Processing OBR Resources

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 the OBR index

Optra & Clement are working on a instruction document to be posted here soon.

Image Resource:

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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.