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Alan Ruttenberg!
Neuroinformatics 2009!
ASeman(cWebforNeuroscience?
Whatcouldthatmean?
AlanRu(enbergScienceCommons
h(p://neurocommons.org/
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Alan Ruttenberg!
Neuroinformatics 2009!
ScienceCommons • ScienceCommonsisaprojectofCrea(veCommons
• Crea-veCommonsprovidesfreetoolsthatletauthors,scien-sts,ar-sts,andeducatorseasilymarktheircrea-veworkwiththefreedomstheywantittocarry
• 140,000,000objectsontheWebunderCClicensesin40+countries
• 800+peerreviewedjournalscarryCClicensing,includingPublicLibraryofScience
• ScienceCommonsspecializesCCtoscience
• Forconsumersofknowledge:makeiteasytouseandreuseinforma-onandincreasechancesfordiscovery
• Forprovidersofknowledge:providelegalcertaintyandautomatedaHribu-onandtracking
• Forfunders:improvereturnoninvestmentbyencouragingandenablingreuse
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Alan Ruttenberg!
Neuroinformatics 2009!
Goalsofmytalk
• Giveyouasenseforwhatismeanby“Seman-cWeb”
• Showglimpsesofwhatweareaimingfor
• CutandpasteontheSeman-cWebforScience• SPARQLforspecificanswerstopreciseques-ons
• Introducethewhy,whatandhowofOntology
• Talkaboutthefuture
– Whereweareheading
– owyoucanpar-cipate.
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Alan Ruttenberg!
Neuroinformatics 2009!
TheSeman-cWebinaNutshell
• AddstoWebstandardsandprac(cesencouraging
• Unambiguousnamesforthings,classes,andrela-onships
• Wellorganizedanddocumentedinontologies
• Withdataexpressedusinguniformknowledgerepresenta-onlanguages
• Toenablecomputa-onallyassistedexploita-onof
informa-on
• Thatcanbeeasilyintegratedfromdifferentsources
• Bothwithinandacrosspublicandorganiza-onalboundaries
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Alan Ruttenberg!
Neuroinformatics 2009!
WhyshouldyouwantaSeman-cWeb?
• Providesopportuni-esforclearercommunica-onofresearchresults
• Encouragessepara-onofconcernsandpar-cipa-oninresearchbyexpertsineachaspectofmul-facetedwork
• Encouragesnetworkeffects–surprisesofcombiningresources,invi-ngexperiment
• Presentsopportunityforefficienciesatglobalscales.
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Alan Ruttenberg!
Neuroinformatics 2009!
Copy/Paste on the Semantic Web for Science
Allen Brain Institute ServersJavascript
SPARQLAJAX
Q u e r y
U R L
http://www.brainmap.org://….0205032816_B.aff/TileGroup3/1-0-1.jpg
GoogleMaps
API
http://sparql.neurocommons.org/map/#Kcnip3@2850,Kcnd1@2800!
Neurocommons Servers
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Alan Ruttenberg!
Neuroinformatics 2009!
BIRN:“viewedsource”,useourcodeintheirownapplica-ons
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Alan Ruttenberg!
Neuroinformatics 2009!
Specificanswerstopreciseques-ons
Signaltransduc-onpathwaysareconsideredtoberichin“druggable”targetsproteinsthatmightrespondto
chemicaltherapyCA1PyramidalNeuronsareknowntobepar-cularlydamagedinAlzheimer’sdisease.
Cas-ngawidenet,canwefindcandidategenesknowntobeinvolvedinsignal
transduc-onandac-veinPyramidalNeurons?
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Alan Ruttenberg!
Neuroinformatics 2009!
Google:223,000results
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Alan Ruttenberg!
Neuroinformatics 2009!
Pubmed:2800results
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Alan Ruttenberg!
Neuroinformatics 2009!
