Download - BioSharing - Mapping the landscape of Standards, Database and Data Policies in the Life Sciences
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BioSharing.orgMappingthelandscapeofStandards,Databases
andDataPoliciesintheLifeSciences
PeterMcQuilton,PhD(@drosophilic)@BioSharing contentlead
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Outline
• WhatisBioSharing?
• Howdowedescribeandlinkstandards?
• Exploringthelandscapeofstandards,databases
anddatapoliciesinthelifesciences
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Mapping the landscape of ‘standards’ in the life, environmental and biomedical sciences
Mapping the landscape of ‘standards’ in the life, environmental and biomedical sciences
1,400recordsandgrowing
WhatisBioSharing?
Aweb-based,curated andsearchableportalthat monitorsthedevelopmentandevolution ofstandards,theiruse indatabasesandtheadoptionofbothin
datapolicies, toinformandeducatetheusercommunity.
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Mapping the landscape of ‘standards’ in the life, environmental and biomedical sciences
Mapping the landscape of ‘standards’ in the life, environmental and biomedical sciences
WhatisBioSharing?
Launchedin2011,asanevolutionoftheMIBBIportal(2008-2011)ManuallycuratedCommunitydriven
Growinguserbase andvisibilityPromotingtheFAIRprinciples
1,400recordsandgrowing
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alsooperatesasaWG inRunat isalsoan Resource that
TheBioSharing community
1,400recordsandgrowing
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Isthereadatabase,implementingstandards,whereIcandepositmy
metagenomicsdataset?
Myfunder’sdatasharingpolicyrecommendstheuseof
establishedstandards,butwhichonesarewidelyendorsedandapplicabletomytoxicological
andclinicaldata?
AmIusingthemostup-to-dateversion ofthisterminologytoannotatecell-basedassays?
Iunderstandthisformathasbeendeprecated;whathasbeenreplaced by
andhowisleadingthework?
Aretheredatabasesimplementingthisexchangeformat,whosedevelopment
wehavefunded?
Whatarethematurestandards and
standards-compliantdatabasesweshouldrecommendtoour
authors?
Helpingpeoplemaketherightdecision
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Howdowedescribeandlinkstandards?
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de jure de facto
grass-rootsgroups
standard organizations
Nanotechnology Working Group
Communitymobilisationtodevelopcontentstandards
Formats Terminologies Guidelines
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19385
346
miameMIAPA
MIRIAMMIQASMIX
MIGEN
ARRIVEMIAPE
MIASE
MIQE
MISFISHIE….
REMARK
CONSORT
MAGE-TabGCDML
SRAxmlSOFT FASTA
DICOM
MzMLSBRML
SEDML…
GELML
ISA-Tab
CML
MITAB
AAOCHEBI
OBIPATO ENVOMOD
BTOIDO…
TEDDY
PROXAO
DO
VO
Thereareover600standardsinthelifesciences
Formats Terminologies Guidelines
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Guidelines=Minimuminformation
reportingrequirements,checklists
o Reportthesamecore,essential
information
o e.g.ARRIVEguidelines
Terminologies=Controlled
vocabularies,taxonomies,
thesauri,ontologies etc.
o Usethesamewordand
refertothesame‘thing’
o e.g.GeneOntology
Models/Formats=Conceptual
model,conceptualschema,
exchangeformats
o Allowdatatoflowfromone
systemtoanother
o e.g.FASTA
Enablers:tobetterdescribe,shareandquerydata
Formats Terminologies Guidelines
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Model/format formalizingreportingguideline -->
<-- Reportingguidelineusedbymodel/format
Cross-linkingstandardstostandardsanddatabases
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Model/format formalizingreportingguideline -->
<-- Reportingguidelineusedbymodel/format
Cross-linkingstandardstostandardsanddatabases
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LinkingstandardsanddatabasestotrainingmaterialLinkingstandardsanddatabasestotrainingmaterial
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Data- Indicatorsoflifecyclestatus
Readyforuse,implementation,orrecommendation
Indevelopment
Statusuncertain
Deprecatedassubsumedorsuperseded
Manuallycurated,approvedbythecommunity
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Data- Indicatorsoflifecyclestatus
Readyforuse,implementation,orrecommendation
Indevelopment
Statusuncertain
Deprecatedassubsumedorsuperseded
Manuallycurated,approvedbythecommunity
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Exploringthelandscape
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The International Conference on Systems Biology (ICSB), 22-28 August, 2008 Susanna-Assunta Sansone www.ebi.ac.uk/net-project
Search,filter,andrefineusingourfacetedsearchSearch,filter,andrefineusingourfacetedsearch
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CollectionsandRecommendationsCollectionsandRecommendations
Collections grouptogether
oneormoretypesofresource
bydomain,projector
organization.
Recommendations areacore-
setofresourcesthatare
selectedandrecommended
byafunderorjournaldata
policy.
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BioSharing – whatwedo
Inform – what’soutthere,whichdatabasesusewhichstandards.Mapthelandscape.
Educate– whatdatabasesarerecommendedbyyourfunder,orjournalofchoice,whichstandardsshouldyoubeusing,whichstandardsanddatabasesshouldyourecommend?Explorethelandscape.
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Acknowledgements
EamonnMaguire,DPhilSoftwareEngineer(contractor)
PhilippeRocca-Serra,PhDSeniorResearchLecturer
AlejandraGonzalez-Beltran,PhDResearchLecturer
MiloThurston,DPhilResearchSWEngineer
MassimilianoIzzo,PhDResearchSWEngineer
PeterMcQuilton,PhDSeniorKnowledgeEngineer
AllysonLister,PhDKnowledgeEngineer
DavidJohnson,PhDResearchSWEngineer
Susanna-AssuntaSansone,PhDCentre’sAssociateDirector,PrincipalInvestigatorandSpringerNature’sConsultantforScientificData
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Use us!
• Add/linkyourstandardtoBioSharing• Add/linkyourdatabase• Useustoinformyourdatapolicy(andadd/linkyourpolicy)
• Makeacollectionorrecommendationforyourgroup/society
https://biosharing.org@biosharing