Piana
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| - | The icb maintains a local installations of the Protein Interactions And Network Analysis ([http://sbi.imim.es/piana/ PIANA]) database. The MySQL database resides on piana.med.cornell.edu and contains the sample "limited" data distribution and also a locally populated version. | + | The icb maintains a local installations of the Protein Interactions And Network Analysis ([http://sbi.imim.es/piana/ PIANA]) database. The MySQL database resides on piana.med.cornell.edu and contains a locally populated version along with the sample "limited" data distribution. |
| == Local database contents == | == Local database contents == | ||
| - | {| border=1 cellspacing=1 cellpadding=0 | + | {| class="wikitable" style="margin: 1em auto 1em auto; background:#efefef;" valign="top" align="left" border="1" cellpadding="5" |
| + | |- valign="bottom" align="left" style="background:#ffdead;" | ||
| ! databaseName | ! databaseName | ||
| ! databaseVersion | ! databaseVersion | ||
| Line 8: | Line 9: | ||
| ! date | ! date | ||
| ! databaseDescription | ! databaseDescription | ||
| - | ! databaseInteger | ||
| |- | |- | ||
| | ncbi_taxonomy | | ncbi_taxonomy | ||
| Line 15: | Line 15: | ||
| | 2008-4-18 | | 2008-4-18 | ||
| | NCBI Species information | | NCBI Species information | ||
| - | | 1 | ||
| |- | |- | ||
| | swissprot | | swissprot | ||
| Line 22: | Line 21: | ||
| | 2008-4-18 | | 2008-4-18 | ||
| | Uniprot manually curated database | | Uniprot manually curated database | ||
| - | | 2 | ||
| |- | |- | ||
| | trembl | | trembl | ||
| Line 29: | Line 27: | ||
| | 2008-4-18 | | 2008-4-18 | ||
| | Uniprot complete not manually curated database | | Uniprot complete not manually curated database | ||
| - | | 4 | ||
| |- | |- | ||
| | genpept | | genpept | ||
| Line 36: | Line 33: | ||
| | 2008-4-19 | | 2008-4-19 | ||
| | ncbi genbank database | | ncbi genbank database | ||
| - | | 8 | ||
| |- | |- | ||
| | nr | | nr | ||
| Line 43: | Line 39: | ||
| | 2008-4-20 | | 2008-4-20 | ||
| | non-redundant ncbi database | | non-redundant ncbi database | ||
| - | | 16 | ||
| |- | |- | ||
| | ncbi2pdb_pdbaa | | ncbi2pdb_pdbaa | ||
| Line 50: | Line 45: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | correspondence between pdb and gi identifiers | | correspondence between pdb and gi identifiers | ||
| - | | 32 | ||
| |- | |- | ||
| | ncbi2uniprot swissprot | | ncbi2uniprot swissprot | ||
| Line 57: | Line 51: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | correspondences between uniprot and gi identifiers | | correspondences between uniprot and gi identifiers | ||
| - | | 64 | ||
| |- | |- | ||
| | pdbsprotec | | pdbsprotec | ||
| Line 64: | Line 57: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | correspondences between pdb and uniprot identifiers | | correspondences between pdb and uniprot identifiers | ||
| - | | 128 | ||
| |- | |- | ||
| | gene | | gene | ||
| Line 71: | Line 63: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | correspondences between ncbi accession number and geneID identifiers | | correspondences between ncbi accession number and geneID identifiers | ||
| - | | 256 | ||
| |- | |- | ||
| | gene_info | | gene_info | ||
| Line 78: | Line 69: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | Gene NCBI database - gene_info | | Gene NCBI database - gene_info | ||
| - | | 512 | ||
| |- | |- | ||
| | refseq | | refseq | ||
| Line 85: | Line 75: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | NCBI RefSeq Database | | NCBI RefSeq Database | ||
| - | | 1024 | ||
| |- | |- | ||
| | cog-myva=gb | | cog-myva=gb | ||
| Line 92: | Line 81: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | Cluster of orthologous genes | | Cluster of orthologous genes | ||
| - | | 2048 | ||
| |- | |- | ||
| | cog | | cog | ||
| Line 99: | Line 87: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | Cluster of orthologous genes | | Cluster of orthologous genes | ||
| - | | 4096 | ||
| |- | |- | ||
| | kog-kyva=gb | | kog-kyva=gb | ||
| Line 106: | Line 93: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | Eucariotic Cluster of orthologous genes | | Eucariotic Cluster of orthologous genes | ||
| - | | 8192 | ||
| |- | |- | ||
| | kog | | kog | ||
| Line 113: | Line 99: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | Eucariotic Cluster of orthologous genes | | Eucariotic Cluster of orthologous genes | ||
| - | | 16384 | ||
| |- | |- | ||
| | scop | | scop | ||
| Line 120: | Line 105: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | SCOP - Structural Classification of Proteins | | SCOP - Structural Classification of Proteins | ||
| - | | 32768 | ||
| |- | |- | ||
| | go | | go | ||
| Line 127: | Line 111: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | GO. Gene Ontology | | GO. Gene Ontology | ||
| - | | 65536 | ||
| |- | |- | ||
