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BiOnIC:ACatalogofUserInteractionswithBiomedicalOntologies
16thInterna+onalSeman+cWebConference(ISWC)Vienna,21st-25thOctober2017
MAU L I K K AMDA R , S IMON WA L K , T A N I A T U DO R A C H E , MA R K MU S E N
StanfordCenterforBiomedicalInforma:[email protected]
Benefitsofanalyzinguserinterac+ons
Ø OntologyEngineers:v Iden+fyexplora+onandqueryingpaVernsv Understandontologyusageandreusev Pruneunwantedclassesandrela+ons
Ø OntologyRepositoryMaintainers:v Categorizeuserbehaviorsv Developintelligentinterfacesv Providetargetedrecommenda+ons
Ø BiomedicalResearchers:v Iden+fytemporalresearchtrendsv Iden+fyfrequentlyaccessedclasses
BiOnIC:ACatalogofUserInterac+onswithBiomedicalOntologies
hVp://onto-apps.stanford.edu/bionic/datasets
hVp://bioportal.bioontology.org/
hVp://bioportal.bioontology.org/
hVp://bioportal.bioontology.org/
hVp://bioportal.bioontology.org/
hVp://bioportal.bioontology.org/
NCBO API Usage
API R
eque
sts
per M
onth
2013−O
ct
2014−J
an
2014−A
pr
2014−J
ul
2014−O
ct
2015−J
an
2015−A
pr
2015−J
ul
2015−O
ct
2016−J
an
2016−A
pr
2016−J
ul
2016−O
ct
2M8M
32M
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
NCBO Website Traffic
Occ
urre
nces
per
Mon
th
2009−J
an
2010−J
an
2011−J
an
2012−J
an
2013−J
an
2014−J
an
2015−J
an
2016−J
an
010
0K20
0K
Page RequestsUnique IP Addresses
BiOnICdatasetscrea+on
• Removingrobot/invalidrequests
• Normalizingontologyiden+fiersandclassIRIs
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
• January2015version.• Ontologiesshouldhave
classesthatarereusedbyothersORreuseclassesfromotherontologies.
• Ontologiesshouldhaveminimumof10uniqueusersviaWebUIandAPI
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
ClassSta:s:csDatasets
Foreachclassineachontology:• AccessAGributes:
o TotalIPRequests(WebUI/API)o UniqueIPRequests(WebUI/API)
• ReuseAGributes:o Numberofontologiesreusingaclass
• StructuralAGributes:o Numberofparent/child/siblingclasseso Depthfromontologyroot
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
ClassDepth->
2a
1
3a 4a
4b
4c2b
3b
3c
1’
2a’
2b’
2c’
3a’
3b’
3c’
2a’ 1’ 2b’ 3b’
2a 3a 4a 3a1
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
UserInterac:onSequencesDatasets
Ontology1
Ontology2
FilteringAccessLogs
FilteringOntologies
Compu+ngClassCounts
Compu+ngSequences
AnonymizingData
BiOnICdatasetscrea+on
Anonymiza:onSteps
• IPaddressesanonymizedusinguniqueSHA-224hash-encodeduseriden+fiersgeneratedfrom“user_<RandomString>_<Random_Integer>”.• e.g.39fd4e6d569a034973g61bb392a694d4eabe1ef98c43ee68ca2fc86
• AbsoluteTime-stampsconvertedtorela+ve+me-stamps,withrespecttofirstinterac+onwithBioPortalrepository.• e.g.0,2757,2786,3586,3618,3803,3959,4047,5111(s),…
BiOnICschematomodelsta+s+csandsequencesdata
countStat
bionic:CountStat
bionic:ReuseCount- reuseType- reusingOntologies
bionic:RequestCount- accessType- year- totalUsers- uniqueUsers
prov:Agent bionic:Sequence- accessType- totalTime- uniqueClasses
bionic:SeqEn:ty- rela6veTimestamp
bionic:Ontology- skos:prefLabel- totalClasses- maxDepth
owl:Class-skos:prefLabel
skos:Collec:on skos:Concept
begin
end
nextEn6ty
class
class
requests
skos:member
bionic:SeqDataset- accessType
bionic:StatDatasetdcat:Dataset
sequence
classInfo
ontology
ontology
bionic:ClassInfo- siblings- directParents- directChildren- classDepth
class
subClassOf
ontology
SKOS,PROVandDCATstandardsarereusedintheBiOnICschema.
