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


1,400recordsandgrowing

WhatisBioSharing?

Aweb-based,curated andsearchableportalthat monitorsthedevelopmentandevolution ofstandards,theiruse indatabasesandtheadoptionofbothin

datapolicies, toinformandeducatetheusercommunity.



WhatisBioSharing?

Launchedin2011,asanevolutionoftheMIBBIportal(2008-2011)ManuallycuratedCommunitydriven

Growinguserbase andvisibilityPromotingtheFAIRprinciples


alsooperatesasaWG inRunat isalsoan Resource that

TheBioSharing community


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


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


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