biosharing at internatiomnal data week - nih bd2k session, denver 2016

Interna'onalDataWeek,SciDataCon,Denver,12September,2016

Communitystandardsforinteroperability:

BioSharing,aninforma'veandeduca'onalresource

Susanna-AssuntaSansone,PhDAssociateDirector,Oxforde-ResearchCentre,

UniversityofOxford

Interoperability standards - Defini3on

•  Enabletheopera'onalprocessesunderlyingexchangeandsharingofinforma'onbetweendifferentsystemsto

§  ensurealldigitalresearchoutputsareFindable,Accessible,InteroperableandReusable(FAIR)

Interoperability standards - Defini3on

•  Enabletheopera'onalprocessesunderlyingexchangeandsharingofinforma'onbetweendifferentsystemsto

§  ensurealldigitalresearchoutputsareFindable,Accessible,InteroperableandReusable(FAIR)

•  Amongtheinteroperabilitystandards,onecategoryfocuseson

thedescrip'ons(ormetadata)ofdigitalobjects

•  withinthiscategorytherearecontentstandards

Opensdatasetsto

transparent

interpreta'on,

verifica'onand

exchangeand(re)use

Content standards – What for?

Content standards – Three types

Formats Terminologies Guidelines

Minimuminforma+onrepor+ng

requirements,checklists

o  Reportthesamecore,

essen'alinforma'on

o  e.g.MIAMEguidelines

Controlledvocabularies,taxonomies,

thesauri,ontologiesetc.

o  Usethesamewordandreferto

thesame‘thing’

o  e.g.GeneOntology

Conceptualmodel,conceptual

schema,exchangeformatsetc

o  Allowdatatoflowfromone

systemtoanother

o  e.g.FASTA

de jure de facto grass-roots

groups standard

organizations NanotechnologyWorkingGroup

Over 700 content standards in biomedical sciences

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!

Formats Terminologies Guidelines

…….... …….... ……....

Datapoliciesbyfunders,journalsandotherorganiza'ons

(100s+?)

Database,toolsandservices(1000s?)

Contentstandards(700+)

Complex and evolving landscape

Formats Terminologies Guidelines

Fromthestandardsdevelopers’view,incl.:•  Complexlifecycleanddiversestakeholdercommuni'es•  Nocentralauthorityrecognizedbyallthepar'esinvolved•  Mainlyvolunteerac'vitywithli_le/nofund(exceptthecurrentNIHBD2KRFA!)•  Standalone,fragmentedstandards:unnecessaryduplica'onsandgaps•  Socialandtechnicalchallenges,extensivecommunitydynamics•  Lackofrewardsandincen'vesforallcontributors•  Ownershipofopenstandardsandthelegalframeworkareveryembryonic

Fromthestandardsconsumers’viewincl.:•  Li_le/noguidanceandtrainingmaterialtonavigate,select,re-use,extendor

recommendmostappropriatestandards•  Domain-specificfragmentedstandardsthatcannotbeusedincombina'on•  Standardsseenasburdensomeand/orover-prescrip've•  Limitednumberoftools/databasesimplemen'ngstandardsforan‘invisibleuse’•  Li_le/noappropriatefundingmechanismstosupportuseofstandards

Challenges emerged already 10 years ago

Referencepoints:CDISCsince1997

MIAMEpublishedin2001

Isthereadatabase,implemen3ngstandards,wheretodepositmy

metagenomicsdataset?

Myfunder’sdatasharingpolicyrecommendstheuseof

establishedstandards,butwhichonesarewidelyendorsedand

applicabletomytoxicologicalandclinicaldata?

AmIusingthemostup-to-dateversionofthisterminologytoannotatecell-basedassays?

Iunderstandthisformathasbeendeprecated;whathasbeenreplacedby

andhowisleadingthework?

Aretheredatabasesimplemen'ngthisexchangeformat,whosedevelopment

wehavefunded?

Whatarethematurestandardsandstandards-compliantdatabasesweshouldrecommendto

ourauthors?

BioSharing: inform and educate, working with and for the community

What is BioSharing?

Aweb-based,curatedandsearchableportalthatmonitorsthedevelopmentandevolu3onofstandards,theiruseindatabasesandtheadop'onofbothindata

policies,toinformandeducatetheusercommunity.

What is BioSharing?

StandardsaredigitalobjectstooandwemakethemFAIR

Using indicators to describe the ‘status’ of a resource

Readyforuse,implementa'on,orrecommenda'on

Indevelopment

Statusuncertain

Deprecatedassubsumedorsuperseded

Manuallycurated,approvedbythecommunity

Helping you discover standards, databases, data policies and the rela3onships between them

Pre-package the resources to help you find what it is relevant to you

Is BioSharing used?

Success stories?

YES!

“BioSharinganditsinteracAvebrowserwillallowustodiscoverwhichdatabasesandstandardsarenotcurrentlyincludedinourauthorguidelines,enablingustoregularlymonitorandrefineourpoliciesasappropriate,insupportofourmissiontohelpourauthorsenhancethereproducibilityoftheirwork.”–HollyMurray,F1000Research

…to export standards-derived metadata for the crea3on of annota3on templates...next talk!

studyMUST

study titleSHOULD

study descriptionMAY

seriesMUST

series titleMUST

series summaryMUST

ExampleofMIAMEelements:

experimentMUST

experiment titleMUST

experiment descriptionMUST

Advisory Board Opera3onal Team