Susanna-Assunta Sansone, PhD
Associate Director, PI - Oxford e-Research Centre, University of Oxford, UK
Data Consultant - Nature Publishing Group’s Scien4fic Data

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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!
In the life sciences there are >600 content standards
Databases and tools
implemenEng
Standards; also training material
on and around standards

de jure de facto
grass-roots
groups
standard
organizations
Nanotechnology Working Group
• To structure, enrich and report the descripEon of the datasets and the
experimental context under which they were produced
Community-developed content standards

Is there a database, implemen5ng
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deprecated; what has been replaced by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 implemenEng this
exchange format, whose development
we have funded?
What are the mature
standards and standards-
compliant databases we
should recommend to
our authors?
But how do we help users to make informed decisions?

Planned output are
• principles for linking informaEon about databases, content standards
and journal / funder policies in the life sciences
• and a curated registry to access and cross-search the informaEon, on
which a variety of stakeholders can base their decisions

Mapping the landscape of ‘standards’ in the life sciences
1,379 records and growing

Mapping the landscape of ‘standards’ in the life sciences
A web-based, curated and searchable registry ensuring that standards and
databases are registered, informa4ve and discoverable; monitoring
development and evolu5on of standards, their use in databases and adopEon
of both in data policies
1,379 records and growing

The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta
Sansone www.ebi.ac.uk/net-project
Tracking evolution, e.g. deprecations and substitutions

Cross-linking standards to standards and databases
Model/format formalizing reporEng guideline -->
<-- ReporEng guideline used by model/format
We link (descriptions of) standards to
related standards and databases,
implementing them

Conducted a 10 quesEons survey to assess users needs: 532 replies will inform
the acEviEes of the BioSharing WG and further development of the registry
Activities in collaboration with and
The replies to other quesEons tell us about the users’
• level of familiarity with standards
• type of standards they want to see in the registry
• descriptors about standards to help them make
decisions
• desired funcEonality of the registry
• preferred indicator of maturity, adopEon and use of
standards

From simple and advance search interfaces to….
Powered by curated descripEons of each standard
and database records, and their relaEons;
….the recommender system

To inform the creaEon of templates to describe datasets, according to community
standards, but rendering the standards invisible to the researchers
Create standards-derived metadata elements
High-level informa6on about the standards,
their rela6ons and use by databases
RDF or JSON representa6ons
of the standards-derived elements
Elements and their
provenance served to

also operaEng as a WG in Run at is also an contribuEon to