Difference between revisions of "Caltech documentation"

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====For Expression Pattern====
Contact Person: Daniela Raciti
*number of genes with Expression Pattern
*number of genes with Picture

Revision as of 20:03, 1 February 2013

Table of Contents

First-pass flagging

Automation and Text Mining Approaches



Curation Progress


Caltech weekly meetings

Conference Calls


Ontology Annotator


SVMs for First Pass Curation

GSA markup

User Guide 2010

Table of Contents

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 genes with Expression Pattern
  • number of genes with Picture