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 .'''ET table verified by stanford'''. Code | + | *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. | *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: | + | *Status: 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. 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.