Overview of BioSharing, scope, content and role for the community; and relations to BD2K activities too

1. @biosharing
dx.doi.org/10.6084/m9.figshare.4055496.v1

2. de jure de facto
grass-roots
groups
standard
organizations
Nanotechnology Working Group
Formats Terminologies Guidelines
Community-driven efforts, just few examples
Content standards: domain-level descriptors essential for
interpretation, verification and reproducibility of datasets

3. Formats Terminologies Guidelines
212
113
500+
source source
source
miame!
MIRIAM!
MIQAS!
MIX!
MIGEN!
ARRIVE!
MIAPE!
MIASE!
MIQE!
MISFISHIE….!
REMARK!
CONSORT!
SRAxml!
SOFT! FASTA!
DICOM!
MzML!
SBRML!
SEDML…!
GELML!
ISA!
CML!
MITAB!
AAO!
CHEBI!OBI!
PATO! ENVO!
MOD!
BTO!
IDO…!
TEDDY!
PRO!
XAO!
DO
VO!
Content standards – in numbers

4. Data policies by
funders, journals and
other organizaLons
Database, tools
and services
Content standards
Complex and evolving landscape
Formats Terminologies Guidelines

5. A web-based, curated and searchable portal that
monitors the development and evolu2on of standards,
their use in databases and the adopLon of both in data
policies, to inform and educate the user community

6. Helping users make the right decision

10. Ready for use, implementaLon, or recommendaLon
In development
Status uncertain
Deprecated as subsumed or superseded
Manually curated and verified
by the community behind each resource
Indicators to describe ‘status’

11. Tracking evoluEon

16. § We have curated 586 of the 674 standards records (87%)
• 155 are claimed by the relevant, and so confirmed to be
‘acLve’ (23%); 64 standards are deprecated, 8 in
development, 19 uncertain
• 55 standards were generated via a worldwide consorLum/
organisaLon/governing body; 341 involved the USA either
alone or in partnership with another country; 138 the UK;
53 EU; 8 China
• the most adopted standard is FASTA, implemented in 247
databases
• 309 (46%) are implemented in 1 or more databases
o 151 (22%) implemented in 1 database; 64 (9%)
implemented in 2 databases; 157 (23%) implemented
in 2 or more databases
Preliminary analysis – work in progress

17. Standard developing groups: Journal Publishers:
Registry
Cross-links/Data exchange:
Some user communiEes and collaborators
SocieLes and organisaLons:
InsLtuLonal RDM services:
Projects/programmes:

18. bsg-000174
biosharing:
ReporLngGuideline
bsg-000161
MINSEQE
MIMARKS
sample
informaLon
sample
idenLfier
taxonomy
idenLfier
sequence
read
geo locaLon
High-level informa0on about the
metadata standards
Representa0ons
of the standards elements
Template elements for
el-000001
el-000002
el-000003
provenance:
MINSEQE
provenance:
MINSEQE
and
MIMARKS
provenance:
MIMARKS
• Serve machine-readable content metadata standards, providing provenance for their elements
• Inform the creaLon of metadata templates, rendering standards invisible to the researchers
From standards to CDEs-like, to annotaEon templates