Download SSBD: a database of quantitative data and

SSBD: a database of quantitative data and microscopy images
of biological dynamics
h"p://ssbd.qbic.riken.jp/
Yukako Tohsato, Kenneth H.L. Ho, Koji Kyoda, Shuichi Onami
RIKEN Quantitative Biology Center, Kobe, Japan
Motivation
SSBD 2.0: collect/share microscopy images
Recentprogressinbioimageinforma9csandmathema9calmodelingproducedalargeamountof
quan9ta9vedataonspa9otemporaldynamicsofvariouskindsofbiologicalobjects.
Microscopyimageincellanddevelopmentalbiology
Microscopyimagesaremanaged
byusingOMEROplacorm
Molecule
Protein
Virus
Bacteria
Cell
C.elegans
internallyinSSBD.SSBD2.0
beginstostoreandshare
1nm
10nm
100nm
1µm
10µm 100µm 1mm
microscopyimagesthathavenot
two-photon
STED
TEM
beenimageprocessed.Wefocus
confocal
on,butnotlimitedto,9me-lapse
SEM
TIRF
PALM
imagedatathatareobtainedby
usingstate-of-the-artsimaging
systems.Theseimagesprovide
vitalbiologicalresourcesand
Superresolu9on
allowotherstoreuseandto Electronmicroscopy
extractinteres9ngfeatures.
(BrandnerandWithers2010,CIL:12415,41488,38651,36148,41000,35161,36572(PD))
WedevelopSSBDtoprovide
•  aninvaluableresourceforphenotypedata-drivenanalysis,and
•  anovelopportunitytodevelopnewcomputa9onalmethods.
Exampleofquan9ta9vebiologicaldynamicsdata
Datafrombioimageinforma9cs
Datafromcomputersimula9on
Thereisaneedtobringthesedatacentrallyinanopenandunifieddataformat.Wedeveloped
BDML(BiologicalDynamicsMarkupLanguage;Kyodaetal.,BioinformaKcs,2015)andSSBD
(SystemsScienceofBiologicalDynamicsdatabase),withthesupportfromNa9onalBioscience
DatabaseCenterofJapan.SSBDcollectsandsharesquan9ta9vedataandmicroscopyimages.Italso
includessoLwaretoolsforvisualiza9onandanalysis.
ConceptofSSBD
Microscopyimages
Quan9ta9vebiologicaldynamicsdata
WeprovideOpenSSBD,open-sourceversionofSSBDformanagingquan9ta9vedata,inGitHuband
Dockerwebsites.Itenableseachindividualscien9storresearchgrouptosetuptheirowndatabaseon
theirownservertoindependentlystoreandsharetheirquan9ta9vedata.
SoLwaretoolsfordataanalysis
h"p://ssbd.qbic.riken.jp
Collect
Rawformat
BDMLformat
Microscopyimages Quan9ta9vedata
h"ps://github.com/openssbd/
SSBDandOpenSSBDstructures
SSBD
OpenSSBDincludesalltheessen9al
func9onsofSSBD,e.g.,asimplekeyword
searchfunc9on,RESTAPIdirectaccessto
quan9ta9vedata,andasimplebrowserbasedviewerfordatavisualiza9on.Userswill
needtoinstallOMEROseparately.
BDML-compa9ble
SoLware
OpenSSBD: Open-source software platform
OpenSSBD
Webserviceforclients
Search&Download
RDF formatted metadata
Database
WeprovideRDF(ResourceDescrip9onFramework)formaeedmetadataofquan9ta9vedataand
microscopyimagesstoredinSSBD.
Meta-informa9onof
quan9ta9vedata
h"p://metadb.riken.jp/db/SSBD
h"p://integbio.jp/rdf/
Original
files
Microscopyimages
Djangoframework
Database
So4ware
tools
BDML
files
QuanAtaAvedata
(Iietal.2012) (Kelleretal.2010)(Baoetal.2006)
Data resource update
Listofnamespace
Namespaces
rdf:<hep://www.w3.org/1999/02/22-rdf-syntax-ns#>
rdfs:<hep://www.w3.org/2000/01/rdf-schema#>
owl:<hep://www.w3.org/2002/07/owl#>
xsd:<hep://www.w3.org/2001/XMLSchema#>
dc:<hep://purl.org/dc/elements/1.1/>
dct:<hep://purl.org/dc/terms/>
foaf:<hep://xmlns.com/foaf/0.1/>
vcard:<hep://www.w3.org/2006/vcard/ns#>
ma-ont:<hep://www.w3.org/ns/ma-ont#>
bqbiol:<hep://biomodels.net/biology-qualifiers/>
sio:<hep://seman9cscience.org/resource/>
dcterms:<hep://purl.org/dc/terms/>
obo:<hep://purl.obolibrary.org/obo/>
ome:<heps://www.openmicroscopy.org/Schemas/Documenta9on/Generated/
OME-2015-01/ome_xsd.html#>
ssbd:<hep://metadb.riken.jp/db/SSBD/>
SSBDstoresquan9ta9vedataandmicroscopyimagesrangingfrommoleculestocellstoorganisms.
