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 data provided to Stanford for verification
+
*Status: Coding and data processing is done .'''ET table verified by stanford'''. Code will checkedin to SVN,
*Last processed: 3/10/2009.
+
*Stanford needs to then run the RAT against local stanford database.
 +
*Last processed: 3/12/2009.
  
 
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:ET table data provided to Stanford for verification
+
*Status:'''ET table data verified by Stanford'''
 
         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
Line 53: Line 54:
 
         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.
 +
        7. Stanford needs to then run the RAT against local stanford database.
  
 
*Last processed: 3/11/2009.
 
*Last processed: 3/11/2009.
Line 62: Line 65:
 
*Status:Coding verification & local testing in progress.ET table data provided to Stanford for verification
 
*Status:Coding verification & local testing in progress.ET table data provided to Stanford for verification
 
       Changes done as per Stanford suggestions :
 
       Changes done as per Stanford suggestions :
       1.For PM_meshheadings context used ‘MSH’ localOntologyID .
+
       1. For PM_meshheadings context used ‘MSH’ localOntologyID .
       2.Coding and testing  for resource tool using E-Utils is in progress.
+
       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.'''
  
*Last processed: 3/11/2009.
+
*Last processed: 3/12/2009.
  
 
=Writing a new ResourceAccessTools=
 
=Writing a new ResourceAccessTools=

Revision as of 20:41, 11 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 will checkedin to 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:ET table data verified by Stanford
       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. Code is expected to uploaded to SVN on 13th March. 
       7. Stanford needs to then run the RAT against local stanford database.
  • 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. 
  • Last processed: 3/12/2009.

Writing a new ResourceAccessTools

Examples include CaNanoLab.

Ongoing Challenges

Other Updates