hVp://onto-apps.stanford.edu/bionic/datasets
BiOnICdatasets
hVp://onto-apps.stanford.edu/bionic/datasets
BiOnICdatasets
hVp://www.rdjdt.org/
hVp://onto-apps.stanford.edu/bionic/datasets
BiOnICdatasets
hVp://www.rdjdt.org/
SPARQLTriplestore/TriplePaGern
FragmentServer
hVp://onto-apps.stanford.edu/bionic/datasets
BiOnICdatasets
hVp://www.rdjdt.org/
SPARQLTriplestore/TriplePaGern
FragmentServer
BioPortalSPARQLEndpoint
Characteris+csoftheBiOnICCatalog
• WebUIAccess:5.4Mclassrequests,1Muniqueagents• APIAccess:67.2Mclassrequests,205Kuniqueagents• 255biomedicalontologies
VisIOn(VisualizingOntologyInterac+ons)WebApplica+on
hVp://onto-apps.stanford.edu/vision
VisIOn(VisualizingOntologyInterac+ons)WebApplica+on
hVp://onto-apps.stanford.edu/vision
VisIOn(VisualizingOntologyInterac+ons)WebApplica+on
hVp://onto-apps.stanford.edu/vision
Applica+onsofBiOnICandVisIOn
TemporalinfluencesinbrowsingandqueryingFisher’sexacttestwithFDR:Certainclasses(e.g.Ebolavirus)orsetsofclassesarebrowsedorqueriedsignificantlymore,whencomparedbetweendifferent+meperiods.
2016
2015
InterfaceinfluencesinbrowsingandqueryingNum
berofUniqu
eAPIUsers(LogScale)
NumberofUniqueWebUIUsers(LogScale)
1000
10
100
10 100 1000
1
1
Certainclassesbrowsedorqueriedsignificantlymore.
InterfaceinfluencesinbrowsingandqueryingNum
berofUniqu
eAPIUsers(LogScale)
NumberofUniqueWebUIUsers(LogScale)
1000
10
100
10 100 1000
FemaleReproduc:ve
System
1
1
Certainclassesbrowsedorqueriedsignificantlymore.
Dermis
InterfaceinfluencesinbrowsingandqueryingDysmorphicSyndrome
Nightblindness
Num
berofUniqu
eAPIUsers(LogScale)
NumberofUniqueWebUIUsers(LogScale)
1000
10
100
10 100 1000
FemaleReproduc:ve
System
1
1
Certainclassesbrowsedorqueriedsignificantlymore.
Dermis
Explora+onandQueryingbehavioralpaVerns
• Certainclassesinthelowerlevelsoftheontologicalhierarchyarerarelybrowsedandqueried–thismaybeanar+factoftheindentedtreevisualiza+on.
• Moretriangularpolygons(1parent->2childrenclasses,or2parents->1childclass)observedinWebUIAccesspolygonduetoindentedtreevisualiza+on.
ModelinguserbehaviorsthroughMarkovChains
Walk,etal.HowUsersExploreOntologiesontheWeb:AStudyofNCBO'sBioPortalUsageLogs.WWW17
Novelresearchdirec+onsmaybeenabledthroughtheBiOnICandVisIOnresources
• Categorizeuserbrowsingbehaviorsbyincorpora+ngthestructuralfeaturesoftheontologyclasses.
• Developpersonalizeduserinterfacesforontologynaviga+on,whichtakeintoaccounttheusertypeandthepredic+onsofthenextclassthatauserislikelytoaccess.
• Developadvancedmethodsforontologysummariza+onandmodulariza+on,usingBiOnICdatasetsasfeatures.
…
Acknowledgments
MusenLab,Stanford
BMIPhDProgram,Stanford
USNIHGrants
U54-HG004028
GM086587
[email protected]://onto-apps.stanford.edu/bionichVp://onto-apps.stanford.edu/vision