# Presentation: 215453

## Contents

- Poster = 2,4..end
- Move = 3..end

## Towards a Semantic Data Grid for Systems Science

**Problem: ****Major challenges exist realizing semantic grids for systems science research**
- discovery, collection, integration, translation, understanding, provenance
**Approach:** **Design and deploy a coordinated set of semantic grid capabilities benefiting systems science research**

- _Targeted scope:_
- Define core services and infrastructure
- Develop capabilities:
-   Data virtualization and semantically-defined data transformation
-   Provenance capture in workflow
- Deploy pilot implementations  in collaboration with the *Interrogative Cellular Signaling Group*

## Microarray/Protein Interaction

** ****Data Virtualization **

**Grid Data Services Engine**

- Raw
- Microarray

- Cytoscape
- dataset

- Cluster Genes

- Discover

- Query

- Translate

- Combine

- Translate

- DIP GDS

- BIND GDS

- DIP XML
- Cache

-   BIND XML
-  Cache

- DIP Website

-   Translate

- DFDL GDS

- DFDL
- BIND
- Schema

- Schema
- Repository

- Grid Registry

- Protein
- Interaction
- DBs

- XPath
- results

- XPath
- results

- HUPO
- dataset

- HUPO ->
- Cytoscape
- XSL

- BIND
- HUPO-XIN
- XSL

- DIP
- HUPO-XIN
- XSL

- DFDL
- Microarray
- Schema

-    BIND FTP
-  server

- Delimited
- Datasets

- Translate
- GDS

- Combine
- GDS

- NCBI
- WS

**...**

- DFDL
- GDS

- What proteins correspond to genes that are up-regulated at 3hr and 4hr, and what proteins are they known to interact with?

- Query
- GDS

- nGIs

- pGIs

- GDS’s

- HUPO
- dataset

- HUPO
- dataset

## Microarray/Protein Interaction

** ****Data Virtualization **

- Raw
- Microarray

- Cytoscape
- dataset

- Cluster Genes

- Discover

- Query

- Translate

- Combine

- Translate

- DIP GDS

- BIND GDS

- DIP XML
- Cache

-   BIND XML
-  Cache

- DIP Website

-   Translate

- DFDL GDS

- DFDL
- BIND
- Schema

- Schema
- Repository

- Grid Registry

- Protein
- Interaction
- DBs

- XPath
- results

- XPath
- results

- HUPO
- dataset

- HUPO ->
- Cytoscape
- XSL

- BIND
- HUPO-XIN
- XSL

- DIP
- HUPO-XIN
- XSL

- DFDL
- Microarray
- Schema

-    BIND FTP
-  server

- Delimited
- Datasets

- Translate
- GDS

- Combine
- GDS

- NCBI
- WS

- DFDL
- GDS

- What proteins correspond to genes that are up-regulated at 3hr and 4hr, and what proteins are they known to interact with?

- Query
- GDS

- nGIs

- pGIs

- GDS’s

- HUPO
- dataset

- HUPO
- dataset

- Scientist wants to compare their experimental results against other data sources

- Microarray data translated to Xml by the generic DFDL translation service.

- Xml representation queried for requested nucleotide protein identifiers.

- Contact NCBI services to map nucleotide GI numbers to protein GI numbers.

- Discover and query protein interaction data sources.

- Convert query results to HUPO-XIN format.

- Combine HUPO-XIN results sets into one result.

- Translate HUPO-XIN into Cytoscape compatible format.

## Cytoscape Visualization of

- merged outputs
- BIND
- DIP

- This scenario can be expanded to consider additional data sources.  For example,  by adding experimental data sources the scientists can compare predicted and observed results.

## Automated Provenance Capture

- Workflow
- Engine

- Cluster Genes

- Discover

- Query

- Translate

- Combine

- inputs

- Data
- Store

- outputs

- Provenance
- Store
- (rdf)

- Who,
- When,
- Service info
- wfid

- Workflow
- services

- activates

- inputs

- Wfid,
- Provenance store info

- Wfid,
- Provenance store info

- Services called by other services may also document themselves

- outputs

- Capture Interface

- Query Interface

- Portals,
- Client Applications
- PSEs

- activates