biosharing - mapping the landscape of standards, database and data policies in the life sciences

BioSharing.orgMappingthelandscapeofStandards,Databases

andDataPoliciesintheLifeSciences

PeterMcQuilton,PhD(@drosophilic)@BioSharing contentlead

Outline

• WhatisBioSharing?

• Howdowedescribeandlinkstandards?

• Exploringthelandscapeofstandards,databases

anddatapoliciesinthelifesciences

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.

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

alsooperatesasaWG inRunat isalsoan Resource that

TheBioSharing community

1,400recordsandgrowing

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

Howdowedescribeandlinkstandards?

de jure de facto

grass-rootsgroups

standard organizations

Nanotechnology Working Group

Communitymobilisationtodevelopcontentstandards

Formats Terminologies Guidelines

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

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

Model/format formalizingreportingguideline -->

<-- Reportingguidelineusedbymodel/format

Cross-linkingstandardstostandardsanddatabases

Model/format formalizingreportingguideline -->

<-- Reportingguidelineusedbymodel/format

Cross-linkingstandardstostandardsanddatabases

LinkingstandardsanddatabasestotrainingmaterialLinkingstandardsanddatabasestotrainingmaterial

Data- Indicatorsoflifecyclestatus

Readyforuse,implementation,orrecommendation

Indevelopment

Statusuncertain

Deprecatedassubsumedorsuperseded

Manuallycurated,approvedbythecommunity

Data- Indicatorsoflifecyclestatus

Readyforuse,implementation,orrecommendation

Indevelopment

Statusuncertain

Deprecatedassubsumedorsuperseded

Manuallycurated,approvedbythecommunity

Exploringthelandscape

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

CollectionsandRecommendationsCollectionsandRecommendations

Collections grouptogether

oneormoretypesofresource

bydomain,projector

organization.

Recommendations areacore-

setofresourcesthatare

selectedandrecommended

byafunderorjournaldata

policy.

BioSharing – whatwedo

Inform – what’soutthere,whichdatabasesusewhichstandards.Mapthelandscape.

Educate– whatdatabasesarerecommendedbyyourfunder,orjournalofchoice,whichstandardsshouldyoubeusing,whichstandardsanddatabasesshouldyourecommend?Explorethelandscape.

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

Use us!

• Add/linkyourstandardtoBioSharing• Add/linkyourdatabase• Useustoinformyourdatapolicy(andadd/linkyourpolicy)

• Makeacollectionorrecommendationforyourgroup/society

https://biosharing.org@biosharing