Integrated Semantic Search on Structured and Unstructured Data in the ADOnIS System Friederike Klan, Erik Faessler,Alsayed Algergawy, Birgitta König-Ries, and Udo Hahn
The AquaDiva Project model of water fmow CSV throughfall and stemfmow data CSV meteorological data CSV DNA sequencing data mass spectrometry data
Syntactic Search in http://bexis2.uni-jena.de/
Example data referring to alkaline milieu Search samp_ID loc date time pH Fe2+ NO2- temp_1 temp_2 r_mm 23 S1 10.12.2011 15:00 7,1 0,01 0,006 9,2 8,9 2,4 10,3 18 S2 14/10/2011 17:30 7,2 0,03 0,004 9,4 9,1 4 S3 16/10/2011 11:55 7,3 0,02 0,003 10,1 8,9 1,8 7 S1 19/10/2011 17:25 7,3 0,04 0,004 9,6 9,2 7,1 12 S2 21/10/2011 14:50 7,1 0,08 0,005 9,4 9,4 2,3 35 S3 23/10/2011 11:40 7,1 0,15 0,003 9,6 9,3 8,1 5 S4 25/10/2011 15:20 7,1 0,04 0,005 10,3 9,9 21,2 10,3 8 S2 28/10/2011 16:45 7,1 0,02 0,006 10,1 9,8 9 S3 30/10/2011 15:30 7,1 0 0,007 9,3 8,7 23,5 17 S4 11.01.2011 13:30 7,2 0,05 0,03 9,3 8,8 1,8
Example data referring to alkaline milieu Search samp_ID loc date time pH Fe2+ NO2- temp_1 temp_2 r_mm 23 S1 10.12.2011 15:00 7,1 0,01 0,006 9,2 8,9 2,4 18 S2 14/10/2011 17:30 7,2 0,03 0,004 9,4 9,1 10,3 1,8 4 S3 16/10/2011 11:55 7,3 0,02 0,003 10,1 8,9 7 S1 19/10/2011 17:25 7,3 0,04 0,004 9,6 9,2 7,1 12 S2 21/10/2011 14:50 7,1 0,08 0,005 9,4 9,4 2,3 35 S3 23/10/2011 11:40 7,1 0,15 0,003 9,6 9,3 8,1 5 S4 25/10/2011 15:20 7,1 0,04 0,005 10,3 9,9 21,2 8 S2 28/10/2011 16:45 7,1 0,02 0,006 10,1 9,8 10,3 9 S3 30/10/2011 15:30 7,1 0 0,007 9,3 8,7 23,5 1,8 17 S4 11.01.2011 13:30 7,2 0,05 0,03 9,3 8,8 alkaline is a Thing which has a pH value > 7
Semantic Search samp_ID loc date time pH Fe2+ NO2- temp_1 temp_2 r_mm 23 H43 12/10/2011 15:00 7,1 0,01 0,006 9,2 8,9 2,4 18 H41 14/10/2011 17:30 7,2 0,03 0,004 9,4 9,1 10,3 4 H51 16/10/2011 11:55 7,3 0,02 0,003 10,1 8,9 1,8 7 H43 19/10/2011 17:25 7,3 0,04 0,004 9,6 9,2 7,1 12 H41 21/10/2011 14:50 7,1 0,08 0,005 9,4 9,4 2,3 35 H51 23/10/2011 11:40 7,1 0,15 0,003 9,6 9,3 8,1 5 H51 25/10/2011 15:20 7,1 0,04 0,005 10,3 9,9 21,2 8 H51 28/10/2011 16:45 7,1 0,02 0,006 10,1 9,8 10,3 Data 9 H43 30/10/2011 15:30 7,1 0 0,007 9,3 8,7 23,5 S1 17 H41 01/11/2011 13:30 7,2 0,05 0,03 9,3 8,8 1,8 S2 Semantic Annotation located in Bechstedter Grund Search keywords reasoner Knowledge Base alkaline is ...
