BioSharing at Internatiomnal Data Week - NIH BD2K session, Denver 2016
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Transcript of BioSharing at Internatiomnal Data Week - NIH BD2K session, Denver 2016
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Interna'onalDataWeek,SciDataCon,Denver,12September,2016
Communitystandardsforinteroperability:
BioSharing,aninforma'veandeduca'onalresource
Susanna-AssuntaSansone,PhDAssociateDirector,Oxforde-ResearchCentre,
UniversityofOxford
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Interoperability standards - Defini3on
• Enabletheopera'onalprocessesunderlyingexchangeandsharingofinforma'onbetweendifferentsystemsto
§ ensurealldigitalresearchoutputsareFindable,Accessible,InteroperableandReusable(FAIR)
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Interoperability standards - Defini3on
• Enabletheopera'onalprocessesunderlyingexchangeandsharingofinforma'onbetweendifferentsystemsto
§ ensurealldigitalresearchoutputsareFindable,Accessible,InteroperableandReusable(FAIR)
• Amongtheinteroperabilitystandards,onecategoryfocuseson
thedescrip'ons(ormetadata)ofdigitalobjects
• withinthiscategorytherearecontentstandards
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Opensdatasetsto
transparent
interpreta'on,
verifica'onand
exchangeand(re)use
Content standards – What for?
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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
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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
…….... …….... ……....
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Datapoliciesbyfunders,journalsandotherorganiza'ons
(100s+?)
Database,toolsandservices(1000s?)
Contentstandards(700+)
Complex and evolving landscape
Formats Terminologies Guidelines
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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
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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
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What is BioSharing?
Aweb-based,curatedandsearchableportalthatmonitorsthedevelopmentandevolu3onofstandards,theiruseindatabasesandtheadop'onofbothindata
policies,toinformandeducatetheusercommunity.
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What is BioSharing?
StandardsaredigitalobjectstooandwemakethemFAIR
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Using indicators to describe the ‘status’ of a resource
Readyforuse,implementa'on,orrecommenda'on
Indevelopment
Statusuncertain
Deprecatedassubsumedorsuperseded
Manuallycurated,approvedbythecommunity
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Helping you discover standards, databases, data policies and the rela3onships between them
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Pre-package the resources to help you find what it is relevant to you
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Is BioSharing used?
Success stories?
YES!
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“BioSharinganditsinteracAvebrowserwillallowustodiscoverwhichdatabasesandstandardsarenotcurrentlyincludedinourauthorguidelines,enablingustoregularlymonitorandrefineourpoliciesasappropriate,insupportofourmissiontohelpourauthorsenhancethereproducibilityoftheirwork.”–HollyMurray,F1000Research
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…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
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Advisory Board Opera3onal Team