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Mapping the landscape of
interoperability standards:
inform and educate
Susanna-Assunta Sansone, PhD
Consultant,
Founding ...
A	web-based,	curated	and	searchable	portal	that monitors	the	development and	
evolution of	standards,	their	use in	databas...
Formats Terminologies Guidelines
Initial focus on metadata (or content) standards
Formats Terminologies Guidelines
Enhance their findability
220+
115+
548+
source source
source
miame
MIRIAM
MIQAS
MIX
MIGE...
Formats Terminologies Guidelines
Initial focus on life/biomedical sciences, but not limited to
220+
115+
548+
source sourc...
Databases/data
repositories
Metadata standards
Formats Terminologies Guidelines
Ready	for	use,	implementation,	or	recommen...
Help users to understand if and how standards are used
Formats
Guideline
Formats
Terminology
Promote adoption e.g. by educating policy makers
Technologically-delineated
views of the world
Biologically-delineated
views of the world
Generic features (‘common core’)
...
Arrays
Scanning Arrays &
Scanning
Columns
Gels
MS MS
FTIR
NMR
Columns
transcriptomics
proteomics
metabolomics
plant biolog...
Standard developing groups:Journal, publishers:
Cross-links, data exchange:
Societies and organisations: Institutional RDM...
2013
2015
2016
https://doi.org/10.6084/m9.figshare.3795816.v2
https://doi.org/10.6084/m9.figshare.4055496.v1
https://datas...
From BioSharing to FAIRsharing - mapping the standards landscape
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From BioSharing to FAIRsharing - mapping the standards landscape

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Very brief overview of the BioSharing (soon FAIRsharing) resource, mapping the landscape of standards, repositories and policies

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From BioSharing to FAIRsharing - mapping the standards landscape

  1. 1. Mapping the landscape of interoperability standards: inform and educate Susanna-Assunta Sansone, PhD Consultant, Founding Academic Editor Associate Director, Principal Investigator Inter-Union Workshop on 21st Century Scientific and Technical Data Developing a roadmap for data integration Convened by the ICSU-CODATA Commission on Data Standards for Science, Paris, 19-21 June 2017
  2. 2. A web-based, curated and searchable portal that monitors the development and evolution of standards, their use in databases and the adoption of both in data policies, to inform and educate the user community part of FAIR .org
  3. 3. Formats Terminologies Guidelines Initial focus on metadata (or content) standards
  4. 4. Formats Terminologies Guidelines Enhance their findability 220+ 115+ 548+ source source source miame MIRIAM MIQAS MIX MIGEN ARRIVE MIAPE MIASE MIQE MISFISHIE…. REMARK CONSORT SRAxml SOFT FASTA DICOM MzML SBRML SEDML… GELML ISA CML MITAB AAO CHEBIOBI PATO ENVO MOD BTO IDO… TEDDY PRO XAO DO VO 882 -> ~1000
  5. 5. Formats Terminologies Guidelines Initial focus on life/biomedical sciences, but not limited to 220+ 115+ 548+ source source source miame MIRIAM MIQAS MIX MIGEN ARRIVE MIAPE MIASE MIQE MISFISHIE…. REMARK CONSORT SRAxml SOFT FASTA DICOM MzML SBRML SEDML… GELML ISA CML MITAB AAO CHEBIOBI PATO ENVO MOD BTO IDO… TEDDY PRO XAO DO VO 882 -> ~1000 de jure standard organizations de facto grass-roots groups
  6. 6. Databases/data repositories Metadata standards Formats Terminologies Guidelines Ready for use, implementation, or recommendation In development Status uncertain Deprecated as subsumed or superseded All records are manually curated in-house and verified by the community behind each resource Interlink standards among themselves and with repositories, as relevant, and use ‘indicators’ to describe their status Data policies by funders, journals and other organizations
  7. 7. Help users to understand if and how standards are used Formats Guideline Formats Terminology
  8. 8. Promote adoption e.g. by educating policy makers
  9. 9. 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 Highlight the fragmentation of standards
  10. 10. Arrays Scanning Arrays & Scanning Columns Gels MS MS FTIR NMR Columns transcriptomics proteomics metabolomics plant biology epidemiology microbiology Proteomics-based gut microbiota profiling Proteomics and metabolomics based gut microbiota profiling Need for modularization to combine and validate
  11. 11. Standard developing groups:Journal, publishers: Cross-links, data exchange: Societies and organisations: Institutional RDM services: Projects, programmes: part of FAIR .org
  12. 12. 2013 2015 2016 https://doi.org/10.6084/m9.figshare.3795816.v2 https://doi.org/10.6084/m9.figshare.4055496.v1 https://datascience.nih.gov/sites/default/files/bd2k/docs/ExecSumm_CBDMSworkshopFEB2015.pdf

Very brief overview of the BioSharing (soon FAIRsharing) resource, mapping the landscape of standards, repositories and policies

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