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