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 data provided to Stanford for verification
• Last processed: 3/10/2009.

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:ET table data provided to Stanford for verification

       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

• 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.

• Last processed: 3/11/2009.

Writing a new ResourceAccessTools

Examples include CaNanoLab.