Overview of community standards beside Common Data Elements (CDEs) and role of BioSharing

1. Susanna-Assunta Sansone,
Associate Director, Oxford e-Research Centre,
University of Oxford, UK
dx.doi.org/10.6084/m9.figshare.4055496.v1
@biosharing
bioCADDIE – DATS and CDEs Workshop, Bethesda, 8 May 2017

2. Formats Terminologies Guidelines
Common
Data
Elements
Types of content standards
Content standards: descriptors essential for interpretation,
verification, reproducibility, sharing etc. of datasets

3. 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
Types of content standards
Common
Data
Elements

4. de jure de facto
grass-roots
groups
standard
organizations
Nanotechnology Working Group
Formats Terminologies Guidelines
Community-driven efforts, just few examples

5. Formats Terminologies Guidelines
224
115
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
CHEBIOBI
PATO ENVO
MOD
BTO
IDO…
TEDDY
PRO
XAO
DO
VO
Content standards in numbers

8. 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

9. Data policies by
funders, journals and
other organizations
Content standards
Formats Terminologies Guidelines
Map this complex and evolving landscape
Databases

10. Data policies by
funders, journals and
other organizations
Databases
Content standards
Formats Terminologies Guidelines
Using indicators to describe ‘status’
Ready for use, implementation, or recommendation
In development
Status uncertain
Deprecated as subsumed or superseded
All records are manually curated
in-house and verified by the
community behind each resource

13. Understanding how standards are used

14. Understanding how standards are used
Guideline

15. Understanding how standards are used
Formats
Guideline

16. Understanding how standards are used
Formats
Guideline
Formats

17. Understanding how standards are used
Formats
Guideline
Formats
Terminology

18. Technologically-delineated
views of the world
Biologically-delineated
views of the world
Generic features (‘common core’)
- description of source biomaterial
- experimental design components
Arrays
Scanning Arrays &
Scanning
Columns
Gels
MS MS
FTIR
NMR
Columns
transcriptomics
proteomics
metabolomics
plant biology
epidemiology
microbiology
Duplications & lack of interoperability among standards

19. Arrays
Scanning Arrays &
Scanning
Columns
Gels
MS MS
FTIR
NMR
Columns
transcriptomics
proteomics
metabolomics
plant biology
epidemiology
microbiology
Hard to use them in combinations, e.g. to represent:
Proteomics-based gut microbiota profiling
Proteomics and metabolomics based gut
microbiota profiling

20. Arrays
Scanning Arrays &
Scanning
Columns
Gels
MS MS
FTIR
NMR
Columns
transcriptomics
proteomics
metabolomics
plant biology
epidemiology
microbiology
Enhancing modularization
Proteomics-based gut microbiota profiling
Proteomics and metabolomics based gut
microbiota profiling

21. Arrays
Scanning Arrays &
Scanning
Columns
Gels
MS MS
FTIR
NMR
Columns
transcriptomics
proteomics
metabolomics
plant biology
epidemiology
microbiology
Proteomics-based gut microbiota profiling
Proteomics and metabolomics based gut
microbiota profiling
Enhancing modularization

22. bsg-000174
biosharing:
ReportingGuideline
bsg-000161
MINSEQE
MIMARKS
sample
information
sample
identifier
taxonomy
identifier
sequence
read
geo location
High-level information about
the metadata standards
Representations
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 creation of metadata templates, rendering standards invisible to the researchers
Modularize and combine

23. Standard developing groups:Journal, publishers:
Cross-links, data exchange:
Societies and organisations: Institutional RDM services:
Projects, programmes: