https://ecoliwiki.org/colipedia/api.php?action=feedcontributions&feedformat=atom&user=Thawkins 2026-11-06T21:31:26Z User contributions MediaWiki 1.43.11 https://ecoliwiki.org/colipedia/index.php?title=Database_Overview&diff=2253 2006-06-21T19:16:44Z

<p>Thawkins: /* Query by gene name */</p> <hr /> <div>[[Category:Databases]]<br /> =Content &amp; Features at different databases=<br /> <br /> =Query types=<br /> ==Query by gene name==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3'|gene name (e.g. lacY) <br /> | sequence<br /> | <br /> *[[ASAP]] (participant of the NAR 06 paper)<br /> *[[GenoBase]] (participant of the NAR 06 paper)<br /> *[[EcoCyc]] (participant of the NAR 06 paper)<br /> *[[EcoGene]] (participant of the NAR 06 paper)<br /> *[[RegulonDB]] (?)<br /> *[[KEGG]]: AA and nucleotide sequences (imported from Genbank)<br /> |-<br /> |description&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: text definition / functional description (primarily imported from Genbank &amp; other db? + original anotation)<br /> |-<br /> |<br /> function,localization,process (GO definitions )&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | rowspan ='4'|<br /> gene name (namespace1)<br /> |<br /> gene name (namespace2)&lt;BR&gt;<br /> Some namespaces:<br /> |-<br /> |<br /> *genbank id<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: yes + link to GenBank<br /> |-<br /> | <br /> *pdb id<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: id not explicitly shown, but link to PDB<br /> |-<br /> |<br /> *ecogene id<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: no<br /> |-<br /> |gene name<br /> |pathway<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry<br /> |-<br /> | rowspan='3'|gene name<br /> |experimental data<br /> |-<br /> |<br /> *gene expression<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *protein interaction<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name (species 1)<br /> |gene name( species 2)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes<br /> <br /> |-<br /> | rowspan='3'|gene name<br /> |<br /> *mutations<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *sequence difference<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *phenotype<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by pathway==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |pathway<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries<br /> |-<br /> | rowspan ='2' |metabolic process <br /> |<br /> *regulatory circuits<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *transcription factors/sites<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by DNA location or sequence==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |DNA location<br /> |Gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |sequence<br /> |related sequence (BLAST)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by Function==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |gene function (GO term) &lt;BR&gt;<br /> same for process and other GO branches<br /> |gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by strain==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3' |strain ID<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *mutation<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *source<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}</div>

Thawkins https://ecoliwiki.org/colipedia/index.php?title=Database_Overview&diff=2251 2006-06-21T15:35:24Z

<p>Thawkins: /* Query by strain */</p> <hr /> <div>[[Category:Databases]]<br /> =Content &amp; Features at different databases=<br /> <br /> =Query types=<br /> ==Query by gene name==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3'|gene name (e.g. lacY) <br /> | sequence<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: AA and nucleotide sequences<br /> |-<br /> |description&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: text definition / functional description<br /> |-<br /> |<br /> function,localization,process (GO definitions )&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | rowspan ='4'|<br /> gene name (namespace1)<br /> |<br /> gene name (namespace2)&lt;BR&gt;<br /> Some namespaces:<br /> |-<br /> |<br /> *genbank<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | <br /> *pdb<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *ecogene<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name<br /> |pathway<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry<br /> |-<br /> | rowspan='3'|gene name<br /> |experimental data<br /> |-<br /> |<br /> *gene expression<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *protein interaction<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name (species 1)<br /> |gene name( species 2)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes<br /> <br /> |-<br /> | rowspan='3'|gene name<br /> |<br /> *mutations<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *sequence difference<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *phenotype<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by pathway==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |pathway<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries<br /> |-<br /> | rowspan ='2' |metabolic process <br /> |<br /> *regulatory circuits<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *transcription factors/sites<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by DNA location or sequence==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |DNA location<br /> |Gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |sequence<br /> |related sequence (BLAST)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by Function==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |gene function (GO term) &lt;BR&gt;<br /> same for process and other GO branches<br /> |gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by strain==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3' |strain ID<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *mutation<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *source<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}</div>

Thawkins https://ecoliwiki.org/colipedia/index.php?title=Database_Overview&diff=2250 2006-06-21T15:34:41Z

