Database Overview: Difference between revisions
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*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: Yes | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: Yes | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation) | *[[KEGG]]: text definition / functional description (primarily imported from Genbank & other db? + original anotation) | ||
| Line 32: | Line 32: | ||
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*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: Indirectly | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: Included in Description | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | *[[KEGG]]: (no result) | ||
| Line 43: | Line 43: | ||
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*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: Included in Experimental Data | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: No | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | *[[KEGG]]: (no result) | ||
| Line 54: | Line 54: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: No | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: Indirectly | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | *[[KEGG]]: (no result) | ||
| Line 71: | Line 71: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: No | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: Indirectly | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: yes + link to GenBank | *[[KEGG]]: yes + link to GenBank | ||
| Line 81: | Line 81: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: No | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: Indirectly | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: id not explicitly shown, but link to PDB | *[[KEGG]]: id not explicitly shown, but link to PDB | ||
| Line 91: | Line 91: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: Indirectly | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: Yes | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: no | *[[KEGG]]: no | ||
| Line 101: | Line 101: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: No | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: Indirectly | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry | *[[KEGG]]: links to relevant KEGG Pathway entries from retrieved GENES entry | ||
| Line 114: | Line 114: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: Included in Experimental Data | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: No | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | *[[KEGG]]: (no result) | ||
| Line 124: | Line 124: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: Included in Experimental Data | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: No | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | *[[KEGG]]: (no result) | ||
| Line 134: | Line 134: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: No | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: No | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes | *[[KEGG]]: KEGG orthologs (manually assigned), Orhtologs and Paralogs by Smith-Waterman alignment to all KEGG genomes | ||
| Line 146: | Line 146: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: Included in Experimental Data | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: Indirectly | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | *[[KEGG]]: (no result) | ||
| Line 156: | Line 156: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: Yes | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: No | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | *[[KEGG]]: (no result) | ||
| Line 166: | Line 166: | ||
| | | | ||
*[[ASAP]] | *[[ASAP]] | ||
*[[GenoBase]] | *[[GenoBase]]: Yes | ||
*[[EcoCyc]] | *[[EcoCyc]] | ||
*[[EcoGene]] | *[[EcoGene]]: No | ||
*[[RegulonDB]] | *[[RegulonDB]] | ||
*[[KEGG]]: (no result) | *[[KEGG]]: (no result) | ||
Revision as of 19:33, 21 June 2006
Content & Features at different databases
Query types
Query by gene name
| Input | Output | How this is handled in different databases |
|---|---|---|
| gene name (e.g. lacY) | sequence | |
| description |
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function |
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localization |
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process (GO definitions ) |
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gene name (namespace1) |
gene name (namespace2) | |
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| gene name | pathway | |
| gene name | experimental data | |
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| gene name (species 1) | gene name( species 2) | |
| gene name |
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Query by pathway
| Input | Output | How this is handled in different databases |
|---|---|---|
| pathway |
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| metabolic process |
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Query by DNA location or sequence
| Input | Output | How this is handled in different databases |
|---|---|---|
| DNA location | Gene name | |
| sequence | related sequence (BLAST) |
Query by Function
| 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
| Input | Output | How this is handled in different databases |
|---|---|---|
| strain ID |
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