Integrated Semantic Search on Structured and Unstructured Data in - - PowerPoint PPT Presentation
Integrated Semantic Search on Structured and Unstructured Data in the ADOnIS System Friederike Klan, Erik Faessler,Alsayed Algergawy, Birgitta Knig-Ries, and Udo Hahn The AquaDiva Project model of water fmow CSV throughfall and stemfmow
Friederike Klan, Erik Faessler,Alsayed Algergawy, Birgitta König-Ries, and Udo Hahn
CSV CSV CSV
meteorological data DNA sequencing data mass spectrometry data throughfall and stemfmow data model of water fmow
http://bexis2.uni-jena.de/
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 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 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 0,007 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
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 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 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 0,007 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
alkaline is a Thing which has a pH value > 7
Search keywords
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 9 H43 30/10/2011 15:30 7,1 0,007 9,3 8,7 23,5 17 H41 01/11/2011 13:30 7,2 0,05 0,03 9,3 8,8 1,8S2 S1 located in
Semantic Annotation Data
Bechstedter Grund alkaline is ...
Knowledge Base
reasoner
MD DS PD MD PD TBox (dom ain knowledge) Virtual ABox (Ontop) SA Mappings PubMed/Medline PubMed Central Publication Search Publication Annotator ( extraction of class mentions, nam ed entities and relations) Query Translation SPARQL Endpoint Quest Reasoner (Ontop) J CoRe GeNO LINNEAUS BioSem BExIS 2 Search Interface
( including autocompletion)
BExIS 2 Module ADOnIS
temporal
ObservationType
EntityType MeasurementType
any
hasPrecision usesStandard
C h a r a c t e r i s t i c refersToMeasurementType refersToEntityType hasObservationType hasValue
hasMeasurementType hasEntityType hasMeasurement refersToObservationType
hasMember
EntityTypeClass CharacteristicClass ChEBI-light- module
chemistry ENVO OBI NCIT- module
subClassOf subClassOf
based on the Extensible Observation Ontology (OBOE)
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
1,57 31,87 334
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
1,57 31,87 334
ABox
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
334
Virtual ABox
CHARACTERISTIC-TYPE :crct_{crct_id} a <{crct}> . SELECT DISTINCT crct, chrct_id FROM annotation MEASUREMENT_TYPE-and-VALUE :msmt_{value} a oboe-core:Measurement;
SELECT DISTINCT value FROM measurement_values
MAPPINGS
1,57 31,87 334
SPARQL Endpoint Quest Reasoner + Annotation (entity, characteristic, standard)
Virtual ABox
CHARACTERISTIC-TYPE :crct_{crct_id} a <{crct}> . SELECT DISTINCT crct, chrct_id FROM annotation MEASUREMENT_TYPE-and-VALUE :msmt_{value} a oboe-core:Measurement;
SELECT DISTINCT value FROM measurement_values
MAPPINGS
measurement_values (materialized view) msmt instance id value id literal annotations dataset column id entity characteristic standard id IRI entity IRI characteristic IRI measurement 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;
:msmt_{1_57} a oboe-core:Measurement
:msmt_{31_87} a oboe-core:Measurement
...
EntityTypeClass CharacteristicClass EntityTypeClass
MAPPINGS
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> } SELECT DISTINCT ?dset WHERE { ?dset ad:refersToObservationType ?obstype. ?obstype ad:refersToEntityType ?enttype. ?enttype a <http://../someontology.owl#Groundwater> }
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?
http://www.aquadiva.uni-jena.de/ http://www.semedico.org/ http://bexis2.uni-jena.de/ 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