Database Overview: Difference between revisions

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|+ '''Query inputs and outputs'''
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
! '''Input''' !! '''Output'''
| [[ASAP]]
| '''[[ASAP]]'''
| [[GenoBase]]
| '''[[GenoBase]]'''
| [[EcoCyc]]
| '''[[EcoCyc]]'''
| [[EcoGene]]
| '''[[EcoGene]]'''
| [[RegulonDB]]
| '''[[RegulonDB]]'''
| Other
| '''Other'''
| Notes
| '''Notes'''
|-
|-
| rowspan = '2'|gene name (e.g. lacY) sequence
| rowspan = '2'|gene name (e.g. lacY) sequence
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| Other
| Other
| Notes
| Notes
|-
| rowspan ='2' |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==
==Query by DNA location==
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|-
|-
|*source
|*source
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
| rowspan ='2' |metabolic process
|*regulatory circuits
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|*transcription factors/sites
| [[ASAP]] (replace these)
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[GenoBase]]

Revision as of 16:30, 19 June 2006

Features at different databases

Query types

Query by gene name

Query inputs and outputs
Input Output ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name (e.g. lacY) sequence description
 ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes

function,localization,process (GO definitions )

 ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name (genbank namespace)

more generally
gene name (namespace1)

gene name (ecogene namespace)

more generally
gene name (namespace2)
Some namespaces:

  • genbank
 ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes
  • pdb
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
  • ecogene
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name pathway ASAP GenoBase EcoCyc EcoGene RegulonDB Other Notes

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

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
gene function (GO term)

same for process and other GO branches

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

*gene expression *protein interaction

ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
sequence related sequence (BLAST) ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name (species 1) gene name( species 2) ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
gene name *mutations
  • sequence difference
  • phenotype
 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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