Difference between revisions of "Processing OBR Resources"

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(Reprocessing: Modification of an existing ResourceAccessTool)
(Reprocessing: Modification of an existing ResourceAccessTool)
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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 .'''ET table verified by stanford'''. Code will checkedin to SVN,
+
*Status: Coding and data processing is done .
*Stanford needs to then run the RAT against local stanford database.
+
        '''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.
 
*Last processed: 3/12/2009.
  
Line 48: Line 50:
 
*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:'''ET table data verified by Stanford'''
+
*Status: Changes done as per Stanford suggestions :
        Changes done as per Stanford suggestions :
 
 
         1. Merging Geo Acccess Tool for GDS and GSE Data done
 
         1. Merging Geo Acccess Tool for GDS and GSE Data done
 
         2. localConceptID field  prefixed with ‘GSE’ or ‘GDS’  
 
         2. localConceptID field  prefixed with ‘GSE’ or ‘GDS’  
 
         3. resourceElementURL  moved to  http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=   
 
         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.
 
         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
+
         5. Splitting organism string  by ';' a  and pass it to mapStringToLocalConceptID method.
         6. Code is expected to uploaded to SVN on 13th March.  
+
         6. '''ET table data verified by Stanford'''
        7. Stanford needs to then run the RAT against local stanford database.
+
        7. Code is expected to uploaded to SVN on 13th March.  
 
+
   
 
*Last processed: 3/11/2009.
 
*Last processed: 3/11/2009.
  
Line 69: Line 70:
 
       3. Merging of XML & online processing in progress
 
       3. Merging of XML & online processing in progress
 
       4. '''One pass of local execution is done after code changes.'''  
 
       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: 3/12/2009.

Revision as of 02:05, 12 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: 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.

Ongoing Challenges

Other Updates