<p>Thawkins: /* Query by Function */</p> <hr /> <div>[[Category:Databases]]<br /> =Content &amp; Features at different databases=<br /> <br /> =Query types=<br /> ==Query by gene name==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3'|gene name (e.g. lacY) <br /> | sequence<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: AA and nucleotide sequences<br /> |-<br /> |description&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: text definition / functional description<br /> |-<br /> |<br /> function,localization,process (GO definitions )&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | rowspan ='4'|<br /> gene name (namespace1)<br /> |<br /> gene name (namespace2)&lt;BR&gt;<br /> Some namespaces:<br /> |-<br /> |<br /> *genbank<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | <br /> *pdb<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *ecogene<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name<br /> |pathway<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry<br /> |-<br /> | rowspan='3'|gene name<br /> |experimental data<br /> |-<br /> |<br /> *gene expression<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *protein interaction<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name (species 1)<br /> |gene name( species 2)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes<br /> <br /> |-<br /> | rowspan='3'|gene name<br /> |<br /> *mutations<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *sequence difference<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *phenotype<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by pathway==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |pathway<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries<br /> |-<br /> | rowspan ='2' |metabolic process <br /> |<br /> *regulatory circuits<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *transcription factors/sites<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by DNA location or sequence==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |DNA location<br /> |Gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |sequence<br /> |related sequence (BLAST)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by Function==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |gene function (GO term) &lt;BR&gt;<br /> same for process and other GO branches<br /> |gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by strain==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3' |strain ID<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *mutation<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *source<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}</div>

Thawkins https://ecoliwiki.org/colipedia/index.php?title=Database_Overview&diff=2249 2006-06-21T15:34:12Z

<p>Thawkins: /* Query by DNA location or sequence */</p> <hr /> <div>[[Category:Databases]]<br /> =Content &amp; Features at different databases=<br /> <br /> =Query types=<br /> ==Query by gene name==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3'|gene name (e.g. lacY) <br /> | sequence<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: AA and nucleotide sequences<br /> |-<br /> |description&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: text definition / functional description<br /> |-<br /> |<br /> function,localization,process (GO definitions )&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | rowspan ='4'|<br /> gene name (namespace1)<br /> |<br /> gene name (namespace2)&lt;BR&gt;<br /> Some namespaces:<br /> |-<br /> |<br /> *genbank<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | <br /> *pdb<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *ecogene<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name<br /> |pathway<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry<br /> |-<br /> | rowspan='3'|gene name<br /> |experimental data<br /> |-<br /> |<br /> *gene expression<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *protein interaction<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name (species 1)<br /> |gene name( species 2)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes<br /> <br /> |-<br /> | rowspan='3'|gene name<br /> |<br /> *mutations<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *sequence difference<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *phenotype<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by pathway==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |pathway<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries<br /> |-<br /> | rowspan ='2' |metabolic process <br /> |<br /> *regulatory circuits<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *transcription factors/sites<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by DNA location or sequence==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |DNA location<br /> |Gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |sequence<br /> |related sequence (BLAST)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by Function==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |gene function (GO term) &lt;BR&gt;<br /> same for process and other GO branches<br /> |gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by strain==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3' |strain ID<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *mutation<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *source<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}</div>

Thawkins https://ecoliwiki.org/colipedia/index.php?title=Database_Overview&diff=2248 2006-06-21T15:33:22Z

<p>Thawkins: /* Query by pathway */</p> <hr /> <div>[[Category:Databases]]<br /> =Content &amp; Features at different databases=<br /> <br /> =Query types=<br /> ==Query by gene name==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3'|gene name (e.g. lacY) <br /> | sequence<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: AA and nucleotide sequences<br /> |-<br /> |description&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: text definition / functional description<br /> |-<br /> |<br /> function,localization,process (GO definitions )&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | rowspan ='4'|<br /> gene name (namespace1)<br /> |<br /> gene name (namespace2)&lt;BR&gt;<br /> Some namespaces:<br /> |-<br /> |<br /> *genbank<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | <br /> *pdb<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *ecogene<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name<br /> |pathway<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry<br /> |-<br /> | rowspan='3'|gene name<br /> |experimental data<br /> |-<br /> |<br /> *gene expression<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *protein interaction<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name (species 1)<br /> |gene name( species 2)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes<br /> <br /> |-<br /> | rowspan='3'|gene name<br /> |<br /> *mutations<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *sequence difference<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *phenotype<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by pathway==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |pathway<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries<br /> |-<br /> | rowspan ='2' |metabolic process <br /> |<br /> *regulatory circuits<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *transcription factors/sites<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by DNA location or sequence==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |DNA location<br /> |Gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |sequence<br /> |related sequence (BLAST)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by Function==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |gene function (GO term) &lt;BR&gt;<br /> same for process and other GO branches<br /> |gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by strain==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3' |strain ID<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *mutation<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *source<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}</div>

