fédération de données et de ConnaissancEs Distribuées en Imagerie BiomédicaLE Data fusion, semantic alignment, distributed queries
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1 fédération de données et de ConnaissancEs Distribuées en Imagerie BiomédicaLE Data fusion, semantic alignment, distributed queries Johan Montagnat CNRS, I3S lab, Modalis team on behalf of the CrEDIBLE consortium CNRS/UNS, laboratoire I3S (UMR7271), équipe MODALIS INRIA/CNRS/UNS, laboratoire I3S (UMR 7271), équipe Wimmics INSERM U1099, laboratoire LTSI, équipe MediCIS U. Picardie, laboratoire MIS, équipe Connaissances icube, journée défis masse de données Illkirch, 7/11/2014 1
2 Motivations Biomedical data High heterogeneity: images, clinical data, biomarkers, biology... Increasing amount / number of (open) sources Big Data Large-scale medical studies (statistical medical studies, epidemiology...) Data (re)analysis opportunities Multicentric studies, Translational research Centralized approaches encounter limitations Need for cross-factors analysis Linked Data Multiple data source kinds Large data volumes to transfer / archive / search Sensitive patient data / complex access control policies Need to adopt uniform data model & format Data is de facto distributed over acquisition centers icube, journée défis masse de données Illkirch, 7/11/2014 2
3 Biomedical data mediation & federation Data federation through distributed querying and query rewriting Client Query-based access to data Federator (query decomposition, planning & results federation) Remote sub-queries Site 1 Mediator (ETL or query rewriting) Mediator (ETL or query rewriting) Site 2 Heterogeneous databases schema mediation Medical data & metadata: raw data + models + processing results + models + provenance... icube, journée défis masse de données Illkirch, 7/11/2014 3
4 Domain ontology-based federation Medical domain ontology (reference model) Data querying Client Query-based access to data Federator Data alignment Remote sub-queries Site 1 Mediator Mediator Site 2 icube, journée défis masse de données Illkirch, 7/11/2014 4
5 Exploitation example: ANR GINSENG (epidemiology) Partnership with GINSENG consortium and Mnemotix SME Federation of heterogeneous epidemiology repositories Multiple epidemiology data acquisition networks Cross-correlation with external data (e.g. demographic: IGN) Mediation of the EHR (Electronic Health Record) data schema icube, journée défis masse de données Illkirch, 7/11/2014 5
6 Challenges and expertise Challenges Representation of data semantics for heterogeneous data sources biomedical ontology building Data federation distributed query engine Data mediation RDB2RDF, ontology alignment Partnership Distributed query engine Semantic representation Semantic reference I3S/Modalis INRIA/I3S/Wimmics LTSI/MediCIS MIS/Connaissances Medical applications icube, journée défis masse de données Illkirch, 7/11/2014 6
7 Scientific networking annual workshop Objectives October 2012 Semantic models usage becomes mainstream Medical systems are mostly centralized but strigent need to support multi-centric studies October 2013 Multidisciplinary workshop gathering international experts in biomedical data representation, semantic, distribution, federation, integration... Many distributed data federation engines Work on data partition schemes and data modeling Query language expressivity limitations October 2014 Towards Web-scale databases (bilion of tuples) R/W access and Semantic reasoning increasingly studied icube, journée défis masse de données Illkirch, 7/11/2014 7
8 Reference ontology 3-levels structure: foundational (DOLCE), core, domain Particular Domain-specific rules Inference abilities Endurant Languages Dataset Subjects acquisition equipment Centres DataTop ontology Current focus on measurements Derived relational schema Medical Image formats Action Dataset processings Dataset Expression acquisitions Conceptualization Inscription Studies Investigators Perdurant Medical image files Medical Datasets image expressions icube, journée défis masse de données Illkirch, 7/11/2014 Examinations 8
9 Ontology modules Modularized ontology to improve reuse and lightweightness ONL-MR-DA: MR Dataset Acquisition ONL-DP: Data Processing ONL-MSA: Mental State Assessment OntoVIP: Medical Image Simulation Wide diffusion icube, journée défis masse de données Illkirch, 7/11/2014 9
