Processing OBR Resources

This wiki page describes the status of the OBR index.

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

OBR workflow execution history

• Aug 24, 2009 [Palani]: Execution of the OBR workflow for DbGap RAT from scratch independently using shell script and property files (on obsdb1.obs_stage schema)

        Started  Date/Time         : Sunday, Aug 23, 2009 10:44 PM        
        Finished Date/Time         : Monday, Aug 24, 2009 04:40 AM  
        Type of workflow execution : Resource update + OBR execution with full 
                                     dictionary of the new delta of resources

• Aug 04, 2009 [Palani]: Execution of the OBR workflow for SMD and DBK RATs from scratch independently using shell script and property files (on obsdb1.obs_stage schema)

        Started  Date/Time         : Monday,  Aug 03, 2009 11:28 PM 
        Finished Date/Time         : Tuesday, Aug 04, 2009 02:12 PM
        Type of workflow execution : Resource update + OBR execution with full 
                                     dictionary of the new delta of resources

• July 29, 2009 [Palani]: Execution of the OBR workflow for Array Express RAT from scratch independently using shell script and property files (on obsdb1.obs_stage schema)

        Started  Date/Time         : Monday,    July 27, 2009 11:19 PM 
        Finished Date/Time         : Wednesday, July 29, 2009 02:42 AM
        Contexts Populated         : name, description, species
        Type of workflow execution : Resource update + OBR execution with full
                                     dictionary of the new delta of resources

• 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 02:45 AM 
        Finished Date/Time         : Tuesday, July 21, 2009 03:46 AM
        Type of workflow execution : Resource update + OBR execution with full 
                                     dictionary of the new delta of resources

• 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 [Clement]: 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

Resources logs

• Execution of the OBR workflow log files

Log files are available here : /project/obs/docman/logs

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.

Migration to a production architecture & framework

No yet started