Difference between revisions of "Caltech documentation"
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Contact Person: Daniela Raciti | Contact Person: Daniela Raciti | ||
| + | *number of Expression Pattern objects | ||
| + | *number of Picture objects | ||
*number of genes with Expression Pattern | *number of genes with Expression Pattern | ||
*number of genes with Picture | *number of genes with Picture | ||
Revision as of 20:06, 1 February 2013
Contents
- 1 First-pass flagging
- 2 Automation and Text Mining Approaches
- 3 Citace
- 4 Datatype
- 5 Curation Progress
- 6 postgres
- 7 Caltech weekly meetings
- 8 Conference Calls
- 9 Phenote
- 10 Ontology Annotator
- 11 Textpresso
- 12 SVMs for First Pass Curation
- 13 GSA markup
- 14 User Guide 2010
- 15 Interesting, Not-yet-modelled Data Index
- 16 Release note requests from Caltech
First-pass flagging
- First-pass flagging pipelines
- Instructions for the first pass curator:
- Datatypes flagged through the first-pass forms: Datatypes flagged
Automation and Text Mining Approaches
Citace
Datatype
- Antibody
- Concise Descriptions
- Expression Pattern
- Gene Class Descriptions
- Gene Interaction
- Gene Ontology
- Gene-Paper Associations
- Gene Regulation
- Life_Stage
- Molecule
- Movie
- Paper Pipeline
- Phenotypes
- Physical Interactions
- Pictures
- Process pages
- RNAi
- Transgenes
- Disease and Drugs
Curation Progress
postgres
Caltech weekly meetings
Conference Calls
Phenote
Ontology Annotator
Textpresso
SVMs for First Pass Curation
GSA markup
- GSA Markup Workflow
- GSA Markup SOP
- GSA linking pipeline
- Entity classes and problems
- Future Entities for markup
- GSA Markup Meeting Notes
- GO entity markup
User Guide 2010
Interesting, Not-yet-modelled Data Index
Release note requests from Caltech
For Phenotype
Contact persons: Karen Yook
- In particular how many genes have been annotated with a phenotype
- through RNAi observed phenotype (ignore phenotype not observed for this class)
- through variation phenotype (include observed and not observed)
- through overexpression (transgene-phenotype)
The problem with this query is that I need to know this information broken down for genes with alleles, and need to filter out snps from the variation class and filter out all MM, WGS mutations as well. It would be good to have a list of all putative coding changing snps, but I do not want to mix up granular gene function characterization efforts with large scale sequencing projects that do not focus on gene-phenotype analysis.
- I would like to also get this list of genes with alleles and no phenotype.
For Disease
Contact Persons: Paul Davis, Ranjana Kishore
Information under 'Disease_info' tag for gene.
- number of genes with 'Potential model' tag
- number of genes with 'Experimental model' tag
- number of genes with 'Disease_relevance' descriptions
- number of Disease Ontology terms (DO) terms in database
- number of DO terms linked to genes (add DO terms used in Potential_model and Experimental_model tags)
For Expression Pattern
Contact Person: Daniela Raciti
- number of Expression Pattern objects
- number of Picture objects
- number of genes with Expression Pattern
- number of genes with Picture
