Difference between revisions of "Processing OBR Resources"

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*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
 
*Person responsible: Kuladip Yadav(Optra),Sanjay Jadhav(Optra).
 
*Notes: Fixed issue of authentication, fixed other xml related issues.
 
*Notes: Fixed issue of authentication, fixed other xml related issues.
−
*Status: Coding and data processing is done .
+
*Status:  
−
        '''ET table verified by stanford'''.  
+
        Changes done as per suggestions :
−
        Code is checked in SVN.
+
        1. Decrease request delay from 1000 ms to 800ms.
−
        Stanford needs to then run the RAT against local stanford database.
+
        2. Implement log4j logger mechanism.
−
*Last processed: 3/12/2009.
+
 
 +
*Last processed: 3/20/2009.
  
 
2. Resource: Geo- GSE  
 
2. Resource: Geo- GSE  
 
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
 
*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).
 
*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 :
+
*Status:   
−
         1. Merging Geo Acccess Tool for GDS and GSE Data done
+
        Changes done as per suggestions :
−
        2. localConceptID field  prefixed with ‘GSE’ or ‘GDS’
+
 
−
        3. resourceElementURL  moved to  http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc= 
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         1. Implement log4j logger mechanism.         
−
        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.
+
*Last processed: 3/20/2009.
  
 
3. Resource: Pubmed  
 
3. Resource: Pubmed  
 
*Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
 
*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 .
+
*Notes:Built a new resource access tool from existing PubMedAccessTool to populate data from eutils and pubmed xml files .
−
*Status:Coding verification & local testing in progress.ET table data provided to Stanford for verification
+
*Status:  
−
      Changes done as per Stanford suggestions :
+
      Changes done as per suggestions :
−
       1. For PM_meshheadings context used ‘MSH’ localOntologyID .
+
 
−
       2. Coding and testing  for resource tool using E-Utils is in progress.
+
       1. Make changes to Pub Med structure element as per GEO RAT.
−
       3. Merging of XML & online processing in progress
+
       2. Implement log4j logger mechanism.         
−
      4. '''One pass of local execution is done after code changes.'''
 
−
      5. SVN checkin is expected by 18th March.
 
  
−
*Last processed: 3/12/2009.
+
*Last processed: 3/20/2009.
  
 
=Writing a new ResourceAccessTools=
 
=Writing a new ResourceAccessTools=

Revision as of 06:09, 20 March 2009

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:
       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- 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 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. Make changes to Pub Med structure element as per GEO RAT.
      2. Implement log4j logger mechanism.
  • Last processed: 3/20/2009.

Writing a new ResourceAccessTools

Examples include CaNanoLab.

Others in queue

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

Ongoing Challenges

Other Updates

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