1. 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

2. 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

3. 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

4. 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. 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

6. 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?

7. Lunched in Jan 2011

8. 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

9. The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta
Sansone www.ebi.ac.uk/net-project
9

12. curated crowdsourcing"

14. 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...

15. 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

16. 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

17. 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

18. Dashboard/Visualizations

19. Dashboard/Visualizations

20. 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:

21. endorsed by data publication platforms:

22. endorsed by data publication platforms:

23. 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"

24. 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)

25. MICheckout: Supporting Users"

26. funders
core BioSharing team

27. 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!