Difference between revisions of "Processing OBR Resources"

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−
== Resources Access Tools ==
+
This wiki page describes the status of the OBR index.
  
−
This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main activities: 1) Reprocessing resources and writing access tools for new resources, 2) Executing the annotation workflow, and 3) Migrating to a production architecture.
+
= Execution of the OBR worklow =
  
−
== How to write Resources Access Tools ==
+
== Technical documentation ==
 +
[[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
 +
* '''Population And Maintenance Of The OBR Index'''
 +
Population of OBR and OBS tables is described in document [http://www.bioontology.org/wiki/images/5/5f/Population_And_Maintenance_Of_The_OBR_Index.doc Population_And_Maintenance_Of_The_OBR_Index]
  
−
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.
+
* '''Technical Instructions for Configuring OBR Workflow'''
 +
Population of OBR and OBS tables using properties files and shell script is described in document [http://www.bioontology.org/wiki/images/4/47/Technical_Instructions_for_Configuring_OBR_Workflow.doc 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) ==
 +
 
 +
{| class="wikitable" border="1" cellspacing="0" cellpadding="1" width="150%"
 +
|-
 +
!  RAT
 +
!  Date first processed
 +
!  Date last processed
 +
!  Database/schema
 +
!  Executed by
 +
!  Type of work flow execution
 +
|-
 +
| valign="top" width="5%" |BSM
 +
| valign="top" width="25%" |Tuesday Dec 01, 2009 11:23 PM
 +
| valign="top" width="25%" |Tuesday Dec 01, 2009 11:38 PM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
 +
|-
 +
| valign="top" width="5%" |MICAD
 +
| valign="top" width="25%" |Monday Nov 09, 2009 05:29 AM
 +
| valign="top" width="25%" |Monday Nov 09, 2009 04:08 PM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
 +
|-
 +
| valign="top" width="5%" |SMD
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 04:14 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |GM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 03:26 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |REAC
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 03:23 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |DBK
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 02:01 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |PCM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 01:59 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |BSM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 01:45 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |AE
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 01:39 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |PC
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 00:23 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |GAP
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 00:19 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |WP
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 00:17 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |GEO
 +
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
 +
| valign="top" width="25%" |Thursday Nov 05, 2009 00:15 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |PGGE
 +
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:34 PM
 +
| valign="top" width="25%" |Wednesday Nov 04, 2009 10:38 PM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |PGDI
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:19 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |UPKB
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:13 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |CDD
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 01:09 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |PGDR
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:56 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" |OMIM
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:39 AM
 +
| valign="top" width="25%" |Tuesday Nov 03, 2009 00:52 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |GM
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 05:11 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |REAC
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 04:07 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |BSM
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:15 AM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |WP
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM 
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:08 AM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |PGGE
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM 
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 02:06 AM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |PGDI
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM 
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:52 AM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |UPKB
 +
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM 
 +
| valign="top" width="25%" |Tuesday Oct 27, 2009 01:35 AM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |CDD
 +
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM 
 +
| valign="top" width="25%" |Monday Oct 26, 2009 10:56 PM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |PGDR
 +
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM 
 +
| valign="top" width="25%" |Monday Oct 26, 2009 08:07 AM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |OMIM
 +
| valign="top" width="25%" |Monday Oct 26, 2009 05:24 AM 
 +
| valign="top" width="25%" |Monday Oct 26, 2009 07:46 AM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |PC
 +
| valign="top" width="25%" |Wednesday Oct 14, 2009 10:47 PM 
 +
| valign="top" width="25%" |Wednesday Oct 14, 2009 11:00 PM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
 +
 
