1. An Extensible Model-Based Mediator System with Domain Maps Amarnath Gupta * Bertram Ludäscher * Maryann E. Martone + * San Diego Supercomputer Center (SDSC) + National Center for Microscopy and Imaging Research (NCMIR) University of California, San Diego (UCSD)

2. Federation of Brain Data using Model-Based Medition CCBCCB, Montana SU Surface atlas, Van Essen LabVan Essen Lab NCMIRNCMIR, UCSD stereotaxic atlas LONILONI MCell, CNL, SalkCNL ANATOM PROTLOC ResultResult (VML) ResultResult (XML/XSLT)  MODEL-BASED Mediation

3. The Need for Semantic Integration protein localization What is the cerebellar distribution of rat proteins with more than 70% homology with human NCS-1? Any structure specificity? How about other rodents? morphometry neurotransmission ???Mediator ??? Web CaBP, Expasy Wrapper ??? Integrated View ??? ??? Integrated View Definition ??? Data, relationships, constraints are modeled (CMs) Cross-source relationships are modeled Semantic (knowledge- based) mediation services Cross-source queries

4. XML-Based vs. Model-Based Mediation Raw Data IF  THEN  Logical Domain Constraints Integrated-CM := CM-QL(Src1-CM,...)...... (XML) Objects Conceptual Models XML Elements XML Models C2 C3 C1 R Classes, Relations, is-a, has-a,... DOMAIN MAP Integrated-DTD := XML-QL(Src1-DTD,...) No Domain Constraints A = (B*|C),D B =... Structural Constraints (DTDs), Parent, Child, Sibling,... CM ~ {Descr.Logic, ER, UML, RDF/XML(-Schema), …} CM-QL ~ {F-Logic, OIL, DAML, …}

5. Model-Based Mediation with DOMAIN MAPS (DMs) Integrated-CM(Z1,...) := get X1,... from Src1; get X2,... from Src2; LINK (Xi, Yj); Zj = CM-QL(X1,...,Y1,...) LINK(X,Y): X.zip = Y.zip X.addr in Y.zip X.zip overlaps Y.county... “Semantic Road Maps” for situating source data => navigational aid (browsing source classes at the conceptual level) => basis for integrated views across multiple worlds => link points (concepts) and labeled arcs (roles) => formal semantics (in FL and/or DLs) Example: ANATOM DM = antatomical entities (concepts) + is_a, has_a, overlaps,... (roles) => from syntactic equality to semantic joins

6. ANATOM Domain Map

7. ANATOM Domain Map with Registered Data ANATOM DATA

8. Query Processing Integrated View Definition DERIVE protein_distribution(Protein, Organism, Brain_region, Feature_name, Anatom, Value) FROM I:protein_label_image[ proteins ->> {Protein}; organism -> Organism; anatomical_structures ->> {AS:anatomical_structure[name->Anatom]}], % from PROLAB NAE:neuro_anatomic_entity[name->Anatom; % from ANATOM located_in->>{Brain_region}], AS..segments..features[name->Feature_name; value->Value]. provided by the domain expert and mediation engineer declarative language (here: F-logic)

9. Client-Side Result Visualization (using AxioMap Viewer: Ilya Zaslavsky) PROTLOC-AxioMap

10. Model-Based Mediator Prototype USER/Client USER/Client S1 S2 S3 XML-Wrapper CM-Wrapper XML-Wrapper CM-Wrapper XML-Wrapper CM-Wrapper GCM CM S1 GCM CM S2 GCM CM S3 CM (Integrated View) Mediator Engine FL rule proc. LP rule proc. Graph proc. XSB Engine Domain Map DM Integrated View Definition IVD Logic API (capabilities) CM Queries & Results (exchanged in XML) CM Plug-In

11. Mediation Services: Semantic Annotation Tools line drawing =annotate=> (spatial) DB for mediation