Database Overview: Difference between revisions

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|+ '''Query inputs and outputs'''
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
! '''Input''' !! '''Output'''
| '''[[ASAP]]'''
| '''How this is handled in different databases'''
| '''[[GenoBase]]'''
| '''[[EcoCyc]]'''
| '''[[EcoGene]]'''
| '''[[RegulonDB]]'''
| '''Other'''
| '''Notes'''
|-
|-
| rowspan = '3' |strain ID
| rowspan = '3' |strain ID
|*gene name
|
| [[ASAP]]
*gene name
| [[GenoBase]]
|  
| [[EcoCyc]]
*[[ASAP]]
| [[EcoGene]]
*[[GenoBase]]
| [[RegulonDB]]
*[[EcoCyc]]
| Other
*[[EcoGene]]
| Notes
*[[RegulonDB]]
|-
|-
|*mutation
|
| [[ASAP]] (replace these)
*mutation
| [[GenoBase]]
|  
| [[EcoCyc]]
*[[ASAP]]
| [[EcoGene]]
*[[GenoBase]]
| [[RegulonDB]]
*[[EcoCyc]]
| Other
*[[EcoGene]]
| Notes
*[[RegulonDB]]
|-
|-
|*source
|
| [[ASAP]] (replace these)
*source
| [[GenoBase]]
|  
| [[EcoCyc]]
*[[ASAP]]
| [[EcoGene]]
*[[GenoBase]]
| [[RegulonDB]]
*[[EcoCyc]]
| Other
*[[EcoGene]]
| Notes
*[[RegulonDB]]
|}
|}

Revision as of 22:20, 19 June 2006

Content & Features at different databases

Query types

Query by gene name

Query inputs and outputs
Input Output How this is handled in different databases
gene name (e.g. lacY) sequence
description

function,localization,process (GO definitions )

gene name (namespace1)

gene name (namespace2)
Some namespaces:

  • genbank
  • pdb
  • ecogene
gene name pathway
gene name experimental data
  • gene expression
  • protein interaction
gene name (species 1) gene name( species 2)
gene name
  • mutations
  • sequence difference
  • phenotype

Query by pathway

Query inputs and outputs
Input Output How this is handled in different databases
pathway
  • gene name
metabolic process
  • regulatory circuits
  • transcription factors/sites

Query by DNA location or sequence

Query inputs and outputs
Input Output How this is handled in different databases
DNA location Gene name
sequence related sequence (BLAST)

Query by Function

Query inputs and outputs
Input Output How this is handled in different databases
gene function (GO term)

same for process and other GO branches

gene name

Query by strain

Query inputs and outputs
Input Output How this is handled in different databases
strain ID
  • gene name
  • mutation
  • source
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