BioSharing for the NIH BD2K community

@biosharing

dx.doi.org/10.6084/m9.figshare.4055496.v1

de jure de facto grass-roots

groups standard

organizations

NanotechnologyWorkingGroup

Formats Terminologies Guidelines

Community-driven efforts, just few examples

Content standards: domain-level descriptors essential for

interpretation, verification and reproducibility of datasets

Formats Terminologies Guidelines

212

113

500+

source sourcesource

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

Datapoliciesbyfunders,journalsandotherorganizaLons

Database,toolsandservices

Contentstandards

Complex and evolving landscape

Formats Terminologies Guidelines

Aweb-based,curatedandsearchableportalthatmonitorsthedevelopmentandevolu2onofstandards,theiruseindatabasesandtheadopLonofbothindatapolicies,toinformandeducatetheusercommunity

Helping users make the right decision

Readyforuse,implementaLon,orrecommendaLon

Indevelopment

Statusuncertain

Deprecatedassubsumedorsuperseded

Manuallycuratedandverifiedbythecommunitybehindeachresource

Indicators to describe ‘status’

Tracking evoluEon

§  Wehavecurated586ofthe674standardsrecords(87%)•  155areclaimedbytherelevant,andsoconfirmedtobe

‘acLve’(23%);64standardsaredeprecated,8indevelopment,19uncertain

•  55standardsweregeneratedviaaworldwideconsorLum/organisaLon/governingbody;341involvedtheUSAeitheraloneorinpartnershipwithanothercountry;138theUK;53EU;8China

•  themostadoptedstandardisFASTA,implementedin247databases

•  309(46%)areimplementedin1ormoredatabaseso  151(22%)implementedin1database;64(9%)

implementedin2databases;157(23%)implementedin2ormoredatabases

Preliminary analysis – work in progress

Standarddevelopinggroups:JournalPublishers:

Registry

Cross-links/Dataexchange:

Some user communiEes and collaborators SocieLesandorganisaLons:

InsLtuLonalRDMservices:

Projects/programmes:

bsg-000174

biosharing:ReporLngGuideline

bsg-000161

MINSEQE

MIMARKS

sampleinformaLon

sampleidenLfier

taxonomyidenLfier

sequenceread

geolocaLon

High-levelinforma0onaboutthemetadatastandards

Representa0onsofthestandardselements

Templateelementsfor

el-000001

el-000002

el-000003

provenance:MINSEQE

provenance:MINSEQE

andMIMARKS

provenance:MIMARKS

•  Servemachine-readablecontentmetadatastandards,providingprovenancefortheirelements•  InformthecreaLonofmetadatatemplates,renderingstandardsinvisibletotheresearchers

From standards to CDEs-like, to annotaEon templates