User Guide 2010:TOC

Introduction

WormBase is a biological database of all genomic and genetic data of the model nematode Caenorhabditis elegans and related nematodes. This is a guide for using WormBase WormBase the genetic and genomic database of the model organism Caenorhabditis elegans and related nematodes. WormBase is developed by an international consortium of researchers and computer scientists.

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Getting Started

• What is WormBase?
• Machine/Browser compatibility
• What types of nematodes does WB collect data for?
• What types of information does WB contain?
• How are WormBase data organized?
• How does data get into WormBase?
• Can I view WormBase data offline?
• With what other formats are WB data compatible?
• Who are the worm community?
• Who are the WB database people?
• Who funds WB?

Contacting WormBase

• Who do I contact if I want to submit data?
• Who do I contact if I see an error on the page?
• Who do I contact if WormBase stops working for me?

Viewing and Navigating WB Data

Individual Pages

• Gene Page
• Sequence Page
• Protein Page
• Allele Page
• Clone/Plasmid Page
• Strain Page
• Molecule Page
• Phenotype Page
  • The NOT annotations
• RNAi experiment Page
• Microarray/SPELL

Searching WB

Simple searches

• Finding
  • a gene
  • an allele
  • a strain
  • a sequence

Ontology browsers

• What is an ontology? (What happened to my jargon?)
• What is GO?

Query languages

• AQL
• WQL

Retrieving/Exporting Data

• Bulk data access
  • gff files
• WormMart

WB Community Tools : tools generated/maintained by wormbase for the community

• Sequence analysis
  • orthology/homology predictors
    • Blast / Blat
    • Synteny Viewer
  • Cis-Elements (CisOrtho)

Experiment tools

• e-PCR
• Balancers
• Transgene markers

Keeping in Touch with WB

• Database release schedule
• Feeds
• Twitter

Glossary

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based on Reactome User's Guide