 +
|-
 +
| valign="top" width="5%" |SMD
 +
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM 
 +
| valign="top" width="25%" |Monday Oct 12, 2009 08:06 AM           
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |GM
 +
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM 
 +
| valign="top" width="25%" |Monday Oct 12, 2009 02:31 AM         
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |REAC
 +
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM 
 +
| valign="top" width="25%" |Monday Oct 12, 2009 02:23 AM         
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" |RXRD
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM 
 +
| valign="top" width="25%" |Monday Oct 12, 2009 02:11 AM         
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | DBK
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:52 PM       
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | CT
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 05:29 PM       
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | BSM
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:39 AM       
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | AE
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 04:37 AM         
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | GAP
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM 
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:55 AM       
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | WP
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM 
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:54 AM       
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | GEO
 +
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM 
 +
| valign="top" width="25%" |Tuesday Oct 06, 2009 00:53 AM     
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | PGGE
 +
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM 
 +
| valign="top" width="25%" |Monday Oct 05, 2009 11:47 PM     
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | PGDI
 +
| valign="top" width="25%" |Monday Oct 05, 2009 11:44 PM
 +
| valign="top" width="25%" |Monday Oct 05, 2009 11:46 PM   
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | CDD
 +
| valign="top" width="25%" |  Monday Oct 05, 2009 10:47 PM
 +
| valign="top" width="25%" | Monday Oct 05, 2009 11:27 PM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" | UPKB
 +
| valign="top" width="25%" |  Monday Oct 05, 2009 11:27 PM 
 +
| valign="top" width="25%" | Monday Oct 05, 2009 11:44 PM   
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
 
 +
|-
 +
| valign="top" width="5%" | PGDR
 +
| valign="top" width="25%" |  Monday Oct 05, 2009 10:45 PM 
 +
| valign="top" width="25%" | Monday Oct 05, 2009 10:47 PM 
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" | OMIM
 +
| valign="top" width="25%" |  Monday Oct 05, 2009 10:32 PM
 +
| valign="top" width="25%" | Monday Oct 05, 2009 10:45 PM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" |Ontology update + OBR execution with new delta dictionary of all the resources
 +
|-
 +
| valign="top" width="5%" | PCM
 +
| valign="top" width="25%" |  Sunday, Oct 04, 2009 10:47 PM
 +
| valign="top" width="25%" | Monday, Oct 05, 2009 06:11 PM
 +
| valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
| valign="top" | Resource update + OBR execution with full dictionary of the new delta of resources
 +
|-
 +
|  valign="top" width="5%" |GAP
 +
|  valign="top" width="25%" | Sunday, Aug 23, 2009 10:44 PM
 +
|  valign="top" width="25%" | Monday, Aug 24, 2009 04:40 AM
 +
|  valign="top" width="10%" |obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
|  valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
 +
|-
 +
|  valign="top" width="5%" |SMD, DBK
 +
|  valign="top" width="25%" | Monday,  Aug 03, 2009 11:28 PM
 +
|  valign="top" width="25%" | Tuesday, Aug 04, 2009 02:12 PM
 +
|  valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
|  valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
 +
|-
 +
|  valign="top" width="5%" | AE
 +
|  valign="top"  width="25%" | Monday, July 27, 2009 11:19 PM
 +
|  valign="top" width="25%" | Wednesday, July 29, 2009 02:42 AM
 +
|  valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Palani
 +
|  valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
 +
|-
 +
|  valign="top" width="5%" | (All)
 +
|  valign="top" width="25%" | Monday,  July 13, 2009 02:45 AM
 +
|  valign="top" width="25%" | Tuesday, July 21, 2009 03:46 AM
 +
|  valign="top" width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Kuladip/Palani
 +
|  valign="top" |Resource update + OBR execution with full dictionary of the new delta of resources
 +
|-
 +
|  valign="top" width="5%" | AE
 +
|  valign="top" width="25%" | Wednesday, June 17, 2009  3:45 AM
 +
|  valign="top" width="25%" | Wednesday, June 17, 2009 10:04 AM
 +
|  valign="top"  width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Kuladip
 +
|  valign="top" |Contexts Populated : name, description, species
 +
|-
 +
|  valign="top" width="5%" | (All)
 +
|  valign="top" width="25%" |
 +
|  valign="top" width="25%" | June 8, 2009
 +
|  valign="top"  width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Clement
 +
|  valign="top" |End of execution of the OBR workflow & switch of OBR API to the obsdb1.obs_stage schema
 +
|-
 +
|  valign="top" width="5%" | (All)
 +
|  valign="top" width="25%" |
 +
|  valign="top" width="25%" | May 22, 2009
 +
|  valign="top"  width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Clement
 +
|  valign="top" |OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
 +
|-
 +
|  valign="top" width="5%" | RXRD
 +
|  valign="top" width="25%" |
 +
|  valign="top" width="25%" | May 2009
 +
|  valign="top"  width="10%" | obsdb1.obs_stage
 +
| valign="top" width="10%" |Adrien
 +
|  valign="top" |Execution of the OBR index on RXRD independently
 +
|-
 +
|  valign="top" width="5%" | (All)
 +
|  valign="top" width="25%" |
 +
|  valign="top" width="25%" | March 2009
 +
|  valign="top"  width="10%" |
 +
| valign="top" width="10%" |Clement
 +
|  valign="top" |DB schema use right now: ncbodb2.obs
 +
|}
  
