bionic: a catalog of user interactions with biomedical ontologies

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BiOnIC: A C atalog of User I nteractions with Bi omedical On tologies 16 th Interna+onal Seman+c Web Conference (ISWC) Vienna, 21 st - 25 th October 2017 M AULIK K AMDAR , S IMON W ALK ,T ANIA T UDORACHE ,M ARK M USEN Stanford Center for Biomedical Informa:cs Research [email protected]

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Page 1: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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]

Page 2: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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

Page 3: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

BiOnIC:ACatalogofUserInterac+onswithBiomedicalOntologies

hVp://onto-apps.stanford.edu/bionic/datasets

Page 4: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

hVp://bioportal.bioontology.org/

Page 5: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

hVp://bioportal.bioontology.org/

Page 6: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

hVp://bioportal.bioontology.org/

Page 7: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

hVp://bioportal.bioontology.org/

Page 8: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

hVp://bioportal.bioontology.org/

Page 9: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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

Page 10: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

FilteringAccessLogs

FilteringOntologies

Compu+ngClassCounts

Compu+ngSequences

AnonymizingData

BiOnICdatasetscrea+on

•  January2015version.•  Ontologiesshouldhave

classesthatarereusedbyothersORreuseclassesfromotherontologies.

•  Ontologiesshouldhaveminimumof10uniqueusersviaWebUIandAPI

Page 11: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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

Page 12: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 13: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 14: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 15: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 16: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 17: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 18: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 19: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 20: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 21: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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’

Page 22: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

2a’ 1’ 2b’ 3b’

2a 3a 4a 3a1

FilteringAccessLogs

FilteringOntologies

Compu+ngClassCounts

Compu+ngSequences

AnonymizingData

BiOnICdatasetscrea+on

UserInterac:onSequencesDatasets

Ontology1

Ontology2

Page 23: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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),…

Page 24: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

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.

Page 25: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

hVp://onto-apps.stanford.edu/bionic/datasets

BiOnICdatasets

Page 26: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

hVp://onto-apps.stanford.edu/bionic/datasets

BiOnICdatasets

hVp://www.rdjdt.org/

Page 27: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

hVp://onto-apps.stanford.edu/bionic/datasets

BiOnICdatasets

hVp://www.rdjdt.org/

SPARQLTriplestore/TriplePaGern

FragmentServer

Page 28: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

hVp://onto-apps.stanford.edu/bionic/datasets

BiOnICdatasets

hVp://www.rdjdt.org/

SPARQLTriplestore/TriplePaGern

FragmentServer

BioPortalSPARQLEndpoint

Page 29: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

Characteris+csoftheBiOnICCatalog

•  WebUIAccess:5.4Mclassrequests,1Muniqueagents•  APIAccess:67.2Mclassrequests,205Kuniqueagents•  255biomedicalontologies

Page 30: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

VisIOn(VisualizingOntologyInterac+ons)WebApplica+on

hVp://onto-apps.stanford.edu/vision

Page 31: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

VisIOn(VisualizingOntologyInterac+ons)WebApplica+on

hVp://onto-apps.stanford.edu/vision

Page 32: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

VisIOn(VisualizingOntologyInterac+ons)WebApplica+on

hVp://onto-apps.stanford.edu/vision

Page 33: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

Applica+onsofBiOnICandVisIOn

Page 34: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

TemporalinfluencesinbrowsingandqueryingFisher’sexacttestwithFDR:Certainclasses(e.g.Ebolavirus)orsetsofclassesarebrowsedorqueriedsignificantlymore,whencomparedbetweendifferent+meperiods.

2016

2015

Page 35: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

InterfaceinfluencesinbrowsingandqueryingNum

berofUniqu

eAPIUsers(LogScale)

NumberofUniqueWebUIUsers(LogScale)

1000

10

100

10 100 1000

1

1

Certainclassesbrowsedorqueriedsignificantlymore.

Page 36: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

InterfaceinfluencesinbrowsingandqueryingNum

berofUniqu

eAPIUsers(LogScale)

NumberofUniqueWebUIUsers(LogScale)

1000

10

100

10 100 1000

FemaleReproduc:ve

System

1

1

Certainclassesbrowsedorqueriedsignificantlymore.

Dermis

Page 37: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

InterfaceinfluencesinbrowsingandqueryingDysmorphicSyndrome

Nightblindness

Num

berofUniqu

eAPIUsers(LogScale)

NumberofUniqueWebUIUsers(LogScale)

1000

10

100

10 100 1000

FemaleReproduc:ve

System

1

1

Certainclassesbrowsedorqueriedsignificantlymore.

Dermis

Page 38: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

Explora+onandQueryingbehavioralpaVerns

•  Certainclassesinthelowerlevelsoftheontologicalhierarchyarerarelybrowsedandqueried–thismaybeanar+factoftheindentedtreevisualiza+on.

•  Moretriangularpolygons(1parent->2childrenclasses,or2parents->1childclass)observedinWebUIAccesspolygonduetoindentedtreevisualiza+on.

Page 39: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

ModelinguserbehaviorsthroughMarkovChains

Walk,etal.HowUsersExploreOntologiesontheWeb:AStudyofNCBO'sBioPortalUsageLogs.WWW17

Page 40: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

Novelresearchdirec+onsmaybeenabledthroughtheBiOnICandVisIOnresources

•  Categorizeuserbrowsingbehaviorsbyincorpora+ngthestructuralfeaturesoftheontologyclasses.

•  Developpersonalizeduserinterfacesforontologynaviga+on,whichtakeintoaccounttheusertypeandthepredic+onsofthenextclassthatauserislikelytoaccess.

•  Developadvancedmethodsforontologysummariza+onandmodulariza+on,usingBiOnICdatasetsasfeatures.

Page 41: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies
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Page 43: BiOnIC: A Catalog of User Interactions with Biomedical Ontologies

Acknowledgments

MusenLab,Stanford

BMIPhDProgram,Stanford

USNIHGrants

U54-HG004028

GM086587

[email protected]://onto-apps.stanford.edu/bionichVp://onto-apps.stanford.edu/vision