http://asp.uma.es Ontology-Based Mediation in the Amine System Project Pisa June 2007 Prof. Dr. José F. Aldana Montes (jfam@lcc.uma.es) Prof. Dr. Francisca Sánchez-Jiménez Ismael Navas Delgado Raúl Montañez Almudena Pino-Ángeles Aurelio A. Moya-García José Luis Urdiales
Outline - Family of problems to be solved - Proposed solution: from Semantics to Data Integration - Semantic Directories - Ontology-Based Mediator - Specific Problem: Use Case - Conclusions
Outline - Family of problems to be solved - Proposed solution: from Semantics to Data Integration - Semantic Directories - Ontology-Based Mediator - Specific Problem: Use Case - Conclusions
Family of Problems - Systems biology is the study of an organism, viewed as an integrated and interacting network of genes, proteins and biochemical reactions which give rise to life. (Institute of Systems Biology) - Instead of focusing on individual parts, the focus is on a complete system Need of integrated access to different data sources to enable the study of the system
Outline - Family of problems to be solved - Proposed solution: from Semantics to Data Integration - Semantic Directories - Ontology-Based Mediator - Specific Problem: Use Case - Conclusions
Proposed Solution - Requirements: - Easily extensible with new resources - Reusable elements - Possibility of developing different kind of applications (not only data integration) - Decisions: - Take advantage of the Semantic Web - Annotate data sources with respect to ontologies - Reuse previous works
Proposed Solution - Requirements: - Easily extensible with new databases - Reusable elements - Possibility of developing different kind of applications (not only data integration) - Decisions: - Take advantage of the Semantic Web - Annotate data sources with respect to ontologies - Reuse previous works
Outline - Family of problems to be solved - Proposed solution: from Semantics to Data Integration - Semantic Directories - Ontology-Based Mediator - Specific Problem: Use Case - Conclusions
Semantic Directories
SD-Core Metadata y O r o n t t i o s o l o p g e y R M a e t t a a d d Semantic a a t t e a M Reasoner R Directory e e c p r o u Componen s o i t s o e r R t y Semantic Register OMV SDMO SDMO OMV OMV OMV OMV OMV OMV Instanc e OMV Instance OMV Instance OMV Instance Instance Instance Instance Instance Instance Instance
OMV OMV (ONTOLOGY METADATA VOCABULARY) is described with OWL, and each instance of the class OntologyImplementation represents an ontology registered in the Semantic Directory. It is possible to describe some relationships between ontologies
SDMO - OMV: link resources with registered ontologies. - Resource: store information (query capabilities, schema, query interface, name and URI) about resources. - Mapping: set the relationships between resources and ontologies. Each mapping is related with a similarity instance that establishes the similarity between ontology concepts and resource elements. The mapping class is related with OMV, Resource and Similarity class. - Similarity: contains three properties (concept1, concept2 and similarityValue) to establish the similarity between an ontology concept and a resource element. - User: deal with users in the applications.
