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	Date first processed	Date last processed	Database/schema	Executed by	Type of work flow execution
SMD	Monday Oct 12, 2009 02:31 AM	Tuesday Oct 13, 2009 08:06 AM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
GM	Monday Oct 12, 2009 02:23 AM	Monday Oct 12, 2009 02:31 AM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
REAC	Monday Oct 12, 2009 02:11 AM	Monday Oct 12, 2009 02:23 AM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
RXRD	Tuesday Oct 06, 2009 05:52 PM	Monday Oct 12, 2009 02:11 AM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
DBK	Tuesday Oct 06, 2009 05:29 PM	Tuesday Oct 06, 2009 05:52 PM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
CT	Tuesday Oct 06, 2009 04:39 AM	Tuesday Oct 06, 2009 05:29 PM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
BSM	Tuesday Oct 06, 2009 04:37 AM	Tuesday Oct 06, 2009 04:39 AM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
AE	Tuesday Oct 06, 2009 00:55 AM	Tuesday Oct 06, 2009 04:37 AM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
GAP	Tuesday Oct 06, 2009 00:54 AM	Tuesday Oct 06, 2009 00:55 AM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
WP	Tuesday Oct 06, 2009 00:53 AM	Tuesday Oct 06, 2009 00:54 AM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
GEO	Monday Oct 05, 2009 11:47 PM	Tuesday Oct 06, 2009 00:53 AM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
PGGE	Monday Oct 05, 2009 11:46 PM	Monday Oct 05, 2009 11:47 PM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
PGDI	Monday Oct 05, 2009 11:44 PM	Monday Oct 05, 2009 11:46 PM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
CDD	Monday Oct 05, 2009 10:47 PM	Monday Oct 05, 2009 11:27 PM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
UPKB	Monday Oct 05, 2009 11:27 PM	Monday Oct 05, 2009 11:44 PM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
PGDR	Monday Oct 05, 2009 10:45 PM	Monday Oct 05, 2009 10:47 PM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
OMIM	Monday Oct 05, 2009 10:32 PM	Monday Oct 05, 2009 10:45 PM	obsdb1.obs_stage	Palani	Ontology update + OBR execution with new delta dictionary of all the resources
PCM	Sunday, Oct 04, 2009 10:47 PM	Monday, Oct 05, 2009 06:11 PM	obsdb1.obs_stage	Palani	Resource update + OBR execution with full dictionary of the new delta of resources
GAP	Sunday, Aug 23, 2009 10:44 PM	Monday, Aug 24, 2009 04:40 AM	obsdb1.obs_stage	Palani	Resource update + OBR execution with full dictionary of the new delta of resources
SMD, DBK	Monday, Aug 03, 2009 11:28 PM	Tuesday, Aug 04, 2009 02:12 PM	obsdb1.obs_stage	Palani	Resource update + OBR execution with full dictionary of the new delta of resources
AE	Monday, July 27, 2009 11:19 PM	Wednesday, July 29, 2009 02:42 AM	obsdb1.obs_stage	Palani	Resource update + OBR execution with full dictionary of the new delta of resources
(All)	Monday, July 13, 2009 02:45 AM	Tuesday, July 21, 2009 03:46 AM	obsdb1.obs_stage	Kuladip/Palani	Resource update + OBR execution with full dictionary of the new delta of resources
AE	Wednesday, June 17, 2009 3:45 AM	Wednesday, June 17, 2009 10:04 AM	obsdb1.obs_stage	Kuladip	Contexts Populated : name, description, species
(All)		June 8, 2009	obsdb1.obs_stage	Clement	End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
(All)		May 22, 2009	obsdb1.obs_stage	Clement	OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
RXRD		May 2009	obsdb1.obs_stage	Adrien	Execution of the OBR index on RXRD independently
(All)		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