Break out session - Communication and Engagement of Stakeholders
Overview of standards/stakeholders in life science (RDA Engagement Interest Group)
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Transcript of Overview of standards/stakeholders in life science (RDA Engagement Interest Group)
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Data Consultant, Honorary Academic Editor
Susanna-Assunta Sansone, PhD Associate Director, Principal Investigator
RDA Engagement IG, Sept, 2013
Mapping the landscape of stakeholders and
standards in the life sciences
@
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§ Researchers and bioinformaticians in both
academic and commercial arenas, along with
funding agencies and publishers, embrace
the concept that community-developed, open, common reporting standards are pivotal to
structure and enrich the annotation of
• entities of interest (e.g., genes,
metabolites, phenotypes) and
• experimental steps (e.g.,
provenance of study materials,
technology and measurement types)
Standards for describing and reporting datasets
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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
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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
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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!
To track provenance of the information
and ensure richness of data and experimental
metadata descriptions, to
maximize reusability
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But how much do we know about these standards
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• A coherent, curated and searchable registry of standards for describing and reporting experiments in life science, environmental, biomedical and biotechnological domains
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• 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
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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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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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Users can claim entries and maintain them
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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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§ Existence of a formal specification, with: • good level of documentation, with scope and use cases • ease of implementation • human and machine readability
§ Broad adoption and implementation, outside the initial group by: • community databases (hence existence of standards-annotated datasets) • software (e.g. for reporting, editing, curating, submitting to databases)
§ Active user community, also providing: • support • responsiveness to community requests • examples
§ Interoperability with and extensibility to other standards, ranging from: • compatibility with other standards • flexibility to cover new domains • conversion and mapping, if applicable
§ Openness
Criteria to be used in evaluating standards for adoption:
Jessica D. Tenenbaum Duke Translational Medicine Institute
Melissa Haendel OHSU Library
Susanna-Assunta Sansone University of Oxford
also as part of the NIH Clinical and Translational Science Award (CTSA) program
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§ Database name § Main resource URL § Contact information § Date resource established (year) § Conditions of use (free, or type of license) § Scope: data types captured, curation polic § Standards implemented: checklists, terminologies, formats § Taxonomic coverage § Data accessibility/output options § Data release frequency § Versioning period and access to historical files § Documentation available § User support options § Data submission policy § Relevant publications § Tools available
Core attributes to describe databases and assist in evaluating scope and relevance as well as access to data:
Gaudet et al. NAR Database, 2011
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Beside grass-roots initiatives and formal
standardization initiatives,
which other stakeholders are relevant and
operative in the data area?
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Data publication platforms, e.g.:
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§ Pharma R&D has invested heavily in procedures and tools that integrate external information with their own data to enhance the decision-making process
§ Now pre-competitive initiatives and private-public partnerships are blooming as solutions towards reducing costs, associated to data management and curation, and maximize data interoperability
Pre-competitive initiative
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Company
Proprietary content provider
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The information landscape in the industrial sector …evolving…
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Our industry needs a Disruptive Innovation. That Disruption...is Pistoia
Credit to: Pistoia Alliance
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