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'|gene name (e.g. lacY)
| rowspan = '3'|gene name (e.g. lacY)
| sequence
| sequence
| [[ASAP]]
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|-
|-
|description<BR>
|description<BR>
| [[ASAP]]
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|-
|-
|
|
function,localization,process (GO definitions )<BR>
function,localization,process (GO definitions )<BR>
| [[ASAP]]
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|-
|-
| rowspan ='4'|
| rowspan ='4'|
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|
|
*genbank
*genbank
| [[ASAP]]  
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|-
|-
|  
|  
*pdb
*pdb
| [[ASAP]] (replace these)
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|-
|-
|
|
*ecogene
*ecogene
| [[ASAP]] (replace these)
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|-
|-
|gene name
|gene name
|pathway
|pathway
| [[ASAP]]
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
 
|-
|-
| rowspan='3'|gene name
| rowspan='3'|gene name
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|
|
*gene expression
*gene expression
| [[ASAP]] (replace these)
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|-
|-
|
|
*protein interaction
*protein interaction
| [[ASAP]] (replace these)
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
 
|-
|-
|gene name (species 1)
|gene name (species 1)
|gene name( species 2)
|gene name( species 2)
| [[ASAP]] (replace these)
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes


|-
|-
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|
|
*mutations
*mutations
| [[ASAP]] (replace these)
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|-
|-
|
|
*sequence difference
*sequence difference
| [[ASAP]] (replace these)
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|-
|-
|
|
*phenotype
*phenotype
| [[ASAP]] (replace these)
|  
| [[GenoBase]]
*[[ASAP]]
| [[EcoCyc]]
*[[GenoBase]]
| [[EcoGene]]
*[[EcoCyc]]
| [[RegulonDB]]
*[[EcoGene]]
| Other
*[[RegulonDB]]
| Notes
|}
|}


Revision as of 22:14, 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 ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
pathway gene name ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
metabolic process *regulatory circuits ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
*transcription factors/sites ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes

Query by DNA location or sequence

Query inputs and outputs
Input Output ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
DNA location Gene name ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
sequence related sequence (BLAST) ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes

Query by Function

Query inputs and outputs
Input Output ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene function (GO term)

same for process and other GO branches

gene name ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes

Query by strain

Query inputs and outputs
Input Output ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
strain ID *gene name ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
*mutation ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
*source ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
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