Difference between revisions of "Processing OBR Resources"
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1. Resource: CDD | 1. Resource: CDD | ||
| − | *Person responsible: Adrien | + | *Person responsible: Adrien (on the way to be managed by Optra) |
*Status: annotations to process | *Status: annotations to process | ||
| − | *Last processed: 3/ | + | *Last processed: 3/9/2009 |
2. Resource: OMIM | 2. Resource: OMIM | ||
| − | *Person responsible: Adrien | + | *Person responsible: Adrien (on the way to be managed by Optra) |
*Status: annotations to process | *Status: annotations to process | ||
| − | *Last processed: 3/ | + | *Last processed: 3/9/2009 |
| − | 3. Resource: PharmGKB | + | 3. Resource: PharmGKB (on the way to be managed by Optra) |
| − | *Person responsible: Adrien | + | *Person responsible: Adrien |
*Status: annotations to process | *Status: annotations to process | ||
| − | *Last processed: 3/ | + | *Last processed: 3/9/2009 |
| − | 4. Resource: Reactome | + | 4. Resource: Reactome (on the way to be managed by Optra) |
| − | *Person responsible: Adrien | + | *Person responsible: Adrien |
*Status: annotations to process | *Status: annotations to process | ||
| − | *Last processed: 3/ | + | *Last processed: 3/9/2009 |
5. Resource: ResearchCrossroads | 5. Resource: ResearchCrossroads | ||
| − | *Person responsible: Adrien | + | *Person responsible: Adrien (on the way to be managed by Optra) |
*Status: annotations to process | *Status: annotations to process | ||
*Last processed: 3/4/2009 | *Last processed: 3/4/2009 | ||
6. Resource: UniProt | 6. Resource: UniProt | ||
| − | *Person responsible: Adrien | + | *Person responsible: Adrien (on the way to be managed by Optra) |
*Status: annotations to process | *Status: annotations to process | ||
| − | *Last processed: 3/ | + | *Last processed: 3/9/2009 |
Revision as of 10:38, 23 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 (on the way to be managed by Optra)
- Status: annotations to process
- Last processed: 3/9/2009
2. Resource: OMIM
- Person responsible: Adrien (on the way to be managed by Optra)
- Status: annotations to process
- Last processed: 3/9/2009
3. Resource: PharmGKB (on the way to be managed by Optra)
- Person responsible: Adrien
- Status: annotations to process
- Last processed: 3/9/2009
4. Resource: Reactome (on the way to be managed by Optra)
- Person responsible: Adrien
- Status: annotations to process
- Last processed: 3/9/2009
5. Resource: ResearchCrossroads
- Person responsible: Adrien (on the way to be managed by Optra)
- Status: annotations to process
- Last processed: 3/4/2009
6. Resource: UniProt
- Person responsible: Adrien (on the way to be managed by Optra)
- Status: annotations to process
- Last processed: 3/9/2009
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
- Person responsible: Kuladip Yadav(Optra), Sanjay Jadhav(Optra).
- Notes:Modified GEO resource access tool to get data from both GSE and GDS database.
- 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. Remove direct database call from PubMed RAT.
2. Implement mapStringsToLocalConceptIDs method into ObsOntologiesAccessTool and TermTable.
3. Implement log4j logger in related classes.
4. Code changes pushed in SVN.
- Last processed: 3/23/2009.
Writing a new ResourceAccessTools
Examples include CaNanoLab.
Others in queue
- PathwayCommons
- ChemSpider
- Stanford Microarray Database
- Human Gene Mutation Database