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

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Population of the OBR tables

• Population And Maintenance Of The OBR Index

Population of OBR and OBS tables is described in document Population_And_Maintenance_Of_The_OBR_Index

• Technical Instructions for Configuring OBR Workflow

Population of OBR and OBS tables using properties files and shell script is described in document Technical_Instructions_for_Configuring_OBR_Workflow

Execution history

• July 21, 2009 [Kuladip/Palani]: Execution of the OBR workflow for all resources independently using shell script and property files (on obsdb1.obs_stage schema)

        Started  Date/Time : Monday, July 13, 2009  02:14:26 AM 
        Finished Date/Time : Tuesday, July 21, 2009 03:46:09 AM

• June 17, 2009 [Kuladip]: Execution of the OBR workflow for Array Express RAT independently using shell script and property files (on obsdb1.obs_stage schema)

        Started  Date/Time : Wednesday, June 17, 2009  3:45 AM 
        Finished Date/Time : Wednesday, June 17, 2009 10:04 AM
        Contexts Populated : name, description, species      

• 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.