| | dip | | dip | ||
| Line 134: | Line 117: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | DIP (Database of Interacting Proteins) | | DIP (Database of Interacting Proteins) | ||
| - | | 131072 | ||
| |- | |- | ||
| | mips | | mips | ||
| Line 141: | Line 123: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | The MIPS Mammalian Protein-Protein Interaction Database | | The MIPS Mammalian Protein-Protein Interaction Database | ||
| - | | 262144 | ||
| |- | |- | ||
| | hprd | | hprd | ||
| Line 148: | Line 129: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | Human Protein Reference Database | | Human Protein Reference Database | ||
| - | | 524288 | ||
| |- | |- | ||
| | bind | | bind | ||
| Line 155: | Line 135: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | Biomolecular Interaction Network Database | | Biomolecular Interaction Network Database | ||
| - | | 1048576 | ||
| |- | |- | ||
| | intact | | intact | ||
| Line 162: | Line 141: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | IntAct protein-protein interaction database | | IntAct protein-protein interaction database | ||
| - | | 2097152 | ||
| |- | |- | ||
| | biogrid | | biogrid | ||
| Line 169: | Line 147: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | The BioGRID's curated set of physical and genetic interactions | | The BioGRID's curated set of physical and genetic interactions | ||
| - | | 4194304 | ||
| |- | |- | ||
| | mint | | mint | ||
| Line 176: | Line 153: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | the Molecular INTeraction database | | the Molecular INTeraction database | ||
| - | | 8388608 | ||
| |- | |- | ||
| | ori | | ori | ||
| Line 183: | Line 159: | ||
| | 2008-4-21 | | 2008-4-21 | ||
| | predicted interactions from distant structure/sequence patterns | | predicted interactions from distant structure/sequence patterns | ||
| - | | 16777216 | ||
| |} | |} | ||
Revision as of 19:01, 8 May 2008
The icb maintains a local installations of the Protein Interactions And Network Analysis (PIANA) database. The MySQL database resides on piana.med.cornell.edu and contains a locally populated version along with the sample "limited" data distribution.
Local database contents
| databaseName | databaseVersion | parsed_file | date | databaseDescription |
|---|---|---|---|---|
| ncbi_taxonomy | April 18 2008 | names.dmp | 2008-4-18 | NCBI Species information |
| swissprot | April 08 2008 | uniprot_sprot_rg_rx_oh_pe_deleted.dat | 2008-4-18 | Uniprot manually curated database |
| trembl | April 08 2008 | uniprot_trembl_rg_rx_oh_pe_deleted.dat | 2008-4-18 | Uniprot complete not manually curated database |
| genpept | April 18 2008 (release 165) | rel165.fsa_aa | 2008-4-19 | ncbi genbank database |
| nr | April 16 2008 | nr | 2008-4-20 | non-redundant ncbi database |
| ncbi2pdb_pdbaa | April 16 2008 | pdbaa | 2008-4-21 | correspondence between pdb and gi identifiers |
| ncbi2uniprot swissprot | April 16 2008 | swissprot | 2008-4-21 | correspondences between uniprot and gi identifiers |
| pdbsprotec | March 12 2008 | mapping.txt | 2008-4-21 | correspondences between pdb and uniprot identifiers |
| gene | April 18 2008 | gene2accession | 2008-4-21 | correspondences between ncbi accession number and geneID identifiers |
| gene_info | April 18 2008 | gene_info | 2008-4-21 | Gene NCBI database - gene_info |
| refseq | March 13 2008 (release 28) | RefSeq-release28.catalog | 2008-4-21 | NCBI RefSeq Database |
| cog-myva=gb | September 26 2002 | myva=gb | 2008-4-21 | Cluster of orthologous genes |
| cog | March 05 2003 | whog | 2008-4-21 | Cluster of orthologous genes |
| kog-kyva=gb | June 06 2003 | kyva=gb | 2008-4-21 | Eucariotic Cluster of orthologous genes |
| kog | July 21 2003 | kog | 2008-4-21 | Eucariotic Cluster of orthologous genes |
| scop | Release 1.73 | dir.cla.scop.txt_1.73 | 2008-4-21 | SCOP - Structural Classification of Proteins |
| go | April 14 2008 | mysql_database_GO | 2008-4-21 | GO. Gene Ontology |
| dip | April 07 2008 | dip20080407.txt | 2008-4-21 | DIP (Database of Interacting Proteins) |
| mips | June 01 2004 | temporal_mysql_database | 2008-4-21 | The MIPS Mammalian Protein-Protein Interaction Database |
| hprd | September 01 2007 (Release_7) | HPRD_Release_7_09012007.txt | 2008-4-21 | Human Protein Reference Database |
| bind | April 15 2008 | temporal_mysql_database | 2008-4-21 | Biomolecular Interaction Network Database |
| intact | March 29 2008 | intact.txt | 2008-4-21 | IntAct protein-protein interaction database |
| biogrid | 2.0.39 | BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt | 2008-4-21 | The BioGRID's curated set of physical and genetic interactions |
| mint | April 08 2008 | 2008-04-08-full.mitab25.txt | 2008-4-21 | the Molecular INTeraction database |
| ori | January 16 2007 | interact.dat | 2008-4-21 | predicted interactions from distant structure/sequence patterns |
