Difference between revisions of "Processing OBR Resources"

From NCBO Wiki
Jump to navigation Jump to search
 
(105 intermediate revisions by 3 users not shown)
Line 1: Line 1:
−
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.
+
This wiki page describes the status of the OBR index.
  
−
=Reprocessing:  Simple re-run of an existing ResourceAccessTool=
+
= Execution of the OBR worklow =
  
 +
== 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]
  
−
1. Resource: CDD
+
* '''Technical Instructions for Configuring OBR Workflow'''
−
*Person responsible: Adrien (on the way to be managed by Optra)
+
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]
−
*Status: annotations to process
 
−
*Last processed: 3/9/2009
 
  
−
2. Resource: OMIM
+
RAT Start Date End Date Database Type of workflow execution
−
*Person responsible: Adrien (on the way to be managed by Optra)
+
PCM Sunday, Oct 04, 2009 10:47 PM
−
*Status: annotations to process
+
Monday, Oct 05, 2009 06:11 PM
−
*Last processed: 3/9/2009
+
Obsdb1.obs_stage Resource update + OBR execution with full                      dictionary of the new delta of resources
  
−
3. Resource: PharmGKB
 
−
*Person responsible: Adrien (on the way to be managed by Optra)
 
−
*Status: annotations to process
 
−
*Last processed: 3/9/2009
 
  
−
4. Resource: Reactome
+
== Resource Index v2.0 execution history ==
−
*Person responsible: Adrien (on the way to be managed by Optra)
 
−
*Status: annotations to process
 
−
*Last processed: 3/9/2009
 
  
−
5. Resource: ResearchCrossroads
+
Please refer to: http://rest.bioontology.org/resource_index/executions/list/
−
*Person responsible: Adrien (on the way to be managed by Optra)
 
−
*Status: annotations to process
 
−
*Last processed: 3/4/2009
 
  
−
6. Resource: UniProt
+
== Resource Index workflow execution history (before v2.0) ==
−
*Person responsible: Adrien (on the way to be managed by Optra)
 
−
*Status: annotations to process
 
−
*Last processed: 3/9/2009
 
  
 +
{| 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
  
−
=Reprocessing:  Modification of an existing ResourceAccessTool =
+
|-
−
Examples include GEO, ClinicalTrials, Pubmed.
+
| 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
 +
|}
 +
 
 +
== 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 =
 +
 
 +
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 [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet.
 +
 
 +
=== Available resources ===
 +
 
 +
Resources fully functional and available in the OBR index are available here: [http://ncbolabs-dev2.stanford.edu:8080/OBS_v1/obr/resources /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  
 
1. Resource: Clinicaltrials.gov  
Line 45: 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 53: 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 67: 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=
 
−
 
 
−
The plan is for Clement to run one resource access tool, Optra runs another one .. compare notes, and repeat once more with two more RATs. That way, at the end of the next week optra should be able to own the *writing to* the OBR index. (i.e. populating all the _ET, _AT, _EAT and _IT tables).
 
−
 
 
−
The server for this is ready. The machine to use is ncbolabs-dev2.stanford.edu. Clement still needs to do the following tasks before Optra can start on this:
 
−
 
 
−
* change the weight of is_a closure annotations using a function dependent on the level
 
−
* move some files (mgrep, files read/generated by the workflow) to folder accessible by everyones.
 
−
* move the workflow execution to db1
 
−
 
 
−
=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 14:11, 11 August 2010

This wiki page describes the status of the OBR index.

Execution of the OBR worklow

Technical documentation

Error creating thumbnail: /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 61: ulimit: cpu time: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 84: ulimit: virtual memory: cannot modify limit: Permission denied /srv/www/vhosts/www.bioontology.org/app/mediawiki-1.35.9/includes/shell/limit.sh: line 90: ulimit: file size: cannot modify limit: Permission denied /bin/bash: /usr/bin/convert: No such file or directory Error code: 127
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

Retrieved from "https://www.bioontology.org//mediawiki/index.php?title=Processing_OBR_Resources&oldid=10110"