Difference between revisions of "Processing OBR Resources"

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== Headline text ==
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== Resource Index v2.0 execution history ==
  
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== OBR workflow execution history ==
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Please refer to: http://rest.bioontology.org/resource_index/executions/list/
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== Resource Index workflow execution history (before v2.0) ==
  
 
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Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]
 
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]
  
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= Resources Access Tools (RATs) development and update =
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= Resources Access Tools =
  
 
This page is for keeping track of Resources Access Tools (RATs) developement.  
 
This page is for keeping track of Resources Access Tools (RATs) developement.  
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       4. Code changes pushed in SVN.
 
       4. Code changes pushed in SVN.
  
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= Migration to a production worflow =
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= Migration to a production workflow =
  
 
No yet started
 
No yet started

Latest revision as of 13:11, 11 August 2010

This wiki page describes the status of the OBR index.

Execution of the OBR worklow

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


Resource Index v2.0 execution history

Please refer to: http://rest.bioontology.org/resource_index/executions/list/

Resource Index workflow execution history (before v2.0)

RAT Date first processed Date last processed Database/schema Executed by Type of work flow execution
BSM Tuesday Dec 01, 2009 11:23 PM Tuesday Dec 01, 2009 11:38 PM obsdb1.obs_stage Palani Resource update + OBR execution with full dictionary of the new delta of resources
MICAD Monday Nov 09, 2009 05:29 AM Monday Nov 09, 2009 04:08 PM obsdb1.obs_stage Palani Resource update + OBR execution with full dictionary of the new delta of resources
SMD Thursday Nov 05, 2009 03:26 AM Thursday Nov 05, 2009 04:14 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
GM Thursday Nov 05, 2009 03:23 AM Thursday Nov 05, 2009 03:26 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
REAC Thursday Nov 05, 2009 02:01 AM Thursday Nov 05, 2009 03:23 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
DBK Thursday Nov 05, 2009 01:59 AM Thursday Nov 05, 2009 02:01 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
PCM Thursday Nov 05, 2009 01:45 AM Thursday Nov 05, 2009 01:59 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
BSM Thursday Nov 05, 2009 01:39 AM Thursday Nov 05, 2009 01:45 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
AE Thursday Nov 05, 2009 00:23 AM Thursday Nov 05, 2009 01:39 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
PC Thursday Nov 05, 2009 00:19 AM Thursday Nov 05, 2009 00:23 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
GAP Thursday Nov 05, 2009 00:17 AM Thursday Nov 05, 2009 00:19 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
WP Thursday Nov 05, 2009 00:15 AM Thursday Nov 05, 2009 00:17 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
GEO Wednesday Nov 04, 2009 10:38 PM Thursday Nov 05, 2009 00:15 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
PGGE Wednesday Nov 04, 2009 10:34 PM Wednesday Nov 04, 2009 10:38 PM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
PGDI Tuesday Nov 03, 2009 01:13 AM Tuesday Nov 03, 2009 01:19 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
UPKB Tuesday Nov 03, 2009 01:09 AM Tuesday Nov 03, 2009 01:13 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
CDD Tuesday Nov 03, 2009 00:56 AM Tuesday Nov 03, 2009 01:09 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
PGDR Tuesday Nov 03, 2009 00:52 AM Tuesday Nov 03, 2009 00:56 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
OMIM Tuesday Nov 03, 2009 00:39 AM Tuesday Nov 03, 2009 00:52 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
GM Tuesday Oct 27, 2009 04:07 AM Tuesday Oct 27, 2009 05:11 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
REAC Tuesday Oct 27, 2009 02:15 AM Tuesday Oct 27, 2009 04:07 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
BSM Tuesday Oct 27, 2009 02:08 AM Tuesday Oct 27, 2009 02:15 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
WP Tuesday Oct 27, 2009 02:06 AM Tuesday Oct 27, 2009 02:08 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
PGGE Tuesday Oct 27, 2009 01:52 AM Tuesday Oct 27, 2009 02:06 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
PGDI Tuesday Oct 27, 2009 01:35 AM Tuesday Oct 27, 2009 01:52 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
UPKB Monday Oct 26, 2009 10:56 PM Tuesday Oct 27, 2009 01:35 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
CDD Monday Oct 26, 2009 08:07 AM Monday Oct 26, 2009 10:56 PM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
PGDR Monday Oct 26, 2009 07:46 AM Monday Oct 26, 2009 08:07 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
OMIM Monday Oct 26, 2009 05:24 AM Monday Oct 26, 2009 07:46 AM obsdb1.obs_stage Palani Ontology update + OBR execution with new delta dictionary of all the resources
PC Wednesday Oct 14, 2009 10:47 PM Wednesday Oct 14, 2009 11:00 PM obsdb1.obs_stage Palani Resource update + OBR execution with full dictionary of the new delta of resources
SMD Monday Oct 12, 2009 02:31 AM Monday Oct 12, 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

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 workflow

No yet started

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