Database Overview: Difference between revisions

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=Features at different databases=
=Features at different databases=
=Query types=
=Query types=
==Query by gene name=
==Query by gene name==
{| border="1" align="TOP"
{| border="1" align="TOP"
|+ '''Query inputs and outputs'''
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
! '''Input''' !! '''Output'''
| [[ASAP]]
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|gene name (e.g. lacY) sequence
|gene name (e.g. lacY) sequence
|description<BR>
|description<BR>
function,localization,process (GO definitions )<BR>
function,localization,process (GO definitions )<BR>
|-
| [[ASAP]] (replace these)
|gene name
| [[GenoBase]]
|pathway
| [[EcoCyc]]
|-
| [[EcoGene]]
|pathway
| [[RegulonDB]]
|gene name
| Other
| Notes
|-
|-
|gene name (genbank namespace)<BR>
|gene name (genbank namespace)<BR>
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*pdb
*pdb
*ecogene
*ecogene
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|gene name
|pathway
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|}
==Query by pathway==
{| border="1" align="TOP"
|+ '''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
|}
|}
==Query by DNA location==
==Query by DNA location==
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|+ '''Query inputs and outputs'''
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
! '''Input''' !! '''Output'''
| [[ASAP]]
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|DNA location
|DNA location
|Gene name
|Gene name
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|gene function (GO term) <BR>
|gene function (GO term) <BR>
same for process and other GO branches
same for process and other GO branches
|gene name
|gene name
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|gene name
|gene name
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*gene expression
*gene expression
*protein interaction
*protein interaction
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|sequence
|sequence
|related sequence (BLAST)
|related sequence (BLAST)
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|gene name (species 1)
|gene name (species 1)
|gene name( species 2)
|gene name( species 2)
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|gene name
|gene name
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*sequence difference
*sequence difference
*phenotype
*phenotype
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|}
|}
==Query by strain==
==Query by strain==
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|+ '''Query inputs and outputs'''
|+ '''Query inputs and outputs'''
! '''Input''' !! '''Output'''
! '''Input''' !! '''Output'''
| [[ASAP]]
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|strain ID
|strain ID
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*mutation
*mutation
*source
*source
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|-
|-
|metabolic process
|metabolic process
|*regulatory circuits
|*regulatory circuits
*transcription factors/sites
*transcription factors/sites
| [[ASAP]] (replace these)
| [[GenoBase]]
| [[EcoCyc]]
| [[EcoGene]]
| [[RegulonDB]]
| Other
| Notes
|}
|}

Revision as of 16:08, 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

function,localization,process (GO definitions )

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

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
  • mutation
  • source
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
metabolic process *regulatory circuits
  • transcription factors/sites
 ASAP (replace these) GenoBase EcoCyc EcoGene RegulonDB Other Notes
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