Processing OBR Resources

This page is for keeping track of what resources we process and what is done with each ResourceAccessTool. There are three main activities.

Reprocessing: Simple re-run of an existing ResourceAccessTool

1. Resource: CDD

• Person responsible: Adrien
• Status: annotations to process
• Last processed: 3/4/2009

2. Resource: OMIM

• Person responsible: Adrien
• Status: annotations to process
• Last processed: 3/4/2009

3. Resource: PharmGKB

• Person responsible: Adrien
• Status: annotations to process
• Last processed: 3/3/2009

4. Resource: Reactome

• Person responsible: Adrien
• Status: annotations to process
• Last processed: 3/3/2009

5. Resource: ResearchCrossroads

• Person responsible: Adrien
• Status: annotations to process
• Last processed: 3/4/2009

6. Resource: UniProt

• Person responsible: Adrien
• Status: annotations to process
• Last processed: 3/3/2009

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: Coding and data processing is done .

        ET table verified by stanford. 
        Code is checked in SVN.  
        Stanford needs to then run the RAT against local stanford database.

• Last processed: 3/12/2009.

2. Resource: Geo- GSE

• Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
• Notes:Built a new resource access tool to get data from GEO- GSE database(as of now a separate tool not integrated with GDS).
• Status: Changes done as per Stanford suggestions :

       1. Merging Geo Acccess Tool for GDS and GSE Data done
       2. localConceptID field   prefixed with ‘GSE’ or ‘GDS’ 
       3. resourceElementURL  moved to  http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=  
       4. For GEO_organism used mapStringToLocalConceptID method with a restriction 'NCBI' as localOntologyID.
       5. Splitting organism string  by ';' a  and pass it to mapStringToLocalConceptID method.
       6. ET table data verified by Stanford
       7. Code is expected to uploaded to SVN on 13th March. 
    

• Last processed: 3/11/2009.

3. Resource: Pubmed

• Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
• Notes:Built a new resource access tool from existing PubMed3AccessTool to populate data from pubmed xml files .
• Status:Coding verification & local testing in progress.ET table data provided to Stanford for verification

     Changes done as per Stanford suggestions :
      1. For PM_meshheadings context used ‘MSH’ localOntologyID .
      2. Coding and testing  for resource tool using E-Utils is in progress.
      3. Merging of XML & online processing in progress
      4. One pass of local execution is done after code changes. 
      5. SVN checkin is expected by 18th March.

• Last processed: 3/12/2009.

Writing a new ResourceAccessTools

Examples include CaNanoLab.

Others in queue

• PathwayCommons
• ChemSpider
• Stanford Microarray Database
• Human Gene Mutation Database