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BioSharing.org - mapping the landscape of community standards, databases, data policies and their interrelations
 

BioSharing.org - mapping the landscape of community standards, databases, data policies and their interrelations

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    BioSharing.org - mapping the landscape of community standards, databases, data policies and their interrelations BioSharing.org - mapping the landscape of community standards, databases, data policies and their interrelations Presentation Transcript

    • Alejandra González-Beltrán, Ph.D University of Oxford e-Research Centre, UK BioSharing.org mapping the landscape of community standards, databases, data policies and their interrelations alejandra.gonzalezbeltran@oerc.ox.ac.uk BioMedBridges Identifiers and Standards Workshop Amsterdam,The Netherlands 24th - 25th June, 2014
    • A community mobilization to develop standards, e.g.: §  Structural and operational differences •  organization types (open, close to members, society, WG etc.) •  standards development (how to formulate, conduct and maintain) •  adoption, uptake, outreach (link to journals, funders and commercial sector) •  funds (sponsors, memberships, grants, volunteering) de jure de facto grass-roots groups standard organizations Nanotechnology Working Group
    • Types of reporting standards Nanotechnology Working Group Including minimum information reporting requirements, or checklists to report the same core, essential information Including controlled vocabularies, taxonomies, thesauri, ontologies etc. to use the same word and refer to the same ‘thing’ Including conceptual model, conceptual schema from which an exchange format is derived to allow data to flow from one system to another
    • Growing number of reporting standards + 130 + 150 + 303 Source:BioPortal Databases, " annotation," curation " tools " implementing " 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 Source:BioSharing Source:BioSharing
    • 5 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 Fragmentation, duplications and gaps To compare and integrate data we need interoperable standards
    • How much do we know and which standards can we use I work in the field of cell migration research, which one are applicable to me? I us cell migration in translational research, are there specific clinical standards?
    • Lunched in Jan 2011
    • Lunched in Jan 2011 BioSharing scope and goals •  Registering and cataloguing policies, standards and databases •  Curated crowdsourcing approach •  Assessment criteria for usability and popularity of standards (impact, maturity models) •  Association of standards to data policies and databases •  Assemble journal and funder policies related to data sharing, storage, preservation, etc. •  Standards modules: integrate with MICheckout work •  Make fully cross-searchable •  Main goal: to help stakeholders make informed decisions for data interoperability
    • The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 9
    • curated crowdsourcing"
    • The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 1 4 User profiles populated from ORCID...
    • The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 1 5 ... credit for creating, contributing to, maintaining standards Ownership of open standards can be problematic in broad, grass-root collaborations It requires improved models, to encourage maintenance of and contributions to these efforts, rewards and incentives need to be identified for all contributors to supporting the continued development of standards
    • The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 1 6 ... link to data records associated to publications
    • The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project 1 7 ...and associated article-level metrics
    • Dashboard/Visualizations
    • Dashboard/Visualizations
    • 2 0 We need “standards impact metrics” to evaluate use/usability Work started/ongoing in: By Fabien Richard (Merck), Philippe Rocca-Serra (Oxford), Paul Houston (CDISC) Straw-man proposal outlined in:
    • endorsed by data publication platforms:
    • endorsed by data publication platforms:
    • BioSharing.org integrates information from
 " "the MIBBI Project (mibbi.org)" [†] Denotes that a specification is provided as a suite of related documents CONCEPT SPECIALISATION ●CIMR[†] ●MIACA ●MIAME ●MIAME/Env ●MIAME/Nutr ●MIAME/Plant ●MIAME/Tox ●MIAPA ●MIAPE[†] ●MIARE ●MIFlowCyt ●MIGen ●MIGS/MIMS ●MIMIx ●MIMPP ●MINI study inputs study design ● generic organism ● cells / microbes plant animal mouse human population environmental sample environment / habitat in silico model study procedures organism maintenance animal husbandry cell / microbe culture plant cultivation acclimation preconditioning / pretreatment ● organism manipulation assay inputs generic study input organism part ● organism state organism trait biomolecule synthetic analyte ● silencing RNA reagent Version 0.7 (2008-04-10) Comparison of MIBBI-registered projects [21] ● Release Granularity Coarse Medium Fine Maturity ● Planned ● Drafting Analysis of granularity and maturity of the existing checklists"
    • Standard modules - MICheckout work creation and usage of modules within the MIBBI Foundry" Stage one •  MIBBI module schema •  Highly-configurable (mostly XML Schema, partly a configuration file) •  Validates data and exports XML (also saves in a ‘native’ zipped XML) Stage two •  Mini shell scripts for XSL transformation using Saxon —  Initially just to get the (media)wiki code for Foundry pages —  Now have MediaWiki and HTML (both as table & list), tab- delimited text, XML Schema (for MDA) and ISA config (XML) •  Java (command line) tool (using DOM) built to combine and transform modules using the above XSLTs (=MyMICheckout) Stage three •  MICheckout user interface – HTML/Javascript •  Same functionality (same XSLTs), rather nicer UI (i.e., it has one)
    • MICheckout: Supporting Users"
    • funders core BioSharing team
    • Questions? You can email us... biosharing-contact-us@lists.sf.net Follow us onTwitter @biosharing View our website http://www.biosharing.org Thanks for your attention!