Revision as of 22:18, 13 October 2009

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

Headline text

OBR workflow execution history

Oct 06, 2009 [Palani]:

RAT	Start date	End date	Database/schema	Type of work flow 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

Aug 24, 2009 [Palani]:

RAT	Start date	End date	Database/schema	Type of work flow execution
GAP	Sunday, Aug 23, 2009 10:44 PM	Monday, Aug 24, 2009 04:40 AM	obsdb1.obs_stage	Resource update + OBR execution with full dictionary of the new delta of resources

Aug 04, 2009 [Palani]:

RAT	Start date	End date	Database/schema	Type of work flow execution
SMD, DBK	Monday, Aug 03, 2009 11:28 PM	Tuesday, Aug 04, 2009 02:12 PM	obsdb1.obs_stage	Resource update + OBR execution with full dictionary of the new delta of resources

July 29, 2009 [Palani]:

RAT	Start date	End date	Database/schema	Type of work flow execution
AE	Monday, July 27, 2009 11:19 PM	Wednesday, July 29, 2009 02:42 AM	obsdb1.obs_stage	Resource update + OBR execution with full dictionary of the new delta of resources

July 21, 2009 [Kuladip/Palani]:

RAT	Start date	End date	Database/schema	Type of work flow execution
(All)	Monday, July 13, 2009 02:45 AM	Tuesday, July 21, 2009 03:46 AM	obsdb1.obs_stage	Resource update + OBR execution with full dictionary of the new delta of resources

June 17, 2009 [Kuladip]:

RAT	Start date	End date	Database/schema	Type of work flow execution
AE	Wednesday, June 17, 2009 3:45 AM	Wednesday, June 17, 2009 10:04 AM	obsdb1.obs_stage	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

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Difference between revisions of "Processing OBR Resources"