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

RAT Start Date End Date Database Type of workflow execution PCM Sunday, Oct 04, 2009 10:47 PM Monday, Oct 05, 2009 06:11 PM Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

OBR workflow execution history

RAT Start Date End Date Database Type of workflow execution PCM Sunday, Oct 04, 2009 10:47 PM Monday, Oct 05, 2009 06:11 PM Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources

• Oct 06, 2009 [Palani]: Execution of the OBR workflow for PCM RAT from scratch independently using shell script and property files (on obsdb1.obs_stage schema)

        Started  Date/Time         : Sunday, Oct 04, 2009 10:47 PM        
        Finished Date/Time         : Monday, Oct 05, 2009 06:11 PM  
        Type of workflow execution : Resource update + OBR execution with full 
                                     dictionary of the new delta of resources

• 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