Release note requests

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 via Potential_model tag
• number of DO terms linked to genes via Experimental_model tag

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

For Genes

Per species:

• Number of genes of each type (protein-coding, miRNA, rRNA, tRNA, etc.)
• Of those, how many are annotated with an observed phenotype (by RNAi, Allele, Transgene, and Total)
• Number of gene-to-phenotype (observed only) annotations (by RNAi, Allele, Transgene, and Total)
• Number of gene-RNAi annotations
• Number of gene-Allele annotations

For Papers

• Number of papers (primary, published research only? i.e. no meeting abstracts, no gazette articles)
• Number of paper-gene connections
• Number of paper-RNAi connections

Back to Caltech documentation