Caltech documentation

Table of Contents

First-pass flagging

• First-pass flagging pipelines
• Instructions for the first pass curator:
  • Quick summary
  • Detailed instructions
• Datatypes flagged through the first-pass forms: Datatypes flagged

Automation and Text Mining Approaches

• Curation Tasks

• Schedule for Presentations

• WormBase Literature Curation Workflow

Citace

• citace data assignments

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

• Curation status pages
• New 2012 Curation Status pages

postgres

• WBGene information and status pipeline

Caltech weekly meetings

• WormBase-Caltech Weekly Calls

Conference Calls

• November 25, 2009 - Sequence Curation Flags

Phenote

• Phenote cgi wish list

Ontology Annotator

• Ontology Annotator

Textpresso

• Textpresso
• How to make a new Textpresso category
• Textpresso Central

SVMs for First Pass Curation

• What are SVMs?
• SVM Guidelines
• WormBase SVMs
• dictyBase
• FlyBase

GSA markup

• GSA Markup Workflow
• GSA Markup SOP
• GSA linking pipeline
• Entity classes and problems
  • Papers that have been markedup
  • Markup excerpts
• Future Entities for markup
• GSA Markup Meeting Notes
• GO entity markup

User Guide 2010

Table of Contents

Interesting, Not-yet-modelled Data Index

INDI

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