The document summarizes a presentation about BioSharing, an online resource that monitors and curates standards for interoperability in biomedical sciences. It aims to inform and educate users on established standards, databases implementing standards, and data policies recommending standards. Over 700 content standards exist across formats, terminologies and guidelines. Challenges include the complex landscape of standards development and use. BioSharing helps users discover relevant standards, databases, and policies to make digital research outputs findable, accessible, interoperable and reusable. It has been successfully used by organizations like F1000Research to refine data policies.

1. Interna'onal Data Week, SciDataCon, Denver, 12 September, 2016
Community standards for interoperability:
BioSharing, an informa've and educa'onal resource
Susanna-Assunta Sansone, PhD
Associate Director, Oxford e-Research Centre,
University of Oxford

2. Interoperability standards - Defini3on
• Enable the opera'onal processes underlying exchange and
sharing of informa'on between different systems to
§ ensure all digital research outputs are Findable, Accessible,
Interoperable and Reusable (FAIR)

3. Interoperability standards - Defini3on
• Enable the opera'onal processes underlying exchange and
sharing of informa'on between different systems to
§ ensure all digital research outputs are Findable, Accessible,
Interoperable and Reusable (FAIR)
• Among the interoperability standards, one category focuses on
the descrip'ons (or metadata) of digital objects
• within this category there are content standards

4. Opens datasets to
transparent
interpreta'on,
verifica'on and
exchange and (re)use
Content standards – What for?

5. Content standards – Three types
Formats Terminologies Guidelines
Minimum informa+on repor+ng
requirements, checklists
o Report the same core,
essen'al informa'on
o e.g. MIAME guidelines
Controlled vocabularies, taxonomies,
thesauri, ontologies etc.
o Use the same word and refer to
the same ‘thing’
o e.g. Gene Ontology
Conceptual model, conceptual
schema, exchange formats etc
o Allow data to flow from one
system to another
o e.g. FASTA

6. de jure de facto
grass-roots
groups
standard
organizations Nanotechnology Working Group
Over 700 content standards in biomedical sciences
miame!
MIAPA!
MIRIAM!
MIQAS!
MIX!
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!
Formats Terminologies Guidelines
…….... …….... ……....

7. Data policies by
funders, journals and
other organiza'ons
(100s+?)
Database, tools
and services
(1000s?)
Content standards
(700+)
Complex and evolving landscape
Formats Terminologies Guidelines

8. From the standards developers’ view, incl.:
• Complex life cycle and diverse stakeholder communi'es
• No central authority recognized by all the par'es involved
• Mainly volunteer ac'vity with li_le/no fund (except the current NIH BD2K RFA!)
• Standalone, fragmented standards: unnecessary duplica'ons and gaps
• Social and technical challenges, extensive community dynamics
• Lack of rewards and incen'ves for all contributors
• Ownership of open standards and the legal framework are very embryonic
From the standards consumers’ view incl.:
• Li_le/no guidance and training material to navigate, select, re-use, extend or
recommend most appropriate standards
• Domain-specific fragmented standards that can not be used in combina'on
• Standards seen as burdensome and/or over-prescrip've
• Limited number of tools/databases implemen'ng standards for an ‘invisible use’
• Li_le/no appropriate funding mechanisms to support use of standards
Challenges emerged already 10 years ago
Reference points:
CDISC since 1997
MIAME published in 2001

9. Is there a database, implemen3ng
standards, where to deposit my
metagenomics dataset?
My funder’s data sharing policy
recommends the use of
established standards, but which
ones are widely endorsed and
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 implemen'ng this
exchange format, whose development
we have funded?
What are the mature
standards and standards-
compliant databases we
should recommend to
our authors?
BioSharing: inform and educate,
working with and for the community

11. What is BioSharing?
A web-based, curated and searchable portal that monitors the development and
evolu3on of standards, their use in databases and the adop'on of both in data
policies, to inform and educate the user community.

12. What is BioSharing?
Standards are digital objects too and we make them FAIR

16. Using indicators to describe the ‘status’ of a resource
Ready for use, implementa'on, or recommenda'on
In development
Status uncertain
Deprecated as subsumed or superseded
Manually curated, approved by the community

19. Helping you discover standards, databases, data
policies and the rela3onships between them

20. Pre-package the resources to help you find what it is
relevant to you

21. Is BioSharing used?
Success stories?
YES!

25. “BioSharing and its interacAve browser will allow us to
discover which databases and standards are not currently
included in our author guidelines, enabling us to regularly
monitor and refine our policies as appropriate, in support of
our mission to help our authors enhance the reproducibility
of their work.” – Holly Murray, F1000Research

26. …to export standards-derived metadata for the
crea3on of annota3on templates...next talk!
study
MUST
study title
SHOULD
study description
MAY
series
MUST
series title
MUST
series summary
MUST
Example of MIAME elements:
experiment
MUST
experiment title
MUST
experiment description
MUST

27. Advisory Board
Opera3onal Team