Processing OBR Resources

This wiki page describes the status of the OBR index.

Resources Access Tools (RATs) development and update

This page is for keeping track of Resources Access Tools (RATs) developement.

How to write Resources Access Tools

How to write a resource access tool is described in this tutorial by Adrien Coulet.

Available resources

Resources fully functional and available in the OBR index are available here: /obr/resources

On development resources

• PubMed (PM)
• Stanford Microarray Database (SMD)
• Pathway Commons
• CaNanoLab

Others in queue

• ChemSpider
• Human Gene Mutation Database

Development history

1. Resource: Clinicaltrials.gov

• Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
• Notes: Fixed issue of authentication, fixed other xml related issues.
• Status:

       Changes done as per suggestions : 
       1. Decrease request delay from 1000 ms to 800ms.
       2. Implement log4j logger mechanism.

2. Resource: GEO

• Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
• Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
• Status:

       Changes done as per suggestions :
       1. Implement log4j logger mechanism.   

3. Resource: Pubmed

• Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
• Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
• Status:

      Changes done as per suggestions :
      1. Remove direct database call from PubMed RAT.
      2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.       
      3. Implement log4j logger in related classes.
      4. Code changes pushed in SVN.

Execution of the OBR worklow & maintenance of the OBR index

Technical documentation

Optra & Clement are working on a instruction document to be posted here soon.

Image Resource:

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Population of the OBR tables

Execution history

• June 8, 2009 [Cleemnt]: End of execution of the oBR workflow & switch of OBR API to the obsdb1.obs_stage schema
• May 22, 2009 [Clement]: OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
• May 2009 [Adrien]: Execution of the OBR index on RXRD independently (on obsdb1.obs_stage schema)
• March 2009 [Clement]: DB schema use right now: ncbodb2.obs

Migration to a production architecture & framework

The task of writing a skeleton RAT conforming to Cherie's architecture.