Interfaces l + ) o , i ( ( i + ( ) o , i ( l + ) o g l , , i ( r + O « ) o , i + o ( g + ) o , i ) ( i i ( l + ) o , i ( g + i ) ) o , i ( l + ) o + g l , + R : S « ) o , i i ( ( , g o + ) o , i , , ) l o i , i , ) + , ) i , i ( r + ( i ( + i i S S « ) i , i , , r i + l , i , i ( ) i ) + , ) + r l + ( i i ( , r i i , i ( i , o , n n n n n n n n n i n n n n n i n n i n n i n i n n : n n i n n n n n n n i n i i n n e e e e e s s s s s s s s s u u e u u e i u i e u u u e u e u i u u u u e e e e n n n n t t t t t g g t g t t g g t o q o r s r u c o r c u s r q o m c r o u u q r q q r u q s r n n t t t t t t t t t t t t t t t t t t t R O O R m O R M M m m R t t t s e e i e S t e i S i i O O e e e i R e c c o o c o s s n a v r s a u e r v s n v u o v r v u v v n e v n n v r v v v u e u f u r s o o l e a l s l e s e i l s l l l l s e s h c n h n c n h e e e t e t n n e a t e e t m e e e t l t t m e t t e a r a e e r t e e a e a n a e e a r e n n n e l o s e s f o o o s f o o o s o p f u o e e e o e e t h e h e t t r p l c r c c c c c c c t r c c c r c r c t v n o c c r p t a t a a t n n o o o a r r o o r u l l u r o u e l r u e l o l u y y e y r o e o e e o y y y p p o t p t t e t e o t t e m o m o t t t o m a t t t t O R R O R g c t c c t c t l l l C r o o C o C u d o M o i M o o u u o r u r o o r o M o d r i l l l i o o p c m i e o p p m e e g i e g n o g g i g o n o y c c c c c c c r e a r e r r e e r r n r n a r r r r r a n O r n r O r r d a g a a t t g g t e y e g t » g y » e e y » y g g e y e D e c c e c c s a N C M s g N s M M a g i i M t t i R D p N E p M N N F p N y o e y t N n N y e N e e s e e N t t N o n e o s o o s i a h a h h o a a F a i t e s a e a t a e e s s a r e s i s e l s s l u u u a l a a a a e m e o o o o r o o o m e b b b n i t l t t g t m m m e m t m m r l r r m e m m l g c h h g l h d c d a d c e i c o o i i c a i l c e l e l o o t y o y m e i i e s e e i e e e e d e e e o e e g t t g d t t V d t d p d i i i o y y r a e e e e a e e t y s s s t r s t n r c a y a t t s o R R r e e p p o o s s i i t t o o r r y y Our goal is to provide applications which will make the semantics of the resources explicit through their commitment with an ontology registered in the Semantic Directory. The applications that can be developed using the Semantic Directory components depend on the extension of the infrastructure by means of new components (built on top of the Semantic Directory)
SD Conclusions - Generic Infrastructure - Basic Functionality - Extended Functionalities requires Core Extensions: new metadata, interfaces, … - Fully implemented: - V 0.9.A: Java, BD MySQL, Racer (Concepts Classification), Web Services - V 0.9.B: Java, Metadata Files, Jena, Web Services - V 0.9.C: Java, Metadata Files, Jena, Corba CCM
Outline - Family of problems to be solved - Proposed solution: from Semantics to Data Integration - Semantic Directories - Ontology-Based Mediator - Specific Problem: Use Case - Conclusions
Mediator (Data Integration) Users must locate data sources that are available online and can solve their problems Discover available Users must select which data data sources sources include relevant information for themselves Select data Users manually interact with sources & tools each data source getting partial results Interact with each data source Users combine partial results to Combine get a partial solution of the results problem Building the full solution
Approach - GAV (BioBroker): + Easy query rewriting - Extension Global Schema Changes - LAV + Easy addition of new data sources - Complex Rewriting Process simpler components will allow partial improvements
Approach - GAV (BioBroker): + Easy query rewriting - Extension Global Schema Changes - LAV + Easy addition of new data sources - Complex Rewriting Process simpler components will allow partial improvements
Main Characteristics Controller User Query, Ontology (Q,O) Result (ontology Instances ) Q, O, Result (Ontology Instances) Q, O, Query Plan (QP) (Q,O) Q , O Mediator , Q P , { R Query 1 , … , R Technical Users Planner Q, O, Query Plan (QP) n } Q, O, QP, {R1, …, Rn} or Software Query Plan Developers Mappings Search Solver/ Integrator Evaluator Resource Search Ontology Search /reasoning Semantics p t a d a y a o r e t r m e c o u o s e R Semantic Register r t s i t o r y O n t i l o g y o M R s o e p e a t a d t a e Component Reasoner Wrappers developed as Web Services Resource Semantic Data Data Data Data Service Service Service Service Descriptions
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