ASPARQLqueryforprocessesinvolved
inpyramidalneuronsprefixgo:<hHp://purl.org/obo/owl/GO#>prefixrdfs:<hHp://www.w3.org/2000/01/rdfschema#>prefixowl:<hHp://www.w3.org/2002/07/owl#>prefixmesh:<hHp://purl.org/commons/record/mesh/>prefixsc:<hHp://purl.org/science/owl/sciencecommons/>prefixro:<hHp://www.obofoundry.org/ro/ro.owl#>select?gene_name?process_namewhere{?pubmed_record?pmesh:D017966.?ar-clesc:iden-fied_by_pmid?pubmed_record.?gene_recordsc:describes_gene_or_gene_product_men-oned_by?ar-cle.?proteinrdfs:subClassOf?restric-on.?restric-onowl:onPropertyro:has_func-on.?restric-onowl:someValuesFrom?restric-on2.?restric-on2owl:onPropertyro:realized_as.?restric-on2owl:someValuesFrom?process.{{?processro:part_ofgo:GO_0007166}union{?processrdfs:subClassOfgo:GO_0007166}}
?proteinrdfs:subClassOf?parent.?parentowl:equivalentClass?restric-on3.?restric-on3owl:onPropertysc:is_protein_gene_product_of_dna_described_by.?restric-on3owl:hasValue?gene_record.?gene_recordrdfs:label?gene_name.?processrdfs:label?processname.}
Mesh: Pyramidal Neurons
Pubmed: Journal Articles
Entrez Gene: Genes
GO: Signal Transduction
Inference required
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Alan Ruttenberg!
Neuroinformatics 2009!
ResultsDRD1,1812 adenylatecyclaseac-va-onADRB2,154 adenylatecyclaseac-va-onADRB2,154 arres-nmediateddesensi-za-onofGproteincoupledreceptorproteinsignalingpathwayDRD1IP,50632 dopaminereceptorsignalingpathwayDRD1,1812 dopaminereceptor,adenylatecyclaseac-va-ngpathwayDRD2,1813 dopaminereceptor,adenylatecyclaseinhibi-ngpathwayGRM7,2917 GproteincoupledreceptorproteinsignalingpathwayGNG3,2785 GproteincoupledreceptorproteinsignalingpathwayGNG12,55970 GproteincoupledreceptorproteinsignalingpathwayDRD2,1813 GproteincoupledreceptorproteinsignalingpathwayADRB2,154 GproteincoupledreceptorproteinsignalingpathwayCALM3,808 Gproteincoupledreceptorproteinsignalingpathway
TR2A,3356 GproteincoupledreceptorproteinsignalingpathwayDRD1,1812 Gproteinsignaling,coupledtocyclicnucleo-desecondmessengerSSTR5,6755 Gproteinsignaling,coupledtocyclicnucleo-desecondmessengerMTNR1A,4543 Gproteinsignaling,coupledtocyclicnucleo-desecondmessengerCNR2,1269 Gproteinsignaling,coupledtocyclicnucleo-desecondmessengerTR6,3362 Gproteinsignaling,coupledtocyclicnucleo-desecondmessengerGRIK2,2898 glutamatesignalingpathwayGRIN1,2902 glutamatesignalingpathwayGRIN2A,2903 glutamatesignalingpathwayGRIN2B,2904 glutamatesignalingpathwayADAM10,102 integrinmediatedsignalingpathwayGRM7,2917 nega-veregula-onofadenylatecyclaseac-vityLRP1,4035 nega-veregula-onofWntreceptorsignalingpathway
ADAM10,102 NotchreceptorprocessingASCL1,429 NotchsignalingpathwayTR2A,3356 serotoninreceptorsignalingpathwayADRB2,154 transmembranereceptorproteintyrosinekinaseac-va-on(dimeriza-on)PTPRG,5793 transmembranereceptorproteintyrosinekinasesignalingpathwayEPA4,2043 transmembranereceptorproteintyrosinekinasesignalingpathwayNRTN,4902 transmembranereceptorproteintyrosinekinasesignalingpathwayCTNND1,1500 Wntreceptorsignalingpathway
Many of the genes are indeed related toAlzheimerʼs Disease through gammasecretase (presenilin) activity!
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Alan Ruttenberg!
Neuroinformatics 2009!
