n
connecting standards, databases and data policies
Susanna-Assunta Sansone
Associate Director
Oxford e-Research Centre, University of Oxford

• Domain-level descriptors that are essential for interpretation, verification,
reproducibility and reusability of datasets
• The depth and breadth of descriptors vary according to the domain broadly
covering the what, who, when, how and why
Content standards

Formats Terminologies Guidelines
Content standards: three categories

Minimum information reporting
requirements, checklists
o Report the same core, essential
information
o e.g. MIAME guidelines
Controlled vocabularies, taxonomies, thesauri, ontologies etc.
o Unambiguous identification and definition of concepts
o e.g. Gene Ontology
Conceptual model, schema,
exchange formats etc
o Define the structure and
interrelation of information,
and the transmission format
o e.g. FASTA Formats Terminologies Guidelines
Content standards: three categories

Formats Terminologies Guidelines
Community-driven initiatives
de jure de facto
grass-roots
groups
standard
organizations
Nanotechnology Working Group

883 -> ~1000
220+
115+
548
source source
source
Content standards in numbers
Formats Terminologies Guidelines
MIAME
MIRIAM
MIQASMIX
MIGEN
ARRIVE
MIAPE
MIASE
MIQE
MISFISHIE….
REMARK
CONSORT
SRAxml
SOFT FASTA
DICOM
MzML
SBRML
SEDML…
GELML
ISA
CML
MITAB
AAO
CHEBIOBI
PATO ENVO
MOD
BTO
IDO…
TEDDY
PRO
XAO
DO
VO
MIAPPE
Sample-Tab

Content standards
Data policies by
funders, journals and
other organizations
Databases, tools
and services
Formats Terminologies Guidelines
Mapping this evolving landscape

Content standards
Data policies by
funders, journals and
other organizations
Databases, tools
and services
Formats Terminologies Guidelines
a resource of the ELIXIR Interoperability Platform
• A web-based, curated and searchable portal that monitors their
development and evolution to inform and educate

Not just quantity but quality:
rich, curated and community
vetted descriptions

Indicators to describe the status of standards and databases
Ready for use, implementation, or recommendation
In development
Status uncertain
Deprecated as subsumed or superseded
Manually curated and verified
by the community behind each resource

Tracking evolution, e.g.:

Visualizing relations, e.g.:
Data Policy
List of their
recommended
databases and standards

…to inform and educate on
existing and new resources
Data Policy

Working with/for the community and our ‘adopters’, e.g.:
Standard developing groups:Journal, publishers:
Cross-links, data exchange:
Societies and organisations: Institutional RDM services:
Projects, programmes:
533
responders

Progressively cross-linking with other ELIXIR resources
Cross-links, data exchange:
Societies and organisations:
Standard developing groups:Journal, publishers:
Institutional RDM services:
Projects, programmes:

• Increase discoverability (e.g. by search engines), aggregation (e.g. by indices)
and analysis of content in different websites and services
• use of schema.org structured semantic markup (for web pages’ content) by Google, Bing,
Yahoo, Yandex
• coordinate its extension, where needed, in the life science area
Gaining traction and
support by:

Acknowledgements