A 20 minute talk on BioSharing, presented at the COST CHARME data standards conference in Warsaw, Poland, on June 21th 2016

1. BioSharing.org
Mapping the landscape of Standards, Databases
and Data Policies in the Life Sciences
Peter McQuilton, PhD (@drosophilic)
@BioSharing content lead

2. Outline
• What is BioSharing?
• How do we describe and link standards?
• Exploring the landscape of standards, databases
and data policies in the life sciences

3. Mapping the landscape of ‘standards’ in the life, environmental and
biomedical sciences
Mapping the landscape of ‘standards’ in the life, environmental and
biomedical sciences
1,400 records and growing
What is BioSharing?
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.

4. Mapping the landscape of ‘standards’ in the life, environmental and
biomedical sciences
Mapping the landscape of ‘standards’ in the life, environmental and
biomedical sciences
What is BioSharing?
Launched in 2011, as an evolution of the MIBBI portal (2008-2011)
Manually curated
Community driven
Growing userbase and visibility
Promoting the FAIR principles
1,400 records and growing

5. also operates as a WG in Run at is also an Resource that
The BioSharing community
1,400 records and growing

6. Is there a database, implementing
standards, where I can deposit my
metagenomics dataset?
My funder’s data sharing policy
recommends the use of
established standards, but which
ones are widely endorsedand
applicable to my toxicological
and clinical data?
Am I using the most up-to-date
version of this terminology to
annotate cell-based assays?
I understand this format has been
deprecated; what has been replaced by
and how is leading the work?
Are there databases implementing this
exchange format, whose development
we have funded?
What are the mature
standardsand
standards-compliant
databases we should
recommend to our
authors?
Helping people make the right
decision

7. How do we describe and
link standards?

8. de jure de facto
grass-roots
groups
standard
organizations
Nanotechnology Working Group
Community mobilisation to develop
content standards
Formats Terminologies Guidelines

9. 193
85
346
miame
MIAPA
MIRIAM
MIQASMIX
MIGEN
ARRIVE
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
There are over 600 standards in
the life sciences
Formats Terminologies Guidelines

10. Guidelines = Minimum information
reporting requirements, checklists
o Report the same core, essential
information
o e.g. ARRIVE guidelines
Terminologies = Controlled
vocabularies, taxonomies,
thesauri, ontologies etc.
o Use the same word and
refer to the same ‘thing’
o e.g. Gene Ontology
Models/Formats = Conceptual
model, conceptual schema,
exchange formats
o Allow data to flow from one
system to another
o e.g. FASTA
Enablers: to better describe, share
and query data
Formats Terminologies Guidelines

11. Model/format formalizing reporting guideline -->
<-- Reporting guideline used by model/format
Cross-linking standards to
standards and databases

12. Model/format formalizing reporting guideline -->
<-- Reporting guideline used by model/format
Cross-linking standards to
standards and databases

15. Linking standards and databases to
training material
Linking standards and databases to
training material

17. Data - Indicators of life cycle
status
Ready for use, implementation, or recommendation
In development
Status uncertain
Deprecated as subsumed or superseded
Manually curated, approved by the community

18. Data - Indicators of life cycle
status
Ready for use, implementation, or recommendation
In development
Status uncertain
Deprecated as subsumed or superseded
Manually curated, approved by the community

19. Exploring the landscape

21. The International Conference on Systems Biology (ICSB), 22-28 August,2008 Susanna-Assunta
Sansone www.ebi.ac.uk/net-project
Search, filter, and refine using our faceted
search
Search, filter, and refine using our faceted
search

22. Collections and RecommendationsCollections and Recommendations
Collections group together
one or more types of resource
by domain, project or
organization.
Recommendations are a core-
set of resources that are
selected and recommended
by a funder or journal data
policy.

26. BioSharing – what we do
Inform – what’s out there, which databases use
which standards. Map the landscape.
Educate– what databases are recommended by your
funder, or journal of choice, which standards should
you be using, which standards and databases should
you recommend? Explore the landscape.

27. Acknowledgements
Eamonn
Maguire, DPhil
Software Engineer
(contractor)
Philippe
Rocca-Serra, PhD
Senior Research Lecturer
Alejandra
Gonzalez-Beltran, PhD
Research Lecturer
Milo
Thurston, DPhil
Research SW Engineer
Massimiliano
Izzo, PhD
Research SW Engineer
Peter
McQuilton, PhD
Senior Knowledge Engineer
Allyson
Lister, PhD
Knowledge Engineer
David
Johnson, PhD
Research SW Engineer
Susanna-Assunta Sansone, PhD
Centre’s Associate Director, Principal Investigator
and
Springer Nature’s Consultant for Scientific Data

28. Use us!
• Add/link your standard to BioSharing
• Add/link your database
• Use us to inform your data policy (and add/link
your policy)
• Make a collection or recommendation for your
group/society
https://biosharing.org
@biosharing