Thawkins https://ecoliwiki.org/colipedia/index.php?title=Database_Overview&diff=2247 2006-06-21T15:32:11Z

<p>Thawkins: /* Query by gene name */</p> <hr /> <div>[[Category:Databases]]<br /> =Content &amp; Features at different databases=<br /> <br /> =Query types=<br /> ==Query by gene name==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3'|gene name (e.g. lacY) <br /> | sequence<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: AA and nucleotide sequences<br /> |-<br /> |description&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: text definition / functional description<br /> |-<br /> |<br /> function,localization,process (GO definitions )&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | rowspan ='4'|<br /> gene name (namespace1)<br /> |<br /> gene name (namespace2)&lt;BR&gt;<br /> Some namespaces:<br /> |-<br /> |<br /> *genbank<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> | <br /> *pdb<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *ecogene<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name<br /> |pathway<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry<br /> |-<br /> | rowspan='3'|gene name<br /> |experimental data<br /> |-<br /> |<br /> *gene expression<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *protein interaction<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |gene name (species 1)<br /> |gene name( species 2)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes<br /> <br /> |-<br /> | rowspan='3'|gene name<br /> |<br /> *mutations<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *sequence difference<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |-<br /> |<br /> *phenotype<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: (no result)<br /> |}<br /> <br /> ==Query by pathway==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |pathway<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries<br /> |-<br /> | rowspan ='2' |metabolic process <br /> |<br /> *regulatory circuits<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *transcription factors/sites<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by DNA location or sequence==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |DNA location<br /> |Gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |sequence<br /> |related sequence (BLAST)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by Function==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |gene function (GO term) &lt;BR&gt;<br /> same for process and other GO branches<br /> |gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by strain==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3' |strain ID<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *mutation<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *source<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}</div>

Thawkins https://ecoliwiki.org/colipedia/index.php?title=Database_Overview&diff=2246 2006-06-21T15:19:36Z

<p>Thawkins: /* Query by pathway */</p> <hr /> <div>[[Category:Databases]]<br /> =Content &amp; Features at different databases=<br /> <br /> =Query types=<br /> ==Query by gene name==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3'|gene name (e.g. lacY) <br /> | sequence<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |description&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> function,localization,process (GO definitions )&lt;BR&gt;<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> | rowspan ='4'|<br /> gene name (namespace1)<br /> |<br /> gene name (namespace2)&lt;BR&gt;<br /> Some namespaces:<br /> |-<br /> |<br /> *genbank<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> | <br /> *pdb<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *ecogene<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |gene name<br /> |pathway<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> | rowspan='3'|gene name<br /> |experimental data<br /> |-<br /> |<br /> *gene expression<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *protein interaction<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |gene name (species 1)<br /> |gene name( species 2)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> <br /> |-<br /> | rowspan='3'|gene name<br /> |<br /> *mutations<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *sequence difference<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *phenotype<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by pathway==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |pathway<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> *[[KEGG]]: retrieves links to KEGG Pathway and KEGG GENES entries<br /> |-<br /> | rowspan ='2' |metabolic process <br /> |<br /> *regulatory circuits<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *transcription factors/sites<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by DNA location or sequence==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |DNA location<br /> |Gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |sequence<br /> |related sequence (BLAST)<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by Function==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> |gene function (GO term) &lt;BR&gt;<br /> same for process and other GO branches<br /> |gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}<br /> <br /> ==Query by strain==<br /> {| border=&quot;1&quot; align=&quot;TOP&quot;<br /> |+ '''Query inputs and outputs'''<br /> ! '''Input''' !! '''Output'''<br /> | '''How this is handled in different databases'''<br /> |-<br /> | rowspan = '3' |strain ID<br /> |<br /> *gene name<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *mutation<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |-<br /> |<br /> *source<br /> | <br /> *[[ASAP]]<br /> *[[GenoBase]]<br /> *[[EcoCyc]]<br /> *[[EcoGene]]<br /> *[[RegulonDB]]<br /> |}</div>

Thawkins