# Presentation: 192961

## The SDM Center Data Integration Effortand Beyond

**Terence Critchlow**
***Center for Applied Scientific Computing***
***Lawrence Livermore National Laboratory***
*January 2002*

## What are the biggest problems facing genomics data integration?

**Hundreds of data sources each using custom interfaces and unique data formats**

**A lack of standardized semantics.**

**Hundreds of data sources each using custom interfaces and unique data formats **
**and regularly updating both the format and the interface without warning. **

## Example: 	Find everything related to a sequence

**Example: ****	****Find everything related to a sequence**

**MILLAFSSGRRLDFVHRSGVFFFQTLLWILCATVCGTEQYFN**

## Example: 	Find everything related to a sequence

**        **_**Additional Desired Capabilities**_
**Handle multiple sequences **
**Search using other tools**
**Preprocess sequence(s)**
**Use results as input to other queries**
**Pass results to other tools**

**Blast**

## What is the ideal environment?

**What is the ideal environment?**

**A *****single***** location that provides *****effective***** access to ****a *****consistent***** view of data and tools from *****many***** sources through an *****intuitive***** *****and***** *****useful***** interface.**

- Transform	     Map
- data format    similar
- 	     concepts

- Parse 	   Access
- input/	   the data
- output

**:****:**

- User
- applications

## What is the ideal environment?

**What is the ideal environment?**

**A *****single***** location that provides *****effective***** access to ****a *****consistent***** view of data and tools from *****many***** sources through an *****intuitive***** *****and***** *****useful***** interface.**

- Transform	     Map
- data format    similar
- 	     concepts

- Parse 	   Access
- input/	   the data
- output

**:****:**

- User
- applications

## SDM Center Data Integration Infrastructure

**GUI**

- Query
- Dispatch
- and
- Collection
- (QDaC)

**External Tools**

## There are a lot of CS research issues that still need to be addressed. 

**GUI**

- Query
- Dispatch
- and
- Collection
- (QDaC)

**External Tools**

## How does this contribute to a scalable infrastructure?

**GUI**

- Query
- Dispatch
- and
- Collection
- (QDaC)

**DF**

**PDB**

**:**

**Medline**

**XPath**
**Wrapper**

**XPath**
**Wrapper**

**XPath**
**Wrapper**

**XPath**
**Wrapper**

**XPath**
**Wrapper**

**Model-Based Mediator**

**Semantic**
**Wrapper**

**Semantic**
**Wrapper**

**Semantic**
**Wrapper**

**VIPAR Wrapper**

**External Tools**

- Metadata Registry

**XWrap**

**Spider**

- Service Class Descr

## Standards – why don’t we have them yet?

## Standards – why don’t we have them yet?

**Challenges**
**Genomics is a complex field where there are more exceptions to the rules than rules themselves**

**Technology is constantly evolving and the terminology has to keep up**

**Different genomics communities use the same terms in different ways**

## What is the answer?

**?**

## What is the answer?

**What is the answer?**

**Forced standards**
**Won’t work in a evolving scientific environment**
**Ontologies are becoming popular**
**DAML OIL **
**XML based representation for ontology exchange**
**Is being promoted as an approach to dealing with this problem**
**Unclear whether it will be sufficiently robust for this environment**

**Scientists need to decide semantics are important enough to focus time and energy on**

## Conclusions

**Efforts are beginning to address data accessibility issues**
**SciDAC SDM Center - data integration infrastructure**
**DataFoundry - scalable data access **
**Providing consistent semantics is one of the biggest challenges remaining**
**Need support from scientists if current efforts are to be successful**

## People

_**LLNL**_
**Terence Critchlow (lead)**
_**Georgia Tech**_
**Calton Pu**
**Ling Liu****	**
**David Buttler**
**Dan Rocco**
**Henrique Paques**
**Wei Han**

_**SDSC**_
**Bertram Ludaescher**
**Amarnath Gupta**
**Ilkay Altintas**
_**Agent Technology**_
**Tom Potok (ORNL)**
**Mladen Vouk (NCSU)**
_**Target Users**_
**Matt Coleman  (LLNL)**
**Allen Christian (LLNL)**
**Phil Bourne (PDB)**

## Questions?

## This work was performed under the auspices of the U.S. Department of Energy by University of California Lawrence Livermore National Laboratory under contract No. W-7405-ENG-48.