Difference between revisions of "User Guide 2010:TOC"

From WormBaseWiki
Jump to navigationJump to search
m
m
Line 1: Line 1:
''based on Reactome User's Guide''<br>
+
==Introduction==
'''Introduction'''<br>
+
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 [http://www.wormbase.org WormBase] the genetic and genomic database of the model organism [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans] and related nematodes. WormBase is developed by an international consortium of researchers and computer scientists.
'''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 [http://www.wormbase.org WormBase] the genetic and genomic database of the model organism [http://en.wikipedia.org/wiki/Caenorhabditis_elegans Caenorhabditis elegans] and related nematodes. WormBase is developed by an international consortium of researchers and computer scientists.
 
  
 
----
 
----
 
+
==Getting Started==
Getting Started
 
 
*What is WormBase?
 
*What is WormBase?
 
*Machine/Browser compatibility
 
*Machine/Browser compatibility
Line 11: Line 9:
 
*What types of information does WB contain?
 
*What types of information does WB contain?
 
*How are WormBase data organized?
 
*How are WormBase data organized?
<br>
 
*What is an ontology? (What happened to my jargon?)
 
*What is GO?
 
 
*How does data get into WormBase?  
 
*How does data get into WormBase?  
 
*Can I view WormBase data offline?  
 
*Can I view WormBase data offline?  
 
*With what other formats are WB data compatible?
 
*With what other formats are WB data compatible?
<br>
+
*Who are the worm community?  
*What is the worm community?  
 
 
*Who are the WB database people?
 
*Who are the WB database people?
 
*Who funds WB?
 
*Who funds WB?
<br>
+
==Contacting WormBase==
Contacting WormBase
 
 
*Who do I contact if I want to submit data?  
 
*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 I see an error on the page?  
 
*Who do I contact if WormBase stops working for me?
 
*Who do I contact if WormBase stops working for me?
<br>
+
==Viewing and Navigating WB Data==
Viewing and Navigating WB Data
+
===The WB Front page===
*The WB Front page
+
===The Genome Browser===
*The Genome Browser
+
===Individual Pages===
*Individual Pages
+
*Gene Page
**Gene Page
+
*Sequence Page
**Sequence Page
+
*Protein Page
**Protein Page
+
*Allele Page
**Allele Page
+
*Clone/Plasmid Page
**Clone/Plasmid Page
+
*Strain Page
**Strain Page
+
*Molecule Page
**Molecule Page
+
*[[User Guide:Phenotype|Phenotype Page]]  
**[[User Guide:Phenotype|Phenotype Page]]  
+
**The NOT annotations
***The NOT annotations
+
*RNAi experiment Page
**RNAi experiment Page
+
*Microarray/SPELL
**Microarray/SPELL
+
==Searching WB==
<br>
+
===Simple searches===
Searching WB
+
*Finding  
*Simple searches
+
**a gene
**Finding  
+
**an allele
***a gene
+
**a strain
***an allele
+
**a sequence
***a strain
+
===Ontology browsers===
***a sequence
+
*What is an ontology? (What happened to my jargon?)
<br>
+
*What is GO?
*Ontology browsers
+
===Query languages===
*Query languages
+
*AQL
**AQL
+
*WQL
**WQL
+
==Retrieving/Exporting Data==
<br>
 
Retrieving/Exporting Data
 
 
*Bulk data access  
 
*Bulk data access  
 
**gff files
 
**gff files
 
*WormMart
 
*WormMart
<br>
+
==WB Community Tools : tools generated/maintained by wormbase for the community==
WB Community Tools : tools generated/maintained by wormbase for the community
 
 
*Sequence analysis
 
*Sequence analysis
 
**orthology/homology predictors
 
**orthology/homology predictors
Line 67: Line 57:
 
***Synteny Viewer
 
***Synteny Viewer
 
**Cis-Elements (CisOrtho)
 
**Cis-Elements (CisOrtho)
<br>
+
===Experiment tools===
Experiment tools
 
 
*e-PCR
 
*e-PCR
 
*Balancers
 
*Balancers
 
*Transgene markers
 
*Transgene markers
<br>
+
==Downloading WB==
Downloading WB
+
==Citing and Linking to WormBase==
<br>
+
==Keeping in Touch with WB==
Citing and Linking to WormBase
 
<br>
 
Keeping in Touch with WB
 
 
*Database release schedule
 
*Database release schedule
 
*Feeds
 
*Feeds
 
*Twitter
 
*Twitter
<br>
+
==Glossary==
Glossary
+
 
 +
----
  
 +
''based on Reactome User's Guide'' <br>
 
[[Category:User Guide]]
 
[[Category:User Guide]]

Revision as of 22:17, 9 August 2010

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.


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

The WB Front page

The Genome Browser

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

Downloading WB

Citing and Linking to WormBase

Keeping in Touch with WB

  • Database release schedule
  • Feeds
  • Twitter

Glossary


based on Reactome User's Guide