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: B

ioSharing

Source: BioSharing

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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

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curated crowdsourcing"

The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project

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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

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... 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

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... 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

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...and associated article-level metrics

Dashboard/Visualizations

Dashboard/Visualizations

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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 ● C

IMR

[†]

● M

IACA

● M

IAME

● M

IAME

/Env

● M

IAME

/Nut

r

● M

IAME

/Pla

nt

● M

IAME

/Tox

● M

IAPA

● M

IAPE

[†]

● M

IARE

● M

IFlo

wCyt

● M

IGen

● M

IGS/

MIMS

● M

IMIx

● M

IMPP

● M

INI

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 on Twitter @biosharing

View our website http://www.biosharing.org

Thanks for your attention!