Difference between revisions of "Processing OBR Resources"
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== Population of OBS tables == | == Population of OBS tables == | ||
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== Population of the OBR index == | == Population of the OBR index == | ||
Revision as of 13:44, 3 June 2009
Resources Access Tools
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.
How to write Resources Access Tools
How to write a resource access tool is described in this tutorial by Adrien Coulet.
Reprocessing: Simple re-run of an existing ResourceAccessTool
1. Resource: CDD
- Person responsible: Adrien (on the way to be managed by Optra)
- Status: annotations to process
- Last processed: 3/9/2009
2. Resource: OMIM
- Person responsible: Adrien (on the way to be managed by Optra)
- Status: annotations to process
- Last processed: 3/9/2009
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
- Person responsible: Adrien (on the way to be managed by Optra)
- Status: annotations to process
- Last processed: 3/9/2009
5. Resource: ResearchCrossroads
- Person responsible: Adrien (on the way to be managed by Optra)
- Status: annotations to process
- Last processed: 3/4/2009
6. Resource: UniProt
- Person responsible: Adrien (on the way to be managed by Optra)
- Status: annotations to process
- Last processed: 3/9/2009
Reprocessing: Modification of an existing ResourceAccessTool
Examples include GEO, ClinicalTrials, Pubmed.
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.
- Last processed: 3/20/2009.
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.
- Last processed: 3/20/2009.
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.
- Last processed: 3/23/2009.
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 OBS tables
Population of the OBR index
Optra & Clement are working on a instruction document to be posted here soon.
Image Resource:
Migrating to new Architecture
The task of writing a skeleton RAT conforming to Cherie's architecture.