User Interface
System Overview BExIS 2 Module ADOnIS Click to add Title BExIS 2 Search Interface ( including autocompletion) Publication Search Query Translation SPARQL Endpoint Publication Annotator ( extraction of class mentions, nam ed entities and relations) Quest Reasoner (Ontop) Virtual ABox (Ontop) TBox J CoRe GeNO LINNEAUS BioSem (dom ain knowledge) Mappings PubMed/Medline PubMed Central MD PD SA MD DS PD
Semantic Search on Structured Data
Knowledge Base (TBox) refersToObservationType oboe-core:ObservationCollection ObservationType hasObservationType refersToMeasurementType hasMember oboe-core:Precision refersToEntityType hasPrecision usesStandard oboe-core:Observation oboe-core: Entity EntityType MeasurementType oboe-core:Standard o f C h a r a c t e ofEntity hasEntityType r i s t i c hasMeasurement oboe-core:Characteristic hasMeasurementType oboe-core:Measurement subClassOf subClassOf hasValue any EntityTypeClass CharacteristicClass ChEBI-light- module oboe- chemistry OBI oboe- NCIT- temporal ENVO module based on the Extensible Observation Ontology (OBOE)
Semantic Annotation SF_ml Tree-No Species TreeCircum_m BHD_m TreeHeight_m 212 56 Birke 1,56 0,48 26,34 35 28 Eiche 1,19 0,35 24,86 62 34 Eiche 1,55 0,52 28,46 43 96 Buche 1,43 0,43 31,72 334 12 Buche 1,57 0,49 31,87 oboe-core:ObservationCollection 1,57 oboe-core:Characteristic 31,87 oboe-core:Characteristic oboe-core:Observation oboe-core: Entity oboe-core:Observation oboe-core: Entity 334 oboe-core:Characteristic
Semantic Annotation SF_ml Tree-No Species TreeCircum_m BHD_m TreeHeight_m 212 56 Birke 1,56 0,48 26,34 35 28 Eiche 1,19 0,35 24,86 62 34 Eiche 1,55 0,52 28,46 43 96 Buche 1,43 0,43 31,72 334 12 Buche 1,57 0,49 31,87 oboe-core:ObservationCollection 1,57 oboe-core:Characteristic 31,87 oboe-core:Characteristic oboe-core:Observation oboe-core: Entity oboe-core:Observation oboe-core: Entity 334 ABox oboe-core:Characteristic
Virtual Abox using Annotation SPARQL Endpoint SF_ml Tree-No Species TreeCircum_m BHD_m TreeHeight_m (entity, + 212 56 Birke 1,56 0,48 26,34 characteristic, 35 28 Eiche 1,19 0,35 24,86 62 34 Eiche 1,55 0,52 28,46 standard) 43 96 Buche 1,43 0,43 31,72 334 12 Buche 1,57 0,49 31,87 Quest Reasoner 1,57 31,87 CHARACTERISTIC-TYPE MAPPINGS :crct_{crct_id} a <{crct}> . SELECT DISTINCT crct, chrct_id FROM annotation MEASUREMENT_TYPE-and-VALUE :msmt_{value} a oboe-core:Measurement; oboe-core:hasValue {value}^^xsd:string . SELECT DISTINCT value FROM measurement_values 334 334 Virtual ABox
Semantic Annotation measurement_values (materialized view) annotations dataset column id entity characteristic standard msmt instance id value id IRI entity IRI characteristic IRI measurement id literal standard ... :crct_1 a <http://../someontology.owl#Volume> :crct_2 a <http://../someontology.owl#Circumference> :crct_3 a <http://../someontology.owl#Height> ... :msmt_{334} a oboe-core:Measurement; CHARACTERISTIC-TYPE MAPPINGS oboe-core:hasValue "334"^^xsd:string :crct_{crct_id} a <{crct}> . :msmt_{1_57} a oboe-core:Measurement SELECT DISTINCT crct, chrct_id FROM annotation oboe-core:hasValue "1,57"^^xsd:string :msmt_{31_87} a oboe-core:Measurement MEASUREMENT_TYPE-and-VALUE oboe-core:hasValue "31,87"^^xsd:string :msmt_{value} a oboe-core:Measurement; oboe-core:hasValue {value}^^xsd:string . ... SELECT DISTINCT value FROM measurement_values Virtual ABox
From keywords to SPARQL groundwater concentration_of nitrate Search EntityTypeClass CharacteristicClass EntityTypeClass SELECT DISTINCT ?dset WHERE { ?dset ad:refersToObservationType ?obstype. ?obstype ad:refersToEntityType ?enttype. ?enttype a <http://../someontology.owl#Nitrate>. ?obstype ad:refersToMeasurementType ?meastype. ?meastype ad:ofCharacteristic ?crct. ?crct a <http://../someontology.owl#concentration_of> } MAPPINGS SELECT DISTINCT ?dset WHERE { ?dset ad:refersToObservationType ?obstype. ?obstype ad:refersToEntityType ?enttype. ?enttype a <http://../someontology.owl#Groundwater> }
More Supported Queries Show me all datasets that refer to measurements of the nitrate concentration in groundwater. At which locations within the Hainich transect has soil moisture been measured? On which dates has the concentration of nitrate been measured at well H31? Has species XY been observed in aquifer moTK? Which characteristics have been measured at H31?
Semantic Search on Unstructured Data
Publication Search with Semedico
Publication Search with Semedico
http://www.aquadiva.uni-jena.de/ http://bexis2.uni-jena.de/ http://www.semedico.org/ Contact: friederike.klan@uni-jena.de http://fusion.cs.uni-jena.de/fusion/members/friederike-klan/ This is joint work with my colleagues Alsayed Algergawy, Erik Faessler, Birgitta König-Ries, Udo Hahn, Roman Gerlach, Javad Chamanara, David Schöne, Sven Thiel, Martin Hohmuth, Thorsten Hindermann, Nafiseh Navabpour, Markus Steinberg, Valentin Wesp
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