User Guide 2010:TOC

From WormBaseWiki
Revision as of 16:13, 10 August 2010 by Kyook (talk | contribs)
Jump to navigationJump to search

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

To edit this Wiki, please create an account (click on the 'log in/create account' link at the top of the page). Before contributing, please see the WormBaseWiki usage guidelines.

Getting Started

Contacting WormBase

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

These are tools generated and or maintained by WB for the community.

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

Experiment tools

  • e-PCR
  • Balancers
  • Transgene markers

UserGuide:Display Tools UserGuide:Embryonic Cell/Time Correlation Table 1 UserGuide:Embryonic Stage/Time Correlation Table 2 UserGuide:Definitions for Life Stages

UserGuide:Full Text Journals UserGuide:Gene Ontology

UserGuide:Genetic Map

UserGuide:How to Obtain Reagents UserGuide:Life Stage System in WormBase UserGuide:Nomenclature UserGuide:Nomenclature nematode UserGuide:Release Notes UserGuide:Wormpep file descriptions UserGuide:ePCR

Downloading WB Data

Batch downloads, Genome Dumper

General Information

Staying up-to-date

WormBase offers a number of ways to stay up-to-date with new features and datasets, to make feature requests, and to ask for assistance with the database.



  • 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?
  • 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?

Internal Documentation

based on Reactome User's Guide