a semantic web for neuroscience what could that mean

8/3/2019 A Semantic Web for Neuroscience What Could That Mean

http://slidepdf.com/reader/full/a-semantic-web-for-neuroscience-what-could-that-mean 1/39

Alan Ruttenberg!

Neuroinformatics 2009!

ASeman(cWebforNeuroscience?

Whatcouldthatmean?

AlanRu(enbergScienceCommons

h(p://neurocommons.org/



Alan Ruttenberg!


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



Alan Ruttenberg!


Goalsofmytalk

• Giveyouasenseforwhatismeanby“Seman-cWeb”

• Showglimpsesofwhatweareaimingfor

• CutandpasteontheSeman-cWebforScience• SPARQLforspecificanswerstopreciseques-ons

• Introducethewhy,whatandhowofOntology

• Talkaboutthefuture

– Whereweareheading

– owyoucanpar-cipate.



Alan Ruttenberg!


TheSeman-cWebinaNutshell

• AddstoWebstandardsandprac(cesencouraging

• Unambiguousnamesforthings,classes,andrela-onships

• Wellorganizedanddocumentedinontologies

• Withdataexpressedusinguniformknowledgerepresenta-onlanguages

• Toenablecomputa-onallyassistedexploita-onof

informa-on

• Thatcanbeeasilyintegratedfromdifferentsources

• Bothwithinandacrosspublicandorganiza-onalboundaries



Alan Ruttenberg!


WhyshouldyouwantaSeman-cWeb?

• Providesopportuni-esforclearercommunica-onofresearchresults

• Encouragessepara-onofconcernsandpar-cipa-oninresearchbyexpertsineachaspectofmul-facetedwork

• Encouragesnetworkeffects–surprisesofcombiningresources,invi-ngexperiment

• Presentsopportunityforefficienciesatglobalscales.



Alan Ruttenberg!


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



Alan Ruttenberg!


BIRN:“viewedsource”,useourcodeintheirownapplica-ons



Alan Ruttenberg!


Specificanswerstopreciseques-ons

Signaltransduc-onpathwaysareconsideredtoberichin“druggable”targetsproteinsthatmightrespondto

chemicaltherapyCA1PyramidalNeuronsareknowntobepar-cularlydamagedinAlzheimer’sdisease.

Cas-ngawidenet,canwefindcandidategenesknowntobeinvolvedinsignal

transduc-onandac-veinPyramidalNeurons?



Alan Ruttenberg!


Google:223,000results



Alan Ruttenberg!


Pubmed:2800results



Alan Ruttenberg!


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



Alan Ruttenberg!


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!



Alan Ruttenberg!


• /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”



Alan Ruttenberg!


Useinterfacetoolkits–e.g.Exhibitarebeing

builttoacceptRDF/SPARQL

Credit: Eric Neumann



Alan Ruttenberg!


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)



Alan Ruttenberg!


Amomentinthelifeofanontologist:

Untanglingtermsthatmixupfunc-onandmaterial

• Ligand

• NeurotransmiHer• ormone

• Pep-de

Lookingforpep<des?



Alan Ruttenberg!


Refactoringtomaximizeconnec-ons• Pep<deReceptorLigandApep(dethathasa

func-onwhichmakesitabletobindtoareceptor• Pep<deNeurotransmi(erApep(deexpressedina

neuronthathasafunc-onwhichmakesitabletoregulateanotherneuron• Pep<deHormoneApep(dethatproducedinone

organandhavinganregulatoryeffectinanotherorgan.

• Pep$deA“short”polymerofaminoacidsLookingforpep<des?



Alan Ruttenberg!


Pep-desfromCEBI

ChemicalEn--esofBiologicalInterest



Alan Ruttenberg!


HormoneAc<vity from

GOMolecularFunc-on



Alan Ruttenberg!




Alan Ruttenberg!


FromEnglishtoOWL• ALLinstancesofPep$deHormoneareaninstanceofPep$de

thathas_roleSOME instanceofHormoneAc$vity



Alan Ruttenberg!Neuroinformatics 2009

!

chebi:25905=<hGp://purl.org/obo/owl/CHEBI#CHEBI_25905>

From English to OWL




!

EachURIprovidesawaytoaccessusefulinforma-onforpeople

…andmachines




!

<?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!)




!

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!



Alan Ruttenberg! Neuroinformatics 2009!

Inconsistency!

• OnceNeuronDBwasrepresentedusingthismethodology,andanOWLreasonerwasrun,itdeclaredtheontologyinconsistent

• Problem:Therearecontradictoryasser-onsaboutwhetherapar-cularioniccurrentoccursinapar-cularcelltype.