−
==Reprocessing: Simple re-run of an existing ResourceAccessTool==
+
== Resources logs ==
 +
* '''Execution of the OBR workflow log files'''
 +
Log files are available here : [https://bmir-gforge.stanford.edu/gf/project/obs/docman/?subdir=58 /project/obs/docman/logs]
  
 +
= Resources Access Tools =
  
−
1. Resource: CDD
+
This page is for keeping track of Resources Access Tools (RATs) developement.
−
*Person responsible: Adrien (on the way to be managed by Optra)
 
−
*Status: annotations to process
 
−
*Last processed: 3/9/2009
 
  
−
2. Resource: OMIM
+
=== How to write Resources Access Tools ===
−
*Person responsible: Adrien (on the way to be managed by Optra)
+
How to write a resource access tool is described in this [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.
−
*Status:  annotations to process
 
−
*Last processed: 3/9/2009
 
  
−
3. Resource: PharmGKB
+
=== Available resources ===
−
*Person responsible: Adrien (on the way to be managed by Optra)
 
−
*Status: annotations to process
 
−
*Last processed: 3/9/2009
 
  
−
4. Resource: Reactome
+
Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /obr/resources]
−
*Person responsible: Adrien (on the way to be managed by Optra)
 
−
*Status: annotations to process
 
−
*Last processed: 3/9/2009
 
  
−
5. Resource: ResearchCrossroads
+
=== On development resources ===
−
*Person responsible: Adrien (on the way to be managed by Optra)
+
* PubMed (PM)
−
*Status: annotations to process
+
* Stanford Microarray Database (SMD)
−
*Last processed: 3/4/2009
+
* Pathway Commons
 +
* CaNanoLab
  
−
6. Resource: UniProt
+
Others in queue
−
*Person responsible: Adrien (on the way to be managed by Optra)
 
−
*Status: annotations to process
 
−
*Last processed: 3/9/2009
 
  
 +
* ChemSpider
 +
* Human Gene Mutation Database
  
−
=Reprocessing:  Modification of an existing ResourceAccessTool =
+
=== Development history ===
−
Examples include GEO, ClinicalTrials, Pubmed.
 
  
 
1. Resource: Clinicaltrials.gov  
 
1. Resource: Clinicaltrials.gov  
Line 51: Line 495:
 
         1. Decrease request delay from 1000 ms to 800ms.
 
         1. Decrease request delay from 1000 ms to 800ms.
 
         2. Implement log4j logger mechanism.
 
         2. Implement log4j logger mechanism.
−
 
−
*Last processed: 3/20/2009.
 
  
 
2. Resource: GEO  
 
2. Resource: GEO  
Line 59: Line 501:
 
*Status:   
 
*Status:   
 
         Changes done as per suggestions :
 
         Changes done as per suggestions :
−
         1. Implement log4j logger mechanism.        
+
         1. Implement log4j logger mechanism.  
−
   
 
−
*Last processed: 3/20/2009.
 
  
 
3. Resource: Pubmed  
 
3. Resource: Pubmed  
Line 73: Line 513:
 
       4. Code changes pushed in SVN.
 
       4. Code changes pushed in SVN.
  
−
*Last processed: 3/23/2009.
+
= Migration to a production workflow =
−
 
 
−
=Writing a new ResourceAccessTools=
 
−
Examples include CaNanoLab.
 
−
 
 
−
Others in queue
 
−
 
 
−
* PathwayCommons http://www.pathwaycommons.org/pc/ they have a web service, and we should focus on getting all pathways via web services.
 
−
* Stanford Microarray Database
 
−
* ChemSpider
 
−
* Human Gene Mutation Database
 
−
 
 
−
= Executing the Annotation workflow =
 
−
 
 
−
== Population of the OBR index ==
 
−
 
 
−
Optra & Clement are working on a instruction document to be posted here soon.
 
−
Image Resource: [[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]]
 
−
 
 
−
== Population of OBS tables ==
 
−
 
 
−
See [[Populating_OBS_database]]
 
−
 
 
−
=Migrating to new Architecture=
 
−
 
 
−
The task of writing a skeleton RAT conforming to Cherie's architecture.
 
  
−
=Ongoing Challenges=
+
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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