# Presentation: 948079

## Semantic Mediation of Scientific Data via Logic-Based Data Federation Software

- Amarnath Gupta
- Bertram Ludäscher
- Reagan Moore
- San Diego Supercomputer Center
- University of California, San Diego

## Information Integration / Mediation 

- Goal:
- combine data from different sources s.t. the integrated whole is more than the sum of its isolated parts
- => SDSC/CSE **MIX** project (Mediation of Information in XML)
- Standard Scenarios:
- C2B, e.g. comparison shopping:
- AddAll := *IntegratedView**(amazon, barnes&noble, ...)*
- B2B, e.g. marketplaces:
- Virt_Market := *IntegratedView**(supplier_1, ... supplier_n)*
- C2M, e.g. home-buyer:
- Full_Picture := *IntegratedView**(Realtor, Crime, Schools, ...)*

_***One-World***_* Mediation*
*e.g. join on ISBN*

_***Simple Multiple-World***_* Mediation*
*e.g. join on ZIP*

##  MIX Mediation Challenges

- MIX Mediator Architecture (middleware)
- wrappers: wrap different data into common format (XML)
- mediator: combines sources’ XML views into *IntegratedView*
- MIX Mediator Components
- declarative mediator view definition language:
- XMAS (XML Matching And Structuring) *language*, *algebra*, and first *prototype* ~ 1999 [SIGMOD99,EDBT00,...]
*query composition* and *rewriting* esp. with limited source capabilities
*on-demand* (“lazy”) query processing of *virtual XML** docs* (DOM-VXD)
- Blended Browsing and Querying user interface (BBQ)

##  New MIX Challenges from Scientific Applications

- Complex Data (S2S)
- SDSC’s Scientific Data Applications (current/planned, e.g. Neurosciences: SciDAC/SDM, NCMIR, NIH BIRN, Earth sciences, ...) show that syntactic/structural integration is insufficient for ...
-  ***Complex Multiple-World**** Mediation Problems:*
- complex, disjoint, seemingly unrelated data
- “hidden semantics” in complex, indirect relationships
- => Semantic (aka Model/Knowledge-Based) Mediation
- lift mediation to the level of conceptual models (CMs)
- use domain experts’ knowledge formalized as rules over CMs
- => Specialized Extensions
- temporal, geospatial, statistical, DQ/accuracy... operations
- => Extend Mediation Scope and Power via Deductive Rules

## A Neuroscience Question

***What is the cerebellar distribution of rat proteins with more than 70% ***
***homology with human NCS-1? Any structure specificity?***
***How about other rodents?***

**Notes:**
protloc = NCMIR, excel + images
morphometry (measurement) = NCMIR, excel + txt +images
neurotrans (stimulate then electrical responses, probes)  = RDB, SENSELAB, Yale
CaBP (chemical structure, PDB links, function of CaBP, found-in...) = Web, Vanderbilt U
Expasy (Protein-info as Sequence data) = Web, Europe

##  Example for Formalizing Domain Knowledge:Domain Map (Ontology) for SYNAPSE and NCMIR

- A **domain map** comprises
-  Description Logic facts ...
-  - concepts ("classes")
-  - roles ("associations")
-  derived properties ...
-  ... expressed as **logic rules**
- - (e.g. F-logic)

##  Domain Map Refinement

- ... source can register **new concepts** at the mediator ...

## Semantic Annotation Tool for Domain Scientists

## Extended Mediator Architecture for Semantic Mediation

** ****USER/Client**

**S2  **

**S3 **

**CM (Integrated View)**

**Domain Map**
**DM**

**Integrated View **
**Definition IVD**

*Logic API*
*(capabilities)*

***CM Queries & Results***
* **(exchanged in XML)*

***CM Plug-In***

**first results & demos**:
- [SSDBM00] [VLDB00]
- [ICDE01] [NIH-HBP01]

**Mediator**
**Repository**
**DB**

## ANATOM Domain Map with Registered Data 

##  Query Processing

## Mediator System Architecture

## Mediation Services:Source Registration (System Issues)  

## Mediation Services: Source Registration (Semantics Issues)

- Domain Map Registration
- provide concept space/ontology
- ... as a private object (“myANATOM”)
- ... merge with others (give “semantic bridges”)
- ... and check for conflicts
- Conceptual Model Registration
- schema: classes, associations, attributes
- domain constraints
- “put data into context” (linking data to the domain map)

## Mediation Services: Client Registration

## Other Existing Infrastructure

- Transparent Access to Remote Data Collections: Storage Resource Broker (SRB) and Metadata Catalog (MCAT)
- “Production-Level” Software
- PPDG: interface to LBNL Storage Manager, collection creation, replication management
- Use of manual and automatic wrapper technology (*Minerva*, *Roadrunner*, V. Crescenzi, Universita di Roma Tre)
- => XWrap Elite

## SRB and the Particle Physics Data Grid

- esrb.server

- Wisc
- Client 2

- IPC

- SRB Server
- @Wisc

- esrb.driver

- Wisc
- Client 1

- SRB Server @LBL

- SRB Server @LBL

- esrb.driver

- IPC

- Disk cache

- FC

- file caching

- File caching  request

- file purging

- Stage()  purge()   fileStatus()

- Stage()  purge()   fileStatus()

- Stage()  purge()   fileStatus()

- S-Commands

- S-Commands

## Year 1 Deliverables

- define interface metadata format (Critchlow)
- extend XWrap to generate wrappers using the interface metadata description instead of requiring human interaction (GT)
- develop a canonical XML-based query and response format as a dynamic interface between query engine and wrappers (Critchlow, GT, SDSC)
- communication via agent protocols? How about using digital library infrastructure (e.g. Simple Digital Library Interoperability Protocol, SDLIP)
- use extended XWrap to create wrappers for the genomics domain for evaluation (GT)
- extend the SDSC query and metadata architecture to interoperate with the LLNL DataFoundry (SDSC, Critchlow)
- ... interoperation at the wrapper level: Minerva wrappers, XWrap

## References

- _[Model-Based Mediation with Domain Maps](http://www.sdsc.edu/~ludaesch/Paper/icde01.html)_, B. Ludäscher, A. Gupta, M. E. Martone, *17th Intl. Conference on Data Engineering* _[(ICDE)](http://www.acm.org/sigmod/dblp/db/conf/icde/index.html)_, Heidelberg, Germany, IEEE Computer Society, April 2001.
- _[Model-Based Information Integration in a Neuroscience Mediator System](http://www.sdsc.edu/~ludaesch/Paper/vldb00.html)_, B. Ludäscher, A. Gupta, M. E. Martone, *demonstration track, 26th Intl. Conference on Very Large Databases* _[(VLDB)](http://www.acm.org/sigmod/dblp/db/conf/vldb/index.html)_, Cairo, Egypt, September 2000.
- _[Knowledge-Based Integration of Neuroscience Data Sources](http://www.sdsc.edu/~ludaesch/Paper/ssdbm00.html)_, A. Gupta, B. Ludäscher, M. E. Martone, *12th Intl. Conference on Scientific and Statistical Database Management* _[(SSDBM)](http://www.acm.org/sigmod/dblp/db/conf/ssdbm/index.html)_, Berlin, Germany, IEEE Computer Society, July 2000.