10 Data query and federation engine KGRAM (Knowledge Graph Abstract Machine) Semantic query engine: Full support of SPARQL1.1 Generic interface for heterogeneous backends Flexible architecture facilitating different deployment scenarios Mediation interface to access relational data Federated relational schema derived from the ontology icube, journée défis masse de données Illkirch, 7/11/
11 Distributed Query Processing Query federator decoupled from data sources Asynchronous querying of multiple data sources Query planning and parallel querying icube, journée défis masse de données Illkirch, 7/11/
12 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. FILTER (CONTAINS (?name, 'Bob')) } icube, journée défis masse de données Illkirch, 7/11/
13 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 icube, journée défis masse de données Illkirch, 7/11/
14 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q #1 #2 icube, journée défis masse de données Illkirch, 7/11/
15 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q #1 #2 icube, journée défis masse de données Illkirch, 7/11/
16 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q Q1 #1 #2 icube, journée défis masse de données Illkirch, 7/11/
17 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q Q1 #1 #2 icube, journée défis masse de données Illkirch, 7/11/
18 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q Q1 Q2' #1 #2 icube, journée défis masse de données Illkirch, 7/11/
19 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q Q1 Q2' #1 #2 icube, journée défis masse de données Illkirch, 7/11/
20 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q Q1 Q2' Q2'' #1 #2 icube, journée défis masse de données Illkirch, 7/11/
21 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q Q1 Q2' Q2'' #1 #2 icube, journée défis masse de données Illkirch, 7/11/
22 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q Q1 Q2' Q2'' #1 #2 icube, journée défis masse de données Illkirch, 7/11/
23 Distributed Query Processing KGRAM query processing Q SELECT?name?date WHERE {?x foaf:name?name.?x dbpedia:birthdate?date. Q1 FILTER (CONTAINS (?name, 'Bob')) } Q2 Asynchronous execution Interface KGRAM core Q Q1 Q2' Q2'' #1 #2 icube, journée défis masse de données Illkirch, 7/11/
24 Data analysis workflows Data-driven compute-intensive workflow engine icube, journée défis masse de données Illkirch, 7/11/
25 Ontology Provenance capture Concepts & Rules T1-MRI DataSet T2-MRI fmri... DataSetProcessing Segmentation Registration... A B Annotations Processing icube, journée défis masse de données Illkirch, 7/11/
26 Ontology Provenance capture Concepts & Rules T1-MRI DataSet T2-MRI fmri... DataSetProcessing Segmentation Registration... A B Img1 IsA T1-MRI Annotations Processing Img2 IsA T1-MRI icube, journée défis masse de données Illkirch, 7/11/
27 Ontology Provenance capture Concepts & Rules T1-MRI DataSet DataSetProcessing T2-MRI fmri... Segmentation Registration... A B Tool1 HasInput T1-MRI Tool1 IsA Registration Annotations Img1 IsA T1-MRI Img2 IsA T1-MRI Tool1 HasOutput Transfo Processing icube, journée défis masse de données Illkirch, 7/11/
28 Ontology Provenance capture Concepts & Rules T1-MRI DataSet T2-MRI fmri... DataSetProcessing Segmentation Registration... A B Img1 IsA T1-MRI Img2 IsA T1-MRI Tool1 HasInput T1-MRI Tool1 HasOutput Transfo Tool1 IsA Registration Annotations Img1 IsProcessedBy Tool1 Img2 IsProcessedBy Tool1 Processing Tool1 Produced Transfo1 Transfo1 IsA GlobalTransfo icube, journée défis masse de données Illkirch, 7/11/
29 Provenance summarization Fine-grained annotation traces generated at run-time Summary generated by inference rules application Produce relevant and human-tractable experiment summaries icube, journée défis masse de données Illkirch, 7/11/
30 Conclusions Query-based data federation grounded on semantic web standards (SPARQL, RDF, RDFS) Ontology-based Emphasis on query language expressivity Support for both horizontal and vertical data partitioning Broad applicability (given that ontologies are available) Reference model for data alignment and query terms Towards support of Multi-Centric studies Heterogeneous databases (data models, database engines) Inherently distibuted data sets Cross-domains (translational research) support through Linked Data icube, journée défis masse de données Illkirch, 7/11/
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