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.

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

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.