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- Reporting standards
- Hopes and hurdles
- Synergistic efforts
- Overcome the fragmentation of standards
- Our standards-compliant implementation
- Manage experimental metadata
Standards and infrastructure for managing experimental metadata - - PowerPoint PPT Presentation
Standards and infrastructure for managing experimental metadata - - PowerPoint PPT Presentation
Standards and infrastructure for managing experimental metadata BioInvestigation Index (see also poster F4) Susanna-Assunta Sansone, PhD The European Bioinformatics Institute (EMBL-EBI) www.ebi.ac.uk/net-project BioCurator Meeting Berlin,
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Growing complexity of the experiments
Consistent reporting of the experimental metadata
- along with the associated
data- has a positive and long-lasting impact on the value of collective scientific
- utputs
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Microarray and Gene Expression Data (MGED) www.mged.org HUPO- Proteomics Standards Initiative (PSI) Psidev.sf.net Pathways www.biopax.org Systems modelling standards www.sbml.org Genomics Standards Consortium (GSC) gensc.org Metabolomics Standards Initiative (MSI) msi-workgroups.sf.net
Some are loosely connected to regulatory/healthcare-driven initiatives and accredited Standards Developing Organizations (SDOs), e.g. CDISC, SEND, HL7, developing de jure standards.
Grass root omics initiatives (de facto standards), e.g.:
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Three types of reporting standards
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Fragmented standards, fragmented systems, e.g.:
DIFFERENT Access and exchange format DIFFERENT Deposition formats DIFFERENT Core requirements captured DIFFERENT Terminologies
Three EBI omics systems
DIFFERENT Curation practices and tools
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But....how do we manage complex experiments?
How do we encourage submissions
- f experimental metadata and data
and enable consistent reporting and curation in the current scenario?
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- Promote synergies among standards initiatives
- ‘Limit’ the range and variability of formats, in particular
- Create interoperable reporting standards
- Fit neatly into a jigsaw, resolving inconsistency and filling gaps
- Overcome several barriers
- Technical, funds and (overall) sociological......
We need to address the fragmentation of standards
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- Promote synergies among standards initiatives
- ‘Limit’ the range and variability of formats, in particular
- Create interoperable reporting standards
- Fit neatly into a jigsaw, resolving inconsistency and filling gaps
- Overcome several barriers
- Technical, funds and (overall) sociological......
- Our* contribution to address these hurdles
Risen funds to hold workshops, supporting synergistic efforts Initiated new synergistic efforts, where missing Work with our data producers and collaborators to implement standards-compliant systems
We need to address the fragmentation of standards
* Sansone SA, Rocca-Serra P, Field D, Taylor C.
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Synergistic efforts we contribute to
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Several stakeholders play pivotal role as enablers
The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 11
Volume 10, Number 10 October 2008
BioMed Central's journals - with clinical content and BMC Bioinformatics - now include a link to the MIBBI in the instructions for authors and encourage data deposition
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Our infrastructure based on synergistic standards
5 open source components working either as united system
- r as independent units
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Component 1: ISAcreator, standalone editor tool
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Component 1: ISAcreator, standalone editor tool
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Component 1: ISAcreator, standalone editor tool
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Component 2: ISAvalidator
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Component 3: BioInvestigation Index database
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Component 4: ISAconverter
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Component 5: R package for ISA-TAB (ongoing)
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Instance deployed at EBI, as prototype
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http//www.ebi.ac.uk/bioinvindex
Instance deployed at EBI, as prototype
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The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 22
Public studies are visible and searchable
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The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 23
Public studies are visible and searchable
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European Nutrigenomics Organisation
The National Center for Toxicological Research (NCTR) Center for Toxicoinformatics