# Presentation: 778073

## Summary of SDM ETC Kickoff for theData Integration Task

**Terence Critchlow**

**Calton Pu**
**Ling Liu**
**David Buttler**

**Bertram Ludaescher****Amarnath Gupta**
***Mladen Vouk******Tom Potok***

## People involved:

**People**
**Terence Critchlow (LLNL)**
**Calton Pu****	****	****(GT)**
**Ling Liu****	****	****(GT)**
**David Buttler****	****(GT)**
**Bertram Ludaescher (UCSD)**
**Amarnath Gupta****	****(UCSD)**
**TDB:**
**Ph.D. student at Georgia Tech**
**Developer at UCSD**
***Mladen Vouk / Tom Potok******	******	******NCSU / ORNL***

**Commitment per institution**
** ****LLNL**
**0.25 (likely) – 1.0 FTE**
**Georgia Tech**
**2 Ph.D. Students**
**X months Calton’s time**
**Y months Ling’s time**
**UCSD **
**1 FTE**
**1 month Bertram’s time**
**1 month Gupta’s time**
**Agent team**
**2-4 months over the course of the year**

## Application ties 

**Primary domain:  bioinformatics**
**Secondary domains:**
**Material science**
**Air / water quality**
**Scientists (early adopters) **
**Matt Coleman****	****	****(LLNL)**
**Allen Christian****	****(LLNL)**
**Phil Bourn****	****	****(PDB)**

**Contacted by ****Terence**

**Contacted by ****Bertram / Gupta**

## Use Case 1: Finding out everything about a sequence 

**Bob starts with one or several DNA or protein sequences that he wants to analyze **
**OR: Bob finds protein or gene sequences of interest by querying databases/web sites for metabolic pathways/cell signaling pathways (e.g., KEGG); **
**OR: Bob looks at a database of microarray experiments and chooses those genes that exhibit specified patterns of co-occurrence (what subsets of genes “go hand in hand” across a large number of experiments)**
**The relevant sequences are submitted to one or more sequence databases for blast search**
**The homologous sequences found in the searched database(s) are**
** ****directly returned to the user, sorted by score **
**OR: post-processed by the mediator (duplicate elimination, groupings, links to additional contextual data)**
**The resulting sequences can be queried for their associated information**
**Bob can use these sequences for new similarity searches**

## Use Case 1: Additional scenerios

**Helpful features for users**
**Multiple sequences entered through a single file **
**Ability to tie in other  programs to preprocess data before passing it to wrappers / mediator**
**Follow-up searches may be more than just blasts**
**Selection / project / join queries through the interface**
**Tie in other tools such as RasMol **
**Other types of search such as phiblast, psiblast or other structural similarity searches**

## Data Integration Architecture

**df**

**PDB**

**XML**
**Wrapper**

**XML**
**Wrapper**

**VIPAR**

**XML**
**Wrapper**

- API

- Integration
- component /
**KB-Mediator**
- (KBM)

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

**CM**
**Wrapper**

**CM**
**Wrapper**

**CM**
**Wrapper**

- Source / Agent
- MetaData
- Registry

- XWRAP
- Wrapper
- Generator

**XQuery (subsets e.g. Sel/Proj)**

**:**

**Medline**

**XML**
**Wrapper**

**XQuery interface**
**Select/project only**

**if invoked, pre-processes **
**query parameters and **
**post-processes results**

## Architecture comments

**Communication protocol:**
**Use agent technology to communicate between components**
**Don’t use full capabilities when on the same machine**
**Between QDaC and wrappers, QDaC and mediator, mediator and CMs, CMs and wrappers**
**NOT expected between wrappers and source **
**Embedded representation:**
**XML sources are queried using a subset of XQuery (fragments)**
**Primarily concerned with selection and projection – not join**
**Query results are returned in XML**

## Architecture comments 

**Meta-data repository (=metadata server)**
**Contains:**
**Location, schema**
**Query capabilities (blast, keyword, XPath) of sources**
**May be duplicated / shared between QDaC and KBM **
**Eventually may be treated as an agent  **
**External programs **
**Will be included as preprocessing steps**
**May need wrappers to handle translations properly**
**Will be tied in to interface where possible **
**Gives users access to tools they need / want / are familiar with**

## Architecture comments

**Expect most wrappers to be generated by XWrap in practice, but it shouldn’t matter as long as they follow the specified protocol and representation**
**VIPAR used to wrap publication sources**
**Simple SQL wrapper for direct database access**
**Definitions:**
**CM – conceptual mapping: a wrapper that translates source-specific XML into **

## Year 1 deliverables

**Send XQuery command to BLAST sources, combine results, and return to user interface**
**Interact with at least 4 sources**
**Integration component will have at least 2 sources**
**QDaC will directly query NCBI and at least one other**
**Operate QDaC and mediator in a distributed environment**
**Interface / QDaC at LLNL and mediator at UCSD**

**Have agent stubs at UCSD and LLNL passing text strings within 3 months**

## Detailed tasks

**Interface (LLNL)**
**Extended to handle blast against new sources**
**Some of which are not integrated**
**QDaC (LLNL)**
**Identify available wrappers from meta-data **
**This includes the SDSC component**
**Query wrappers using XQuery**
**Collect and sort responses**
**Adopt agent protocol**

## Detailed tasks

**XWrap  (GT)**
**Accept XPath/XQuery input **
**Handle complex BLAST interfaces**
**Adopt agent protocol**
**Mediator (UCSD)**
**Model of pathways, gene and protein expressions ==> ontology to be used for driving BLAST queries and interpreting their results**
**Accept XQuery queries**
**Identify available sources from meta-data**
**Modify CM wrappers to generate XQuery commands**
**Agent technology (ORNL, LLNL, UCSD)**
**Use VIPAR to wrap Medline database**
**Use protocols to communicate between LLNL and SDSC components **

## Administrative

**Reports**
**Quarterly reports **
**to be collected by Terence, (possibly) summarized, and forwarded on to Arie**
**Short – bulleted form (word file or plain text preferred) **
**Center-wide communications**
**Telecon 1****st**** Monday of the month 11:00 – 12:00 PST**
**It is ok to miss this**
**Semi-annual meetings **
**next at ORNL in mid-March**
**Center web site will point to individual task sites**
**Shared CVS repository at NC State**
**Primarily for major releases / sharing code between tasks**

## Administrative

**Advisory committee**
**Potential names from bioinformatics area**
**Carole Goble (Univ of Manchester), Tom Slezak (LLNL), ???**
**Unclear who pays travel for members**
**This is for us, so they will not be generating reports**

## Task specific 

**Mail list**
**For our task ONLY **_**s**__**[dm](mailto:dmctr-integrate@llnl.gov)**__**[ctr](mailto:dmctr-integrate@llnl.gov)**__**[-integrate@llnl.gov](mailto:dmctr-integrate@llnl.gov)**_** ****is being set up **
**Will be archived**
**Site contacts**
**Terence ****	****(LLNL)**
**Bertram ****	****(UCSD)**
**Calton ****	****(GT)**
**Tom ****	****(Agents)**
**Web site**
**Being set up at GT**
**Use main CVS repository for major releases**

**Code sharing option 1**
**Task-only CVS repository for day-to-day work**
**Unlikely LLNL could host this service**
**Code sharing option 2**
**Site specific cvs repositories for day-to-day work**
**Alexandria repository for inter-task code sharing**
_**[https://www-casc.llnl.gov/alexandria/](https://www-casc.llnl.gov/alexandria/)**_
**Disadv: tar-balls **
**Adv: we don’t all need an account on the repository machine**