• /sparql/?query=PREFIX%20owl%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23%3E%0APREFIX%20go%3A%20%3Chttp%3A%2F%2Fpurl.org%2Fobo%2Fowl%2FGO%23%3E%0APREFIX%20obo%3A %20%3Chttp%3A%2F%2Fwww.geneontology.org%2Fformats%2FoboInOwl%23%3E%0APREFIX%20rdfs%3A%20%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0A%0Aselect%20%20%3Fname%20%20%3Fclass%20%3Fdefinition%0Afrom%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2F20070416%3E%0Awhere%0A%7B%20%20%20graph%20%3Chttp%3A%2F%2Fpurl.org%2Fcommons%2Fhcls%2F20070416%2Fclassrelations%3E%0A%20%20%20%20%20%7B%3Fclass%20rdfs%3AsubClassOf%20go%3AGO_0008150%7D%0A %20%20%20%20%3Fclass%20rdfs%3Alabel%20%3Fname.%0A %20%20%20%20%3Fclass%20obo%3AhasDefinition%20%3Fdef.%0A %20%20%20%20%3Fdef%20rdfs%3Alabel%20%3Fdefinition%20%0A %20%20%20%20filter(regex(%3Fname%2C%22%5BDd%5Dendrite%22))%0A %7D%0A !SosomeoneelsecanbuildsomethingbeHer
ButanswersarealsoavailablebyaTTP“GET”
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Alan Ruttenberg!
Neuroinformatics 2009!
Useinterfacetoolkits–e.g.Exhibitarebeing
builttoacceptRDF/SPARQL
Credit: Eric Neumann
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Alan Ruttenberg!
Neuroinformatics 2009!
Wearealwaysaskingques-ons• Forwhatneurologicaldisordersarecelllinesavailable?• ForParkinsonsdisease,what-ssueandcelllinesareavailable?
• Givemeinforma-ononthereceptorsandchannelsexpressedincor-calneurons
• Whatchemicalagentscanbeusedvisualizingthenervous
system?
Aques-onIwasaskedCreate a system that will let us prioritize an expected 2000 siRNA hitsaccording to whether there is chemical matter for studying them, e.g. validated
antibodies, since we can only follow up on 600.
We know how to use Semantic Web technology to answer thesekinds of questions
(but there is no free lunch)
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Alan Ruttenberg!
Neuroinformatics 2009!
Amomentinthelifeofanontologist:
Untanglingtermsthatmixupfunc-onandmaterial
• Ligand
• NeurotransmiHer• ormone
• Pep-de
Lookingforpep<des?
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Alan Ruttenberg!
Neuroinformatics 2009!
Refactoringtomaximizeconnec-ons• Pep<deReceptorLigandApep(dethathasa
func-onwhichmakesitabletobindtoareceptor• Pep<deNeurotransmi(erApep(deexpressedina
neuronthathasafunc-onwhichmakesitabletoregulateanotherneuron• Pep<deHormoneApep(dethatproducedinone
organandhavinganregulatoryeffectinanotherorgan.
• Pep$deA“short”polymerofaminoacidsLookingforpep<des?
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Alan Ruttenberg!
Neuroinformatics 2009!
Pep-desfromCEBI
ChemicalEn--esofBiologicalInterest
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Alan Ruttenberg!
Neuroinformatics 2009!
HormoneAc<vity from
GOMolecularFunc-on
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Alan Ruttenberg!
Neuroinformatics 2009!
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Alan Ruttenberg!
Neuroinformatics 2009!
FromEnglishtoOWL• ALLinstancesofPep$deHormoneareaninstanceofPep$de
thathas_roleSOME instanceofHormoneAc$vity
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Alan Ruttenberg!Neuroinformatics 2009
!
chebi:25905=<hGp://purl.org/obo/owl/CHEBI#CHEBI_25905>
From English to OWL
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Alan Ruttenberg!Neuroinformatics 2009
!
EachURIprovidesawaytoaccessusefulinforma-onforpeople
…andmachines
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Alan Ruttenberg!Neuroinformatics 2009
!
