susanna-assunta sansone: an overview of the evolving portfolio of data sharing enablers: biosharing
DESCRIPTION
Susanna-Assunta Sansone talk at the Genomics Standards Consortium meeting in Shenzhen, March 6th 2012TRANSCRIPT
§ How do we make standards-compliant data sharing culture functional and efficient?
• Several data management, sharing policies and plans have emerged; the number of data journals is growing and guidelines to authors for reporting data are being enriched; there are thousands of biological databases and a wealth of community standards
• Although, funders, journal editors, data producers, consumers and service providers agree in principle that shared, annotated research data and methods offers new discovery opportunities, compliance is challenging in practice
§ Starting from the genomics domain and extending to other areas of life-science, we are looking to highlight the success stories and existing problems
Policies and standards for reproducible research: from theory to practice
§ Representatives from stakeholders involved in complete cycle of data • from funding and regulation, to production, release and re-use
§ Setting the scene: • Susanna-Assunta Sansone, University of Oxford, UK
• Scott Edmunds, GigaScience BGI Shenzhen, China
§ Funders • Rita Colwell, University of Maryland, USA
• Paula J. Olsiewski, Sloan Foundation
§ Service providers and/or data producers
• Philippe Rocca-Serra, University of Oxford, UK • Folker Meyer, Argonne National Laboratory, USA • Srikrishna Subramanian, IMTECH, India
§ Editors • Clare Garvey, Genome Biology/BioMed Central • Craig Mak, Nature Biotechnology
About this session - speakers
§ Data management, preservation and sharing policies – view points
• formulation and enforcement, or
• uptake and compliance
§ Reporting standards – experiences and challenges
• evolutions of standards, costs of compliance, reward for complying etc.
• usability of standards when working across disciplines, also they all have differing community norms
• challenges in integrating data types and how standards can help
§ Tackling the challenges – approaches and lessons learned
• balance needs and expectations (data producers, consumers, reviews, service providers etc.)
• potential role of each stakeholder • new way forwards
About this session - topics
the evolving portfolio of data sharing enablers
Susanna-Assunta Sansone, PhD
University of Oxford,
Oxford e-Research Centre, Oxford, UK
http://uk.linkedin.com/in/sasansone
GSC13th, Shenzhen, China, March 5-7, 2012
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
From reusable data to reproducible research
To make the datasets comprehensible, interoperable and reusable, underpinning future investigations, we need common ways to report and share the experimental details and the associated results.
Consistent reporting will have a positive and long-lasting impact on the value of collective scientific outputs.
A ‘general mobilization’ to develop standards, e.g.:
report the same core, essential information
use the same word and refer to the same ‘thing’ allow data to flow from
one system to another
A ‘general mobilization’ to develop standards…..BUT
§ Fragmentation of the standards is a major issue ! • Being focused on particular communities’ interests, be their individual technologies
or biological/biomedical disciplines, leads to duplication of effort, and more seriously, the development of (largely arbitrarily) different standards
• This severely hinders the interoperability of databases and tools and ultimately the integration of datasets
VO!
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
Growing number of reporting standards
Growing number of reporting standards
+ 130
Estimated
+ 150
Source: MIB
BI,
EQU
ATOR
+ 303
Source: BioPortal
Databases, annotation,
curation tools
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!
But how much do we know about these 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!
Which one are mature enough for
me to use or recommend?
I work on plants, are these just for
biomedical applications?
What are the criteria to evaluate
their status and value?
How can I get involved to
propose extensions or modifications?
Which tools and databases
implement which standards?
I use high throughput sequencing technologies, which one are applicable
to me?
But how much do we know about these standards
Which one are mature enough for
me to use or recommend?
I work on plants, are these just for
biomedical applications?
What are the criteria to evaluate
their status and value?
Which tools and databases
implement which standards?
I use high throughput sequencing technologies, which one are applicable
to me?
How can I get involved to
propose extensions or modifications?
Several policy documentations and guidelines are inconsistent and/or unclear when recommending use of standards, e.g.: “..recommend use of appropriate standards...where these exists…....mature, stable efforts....MIAME format…..standards from accredited standards organizations…..deposition to public repositories, supporting these standards…...”
Often not much …
14
2009
15
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
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A coherent, curated and searchable catalogue of data sharing resources that (collaboratively) works to:
2. Centralizes community-developed bioscience standards and make them discoverable; linking to:
• data sharing, preservation and management policies • other portals e.g. MIBBI, NCBO’s BioPortal, NIF, BioSiteMaps, OBO foundry • related open access, published material e.g. BioMedCentral, Nature Precedings, F1000 • tools and databases implementing the standards e.g. collaboration with NAR Database
3. Identifies and maintain a set of (implicit) criteria for assessing usability and popularity of the standards, including:
• implementations by tools and databases • availability of standards-compliant, public datasets • relations among standards
3. Fosters communication among groups, in particular to: • address overlaps and duplication of efforts and enhance interoperability of standards • produce ‘best practice’ guidelines starting new, or contributing to existing efforts
Ø Will allow stakeholders (funders, journals, service providers and researchers) to make informed decision on 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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The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
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Over 400 entries (public and in curation)
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
Smith et al, 2007
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
Smith et al, 2007
Taylor, Field, Sansone et al, 2008
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
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List of databases, linked to standards a collaboration with Database Issue
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
22
List of databases, linked to standards a collaboration with Database Issue
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
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List of databases, linked to standards a collaboration with Database Issue
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
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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.
Define groups and relations among standards
E.g. in the genomics context: resources from GSC and other communities…
MixS
EnvO
EnvO-light
OBI
etc…
GCDML
ISA-Tab
SRAxml
BIOM (data matrices)
INSDC
GOLD
MG-RAST
CAMERA
SILVA
etc… Disclaimer: draft for illustrative purpose; this is a dynamic environment, work in progress…
E.g. in the genomics context: resources from GSC and other communities…
MixS
EnvO
EnvO-light
OBI
etc…
GCDML
ISA-Tab
SRAxml
BIOM (data matrices)
INSDC
GOLD
MG-RAST
CAMERA
SILVA
etc… Disclaimer: draft for illustrative purpose; this is a dynamic environment, work in progress…
E.g. in the genomics context: resources from GSC and other communities…
MixS
EnvO
EnvO-light
OBI
etc…
GCDML
ISA-Tab
SRAxml
BIOM (data matrices)
INSDC
GOLD
MG-RAST
CAMERA
SILVA
etc… Disclaimer: draft for illustrative purpose; this is a dynamic environment, work in progress…
E.g. in the genomics context: resources from GSC and other communities…
MixS
EnvO
EnvO-light
OBI
etc…
GCDML
ISA-Tab
SRAxml
BIOM (data matrices)
INSDC
GOLD
MG-RAST
CAMERA
SILVA
etc… Disclaimer: draft for illustrative purpose; this is a dynamic environment, work in progress…
E.g. in the genomics context: resources from GSC and other communities…
MixS
EnvO
EnvO-light
OBI
etc…
GCDML
ISA-Tab
SRAxml
BIOM (data matrices)
INSDC
GOLD
MG-RAST
CAMERA
SILVA
etc… Disclaimer: draft for illustrative purpose; this is a dynamic environment, work in progress…
Acknowledgements: Philippe Rocca-Serra (University of Oxford) Eamonn Maguire (University of Oxford) Annapaola Santarsiero (University of Oxford) Susanna Sansone (University of Oxford) Chris Taylor (EMBL-EBI) Dawn Field (NERC-NEBC) with contributions from members of our communities and individuals.