activitiesPart of our software development activities

Rocca-Serra et al,

Bioinformatics, 2010

ISA software suiteopen source: www.isa-tools.org

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Science, 2009

Bioinformatics, 2010

Nature Biotech, (invited)