<?xml version="1.0" encoding="UTF-8"?><?xml-stylesheet type="text/xsl" href="http://ashby.csail.mit.edu/cgi-bin/obiterm.xsl?ref=OBI_0000225"?><owl:Class rdf:about="&obo;OBI_0000225"><obo:OBI_0000274 rdf:datatype="&xsd;string">Jennifer Fostel</obo:OBI_0000274><obo:OBI_0000275 rdf:datatype="&xsd;string">site is a material (building) having the role site</obo:OBI_0000275><obo:OBI_0000275 rdf:datatype="&xsd;string">solution1: is a physical location, should maybe go under processual
context, and then be used in conjunction with the located relation</obo:OBI_0000275><obo:OBI_0000275 rdf:datatype="&xsd;string">solution2: site is related to trial used located_in relation –
site can bear the role</obo:OBI_0000275><obo:OBI_0000281 rdf:resource="&obo;OBI_0000320"/>
<obo:OBI_0000287 rdf:datatype="&xsd;string">A field, a laboratory, a medical institute, a pharmaceutical company</obo:OBI_0000287><obo:OBI_0000288 rdf:datatype="&xsd;string">Investigation site</obo:OBI_0000288><obo:OBI_0000291 rdf:datatype="&xsd;string">Investigation site is a role born by a site or material realized in an investigation
which islocated at the investigation site</obo:OBI_0000291>
<dc:creator rdf:resource="&obo;obi/project"/><rdfs:isDefinedBy rdf:resource="&obo;obi.owl"/><rdfs:label rdf:datatype="&xsd;string">investigation site role</rdfs:label><rdfs:subClassOf rdf:resource="http://www.ifomis.org/bfo/1.1/snap#Role"/>
</owl:Class><doap:Project rdf:about="&obo;obi/project"><doap:browse rdf:resource="http://obi.svn.sourceforge.net/viewvc/obi/"/>
<doap:bug-database rdf:resource="http://sourceforge.net/tracker/?group_id=177891&atid=886178"/><doap:homepage rdf:resource="http://obi.sourceforge.net/"/><doap:mailing-list rdf:resource="mailto:[email protected] "/><doap:release rdf:resource="&obo;obi/version-2008-03-10"/><doap:repository rdf:resource="http://obi.svn.sourceforge.net/svnroot/obi/"/><doap:wiki rdf:resource="https://wiki.cbil.upenn.edu/obiwiki/index.php?title=HomePage"/>
</doap:Project><doap:Version rdf:about="&obo;obi/version-2008-03-10">
<doap:file-release rdf:resource="http://purl.org/obo/2008-03-10/obi.owl"/><doap:file-release rdf:resource="http://purl.org/obo/obi.owl"/>
</doap:Version>
</rdf:RDF>
What’sreallyathHp://purl.org/obo/OBI_0000225
Don’treadthis(butmachinesloveit!)
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Alan Ruttenberg!Neuroinformatics 2009
!
NeuronDB• Startedwithhomegrownontology.Problem:owtolink
withanythingelse
• Eg.Nolinkstoevidence,“receptors”versusproteinswithreceptorac-vity(likeGOA)
• Process:fixingOWL,understandingGOandmakingrepresenta-oncompa-ble
• Augmentedwhatwasinontology,e.g.provenance
• EndedwithsomethingthatlinkedwithGOFunc-onand,
viathat,therestoftheNeurocommons• Takeaway:avingyourownontology:Nice.Beingableto
connectyourdatatotherestofknowledge:Priceless!
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Alan Ruttenberg! Neuroinformatics 2009!
Inconsistency!
• OnceNeuronDBwasrepresentedusingthismethodology,andanOWLreasonerwasrun,itdeclaredtheontologyinconsistent
• Problem:Therearecontradictoryasser-onsaboutwhetherapar-cularioniccurrentoccursinapar-cularcelltype.
• Whattodo?
• InconsistencyisNOTacceptable,butthiscanberesolvedbythinkingaboutabitaboutwhatthe
resourcesistryingtoaccomplish.
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Alan Ruttenberg! Neuroinformatics 2009!
ThreeWaysofRepresen-ng
Scien-ficKnowledge
• Recordlevel :Representdatabaserecords.Inconsistentiftwosourcesdisagreeaboutcontentsofafield.
• Statementlevel :Representwhatresearcherssay.Inconsistentiftwopeopledisagreeaboutwhatapapersaid
• Domainlevel :OBOFoundryapproach.Representyourbestunderstandingofourconsensusofwhatexists.Inconsistentiffactscontradict.
Weneedallthree(butmakeclearwhichiswhich)
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Alan Ruttenberg! Neuroinformatics 2009!
owtoBuildConsensusaroundOntology
• Understandwhattermsmeanbyrela-ngthem(tracingthem)toelementsinreality.Orsaywhenyouarenot.
• Knowwhattheinstancesare
•
Askyourselfhowinstancesarerelatedtoeachother• Defineclassesasgroupsofinstancesthathaveshared
proper-es
• Documentandorganizethisknowledgeinawaythat
canbemanagedinadistributedmanner• TheproductofthiseffortisyourOntology
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Alan Ruttenberg! Neuroinformatics 2009!
