Caltech documentation

From WormBaseWiki

Table of Contents

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

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
• Paper Pipeline
• Phenotypes
• Physical Interactions
• Pictures
• Process pages
• RNAi
• Transgenes
• Disease and Drugs

Curation Progress

• 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