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 And Maintenance Of The OBR Index
Population of OBR and OBS tables is described in document Population_And_Maintenance_Of_The_OBR_Index
- Technical Instructions for Configuring OBR Workflow
Population of OBR and OBS tables using properties files and shell script is described in document Technical_Instructions_for_Configuring_OBR_Workflow
RAT Start Date End Date Database Type of workflow execution PCM Sunday, Oct 04, 2009 10:47 PM Monday, Oct 05, 2009 06:11 PM Obsdb1.obs_stage Resource update + OBR execution with full dictionary of the new delta of resources
Headline text
OBR workflow execution history
- Oct 13, 2009 [Palani]:
| RAT | Date first processed | Date last processed | Database/schema | Executed by | Type of work flow execution |
|---|---|---|---|---|---|
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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