OBOFoundryWhat
AsubsetofOBOontologieswhosedevelopershaveagreedinadvancetoacceptacommonsetofprinciplesreflec-ngbestprac-ceinontologydevelopment
designedtoensure§ -ghtconnec-ontothebiomedicalbasicsciences
§ compa-bility
§ interoperability,commonrela-ons
§ formalrobustness
§ supportforlogicbasedreasoning
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Alan Ruttenberg! Neuroinformatics 2009!
OBOFoundryow
• Collabora-on
• Peerreview
• Designprinciplesevolveaswelearn• AHribu-onatalllevels–Duecredit
• Metricstomeasureprogressand
effec-veness
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Alan Ruttenberg! Neuroinformatics 2009!
SelectedOBOOntologies• GeneOntology(GO)
• Rela-onOntology(RO)
• ChemicalEn--esofBiologicalInterest(CheBI)
• PhenotypeOntology(PATO)
• OntologyforBiomedicalInves-ga-ons(OBI)• CellOntology(CL)
• ProteinOntology(PRO)
• Founda-onalModelofAnatomy(FMA)
•
SequenceOntology(SO)• SubcellularAnatomy(SAO)
• Informa-onAr-fact(IA0)
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Alan Ruttenberg! Neuroinformatics 2009!
INCFProgramforOntologyofNeural
Structures(PONS)• Ini-algoals:Commonsetofiden<fiers,terms,
anddefini<ons,iden-fyingelementsof
neuroanatomicstructureandtypesofneurons• Threetaskforces:
– StructuralLexicon
– NeuronalRegistry
– Representa-onandDeployment
• AlsoliasonwithDigitalAtlasingtaskforce
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Alan Ruttenberg! Neuroinformatics 2009!
TheNeuroCommons
• Builtonopenresources:publicdomain,opendatabases,openliterature
• Encodedusingopenarchitecturesandtechnicalstandards–OWL,SPARQL,OBO
• Promo-nglegalpredictabilityandcertainty• Licensesthatareeasytouseandunderstand
• Thatimposethelowestpossibletransac-oncostsonusers
• Thesupportthefreedomtointegrate
• Scou-ngoutissuestobeimportantinbuildingaseman-cwebforneuroscience
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Alan Ruttenberg! Neuroinformatics 2009!
ElementsofthewebofNeuroscience–
Veryconnected!• structure,connec-vity• physiology,pathophysiology• func-on,malfunc-on
• molecularmechanism• disease,injury• experimentalmaterialsandmethod• pa-ents,clinicaldiagnosis,devices,treatments
• studies,measurements,images• publica-ons• models,simula-ons,hypotheses,predic-ons
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Alan Ruttenberg! Neuroinformatics 2009!
ChallengesonthewaytotheSeman-c
WebforNeuroscience• Neuroscience–largedomain,rapidlyadvance
• Buildingquality,durable,maintainable
ontologiesisdifficult–anotherdevelopingscience
• Sociology–therearebarrierstosharing–we
needtounderstandthemandlearnwaysto
overcomethem
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Alan Ruttenberg! Neuroinformatics 2009!
OBOFoundryWhat
AsubsetofOBOontologieswhosedevelopershaveagreedinadvancetoacceptacommonsetofprinciplesreflec-ngbestprac-ceinontologydevelopmentdesignedtoensure
§ -ghtconnec-ontothebiomedicalbasicsciences
§ compa-bility
§ interoperability,commonrela-ons
§ formalrobustness
§ supportforlogicbasedreasoning
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Alan Ruttenberg! Neuroinformatics 2009!
OBOFoundryow
• Collabora-on
• Peerreview
•
Designprinciplesevolveaswelearn• AHribu-onatalllevels–Duecredit
• Metricstomeasureprogressand
effec-veness
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Alan Ruttenberg! Neuroinformatics 2009!
SelectedOBOOntologies
• GeneOntology(GO)
• Rela-onOntology(RO)
• ChemicalEn--esofBiologicalInterest(CheBI)
•
PhenotypeOntology(PATO)• OntologyforBiomedicalInves-ga-ons(OBI)
• CellOntology(CL)
• Founda-onalModelofAnatomy(FMA)
• SequenceOntology(SO)• SubcellularAnatomy(SAO)
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Alan Ruttenberg! Neuroinformatics 2009!
Wrapup
• It’sworthaHemp-ngtoconstructaseman-cwebforneuroscience
• Seman-cwebtechnologiespresentopportuni-es
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