• Whattodo?

• InconsistencyisNOTacceptable,butthiscanberesolvedbythinkingaboutabitaboutwhatthe

resourcesistryingtoaccomplish.




ThreeWaysofRepresen-ng

Scien-ficKnowledge

• Recordlevel :Representdatabaserecords.Inconsistentiftwosourcesdisagreeaboutcontentsofafield.

• Statementlevel :Representwhatresearcherssay.Inconsistentiftwopeopledisagreeaboutwhatapapersaid

• Domainlevel :OBOFoundryapproach.Representyourbestunderstandingofourconsensusofwhatexists.Inconsistentiffactscontradict.

Weneedallthree(butmakeclearwhichiswhich)




owtoBuildConsensusaroundOntology

• Understandwhattermsmeanbyrela-ngthem(tracingthem)toelementsinreality.Orsaywhenyouarenot.

• Knowwhattheinstancesare

•

Askyourselfhowinstancesarerelatedtoeachother• Defineclassesasgroupsofinstancesthathaveshared

proper-es

• Documentandorganizethisknowledgeinawaythat

canbemanagedinadistributedmanner• TheproductofthiseffortisyourOntology




OBOFoundryWhat

AsubsetofOBOontologieswhosedevelopershaveagreedinadvancetoacceptacommonsetofprinciplesreflec-ngbestprac-ceinontologydevelopment

designedtoensure§ -ghtconnec-ontothebiomedicalbasicsciences

§ compa-bility

§ interoperability,commonrela-ons

§ formalrobustness

§ supportforlogicbasedreasoning




OBOFoundryow

• Collabora-on

• Peerreview

• Designprinciplesevolveaswelearn• AHribu-onatalllevels–Duecredit

• Metricstomeasureprogressand

effec-veness




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)




INCFProgramforOntologyofNeural

Structures(PONS)• Ini-algoals:Commonsetofiden<fiers,terms,

anddefini<ons,iden-fyingelementsof

neuroanatomicstructureandtypesofneurons• Threetaskforces:

– StructuralLexicon

– NeuronalRegistry

– Representa-onandDeployment

• AlsoliasonwithDigitalAtlasingtaskforce




TheNeuroCommons

• Builtonopenresources:publicdomain,opendatabases,openliterature

• Encodedusingopenarchitecturesandtechnicalstandards–OWL,SPARQL,OBO

• Promo-nglegalpredictabilityandcertainty• Licensesthatareeasytouseandunderstand

• Thatimposethelowestpossibletransac-oncostsonusers

• Thesupportthefreedomtointegrate

• Scou-ngoutissuestobeimportantinbuildingaseman-cwebforneuroscience




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




ChallengesonthewaytotheSeman-c

WebforNeuroscience• Neuroscience–largedomain,rapidlyadvance

• Buildingquality,durable,maintainable

ontologiesisdifficult–anotherdevelopingscience

• Sociology–therearebarrierstosharing–we

needtounderstandthemandlearnwaysto

overcomethem




OBOFoundryWhat

AsubsetofOBOontologieswhosedevelopershaveagreedinadvancetoacceptacommonsetofprinciplesreflec-ngbestprac-ceinontologydevelopmentdesignedtoensure

§ -ghtconnec-ontothebiomedicalbasicsciences

§ compa-bility

§ interoperability,commonrela-ons

§ formalrobustness

§ supportforlogicbasedreasoning




OBOFoundryow

• Collabora-on

• Peerreview

•

Designprinciplesevolveaswelearn• AHribu-onatalllevels–Duecredit

• Metricstomeasureprogressand

effec-veness




SelectedOBOOntologies

• GeneOntology(GO)

• Rela-onOntology(RO)

• ChemicalEn--esofBiologicalInterest(CheBI)

•

PhenotypeOntology(PATO)• OntologyforBiomedicalInves-ga-ons(OBI)

• CellOntology(CL)

• Founda-onalModelofAnatomy(FMA)

• SequenceOntology(SO)• SubcellularAnatomy(SAO)




Wrapup

• It’sworthaHemp-ngtoconstructaseman-cwebforneuroscience

• Seman-cwebtechnologiespresentopportuni-es

fordataintegra-onatwebscale(andcorrespondingefficiencies)• Thereisagrowingcommunityofbiologistsand

neuroscien-stsbuildingontologies,viatheOBOFoundry,PONS

• Pleasedevotesomesmallpercentageofyourthoughtstotheopportuni-esforintegra-ngyour workintothiseffort!

a semantic web for neuroscience what could that mean

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