Difference between revisions of "Processing OBR Resources"
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| − | + | This wiki page describes the status of the OBR index. | |
| − | + | = 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 [http://www.stanford.edu/~coulet/obr_tutorial_to_add_new_resources.pdf tutorial] by Adrien Coulet. | 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 | |
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| + | * ChemSpider | ||
| + | * Human Gene Mutation Database | ||
| − | = | + | === Development history === |
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1. Resource: Clinicaltrials.gov | 1. Resource: Clinicaltrials.gov | ||
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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. | ||
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2. Resource: GEO | 2. Resource: GEO | ||
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*Status: | *Status: | ||
Changes done as per suggestions : | Changes done as per suggestions : | ||
| − | 1. Implement log4j logger mechanism. | + | 1. Implement log4j logger mechanism. |
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3. Resource: Pubmed | 3. Resource: Pubmed | ||
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4. Code changes pushed in SVN. | 4. Code changes pushed in SVN. | ||
| − | + | = Execution of the OBR worklow & maintenance of the OBR index = | |
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| + | == Technical documentation == | ||
Optra & Clement are working on a instruction document to be posted here soon. | Optra & Clement are working on a instruction document to be posted here soon. | ||
Image Resource: [[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]] | Image Resource: [[Image:PopulationOBRtables.png|thumb|Population of the OBR tables]] | ||
| − | == | + | == Execution history == |
| − | + | * June 8, 2009 [Cleemnt]: End of execution of the oBR workflow & switch of OBR API to the obsdb1.obs_stage schema | |
| + | * May 22, 2009 [Clement]: OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources | ||
| + | * May 2009 [Adrien]: Execution of the OBR index on RXRD independently (on obsdb1.obs_stage schema) | ||
| + | * March 2009 [Clement]: DB schema use right now: ncbodb2.obs | ||
| − | = | + | = Migration to a production architecture & framework = |
The task of writing a skeleton RAT conforming to Cherie's architecture. | The task of writing a skeleton RAT conforming to Cherie's architecture. | ||
| − | =Ongoing Challenges= | + | = Ongoing Challenges = |
Revision as of 07:03, 8 June 2009
This wiki page describes the status of the OBR index.
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.
Execution of the OBR worklow & maintenance of the OBR index
Technical documentation
Optra & Clement are working on a instruction document to be posted here soon.
Image Resource:
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
Execution history
- June 8, 2009 [Cleemnt]: End of execution of the oBR workflow & switch of OBR API to the obsdb1.obs_stage schema
- May 22, 2009 [Clement]: OBR workflow run (from scratch) on the new schema obsdb1.obs_stage for all resources
- May 2009 [Adrien]: Execution of the OBR index on RXRD independently (on obsdb1.obs_stage schema)
- March 2009 [Clement]: DB schema use right now: ncbodb2.obs
Migration to a production architecture & framework
The task of writing a skeleton RAT conforming to Cherie's architecture.