ListofavailabledataresourcesinSSBD
Species
ExamplesofSPARQLquery
PREFIXssbd:<hep://metadb.riken.jp/db/SSBD/>
PREFIXobo:<hep://purl.obolibrary.org/obo/>
PREFIXbqbiol:<hep://biomodels.net/biology-qualifiers/>
#Searchingforresourcesrelatedwithmouse
SELECT?s?desc　FROM　<hep://metadb.riken.jp/db/SSBD>　WHERE　{
?sobo:RO_0002162obo:NCBITaxon_10090.#mouse
?sssbd:descrip9on?desc.
}
#Searchingforexperimentalresourcesrelatedwithpronuclearmigra9oninC.elegans
SELECT?s?desc　FROM　<hep://metadb.riken.jp/db/SSBD>　WHERE　{
?sobo:RO_0002162obo:NCBITaxon_6239.#C.elegans
?sbqbiol:isVersionOfobo:GO_0035046.#pronuclearmigra9on
?sssbd:basedOn?textFILTERregex(?text,”measurement","i”
?sssbd:descrip9on?desc.
}
Meta-informa9onof
microscopyimages
VisualizaAon
Webapplica1onserver
OMERO
Examplesofvisualiza9onofquan9ta9vedata
Share
RESTAPI
Type
BasedOn
#BDML
#entries
#images
singlemolecule
Simula9on
Arjunan&Tomita2010
1
721
0
D.discoideum
singlemolecule
Experiment
Komatsuzakietal.2014
1
987
1,800
D.discoideum
singlemolecule
Experiment/Simula9on Watabeetal.2015
0
0
20
C.elegans
nucleus
Experiment
Baoetal.2006
2
24,747
0
C.elegans
nucleus
Experiment
Kyodaetal.2013
186
75,955
180x66x186
C.elegans
nucleus
Experiment
Toyoshimaetal.
14
125,426
C.elegans
pronucleus/nucleus
Experiment
Tohsatoetal.
1,582
2,430,536
C.elegans
nucleus
Experiment
Kyodaetal.
1,147
C.elegans
pronucleus/microtubule Simula9on
Kimura&Onami2005
100
2,400,100
0
C.elegans
locomo9on
Experiment
Croninetal.2005
11
15,822
0
D.melanogaster nucleus
Experiment
Kelleretal.2010
2
5,111,828
0
D.rerio
nucleus
Experiment
Kelleretal.2008
7
56,584,840
0
R.norvegicus
singlemolecule
Experiment/Simula9on Watabeetal.2015
0
0
75
M.musculus
nucleus
Experiment
Basharetal.2012
1
2,054
2,800
M.musculus
geneexpression
Experiment
Harimaetal.2013
2
146
2
M.musculus
geneexpression
Experiment
Masumotoetal.2010
8
48
0
14
4,512
360x66x1147
■ newdata,□currentlyavailable,■plannedrelease
IntotalRDFdataconsistof
•  18,319triples(dataen99esofsubject-predicate-objectform),
•  14classes,and
•  33proper9es.
OntologyusedintheRDFdataareasfollows:
• 
• 
• 
• 
• 
Reference
E.coli
NCBITaxon
GO:biologicalprocess
GO:cellularcomponent
OntologyforMediaResources1.0
OME.xml
Examplesofquan9ta9vedataandtheirvisualiza9on
SinglemoleculedynamicsinE.coli(Arjunan&Tomita2010)
NucleardivisiondynamicsinC.elegans(Kyodaetal.2013)
NucleardivisiondynamicsinC.elegans(Baoetal.2006)
NucleardivisiondynamicsinD.melanogaster(Kelleretal.2010)
Ref.:KojiKyoda,YukakoTohsato,KennethH.L.Ho,ShuichiOnami(2015)
BiologicalDynamicsMarkupLanguage(BDML):anopenformatforrepresen9ng
quan9ta9vebiologicaldynamicsdata.Bioinforma9cs31(7):1044-1052.