Piana
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| Revision as of 19:01, 8 May 2008 Marko (Talk | contribs) ← Previous diff |
Revision as of 19:47, 8 May 2008 Marko (Talk | contribs) (→Local database contents) Next diff → |
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| {| class="wikitable" style="margin: 1em auto 1em auto; background:#efefef;" valign="top" align="left" border="1" cellpadding="5" | {| 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;" | |- valign="bottom" align="left" style="background:#ffdead;" | ||
| - | ! databaseName | + | ! Name |
| - | ! databaseVersion | + | ! Version |
| - | ! parsed_file | + | ! Data Source |
| - | ! date | + | ! Description |
| - | ! databaseDescription | + | |
| |- | |- | ||
| | ncbi_taxonomy | | ncbi_taxonomy | ||
| | April 18 2008 | | April 18 2008 | ||
| - | | names.dmp | + | | [ftp://ftp.ncbi.nih.gov/pub/taxonomy/ names.dmp] |
| - | | 2008-4-18 | + | |
| | NCBI Species information | | NCBI Species information | ||
| |- | |- | ||
| | swissprot | | swissprot | ||
| | April 08 2008 | | April 08 2008 | ||
| - | | uniprot_sprot_rg_rx_oh_pe_deleted.dat | + | | [ftp://ftp.expasy.org/databases/uniprot/knowledgebase/ uniprot_sprot_rg_rx_oh_pe_deleted.dat] |
| - | | 2008-4-18 | + | |
| | Uniprot manually curated database | | Uniprot manually curated database | ||
| |- | |- | ||
| | trembl | | trembl | ||
| | April 08 2008 | | April 08 2008 | ||
| - | | uniprot_trembl_rg_rx_oh_pe_deleted.dat | + | | [ftp://ftp.expasy.org/databases/uniprot/knowledgebase/ uniprot_trembl_rg_rx_oh_pe_deleted.dat] |
| - | | 2008-4-18 | + | |
| | Uniprot complete not manually curated database | | Uniprot complete not manually curated database | ||
| |- | |- | ||
| Line 31: | Line 27: | ||
| | April 18 2008 (release 165) | | April 18 2008 (release 165) | ||
| | rel165.fsa_aa | | rel165.fsa_aa | ||
| - | | 2008-4-19 | ||
| | ncbi genbank database | | ncbi genbank database | ||
| |- | |- | ||
| Line 37: | Line 32: | ||
| | April 16 2008 | | April 16 2008 | ||
| | nr | | nr | ||
| - | | 2008-4-20 | ||
| | non-redundant ncbi database | | non-redundant ncbi database | ||
| |- | |- | ||
| Line 43: | Line 37: | ||
| | April 16 2008 | | April 16 2008 | ||
| | pdbaa | | pdbaa | ||
| - | | 2008-4-21 | ||
| | correspondence between pdb and gi identifiers | | correspondence between pdb and gi identifiers | ||
| |- | |- | ||
| Line 49: | Line 42: | ||
| | April 16 2008 | | April 16 2008 | ||
| | swissprot | | swissprot | ||
| - | | 2008-4-21 | ||
| | correspondences between uniprot and gi identifiers | | correspondences between uniprot and gi identifiers | ||
| |- | |- | ||
| Line 55: | Line 47: | ||
| | March 12 2008 | | March 12 2008 | ||
| | mapping.txt | | mapping.txt | ||
| - | | 2008-4-21 | ||
| | correspondences between pdb and uniprot identifiers | | correspondences between pdb and uniprot identifiers | ||
| |- | |- | ||
| Line 61: | Line 52: | ||
| | April 18 2008 | | April 18 2008 | ||
| | gene2accession | | gene2accession | ||
| - | | 2008-4-21 | ||
| | correspondences between ncbi accession number and geneID identifiers | | correspondences between ncbi accession number and geneID identifiers | ||
| |- | |- | ||
| Line 67: | Line 57: | ||
| | April 18 2008 | | April 18 2008 | ||
| | gene_info | | gene_info | ||
| - | | 2008-4-21 | ||
| | Gene NCBI database - gene_info | | Gene NCBI database - gene_info | ||
| |- | |- | ||
| Line 73: | Line 62: | ||
| | March 13 2008 (release 28) | | March 13 2008 (release 28) | ||
| | RefSeq-release28.catalog | | RefSeq-release28.catalog | ||
| - | | 2008-4-21 | ||
| | NCBI RefSeq Database | | NCBI RefSeq Database | ||
| |- | |- | ||
| Line 79: | Line 67: | ||
| | September 26 2002 | | September 26 2002 | ||
| | myva=gb | | myva=gb | ||
| - | | 2008-4-21 | ||
| | Cluster of orthologous genes | | Cluster of orthologous genes | ||
| |- | |- | ||
| Line 85: | Line 72: | ||
| | March 05 2003 | | March 05 2003 | ||
| | whog | | whog | ||
| - | | 2008-4-21 | ||
| | Cluster of orthologous genes | | Cluster of orthologous genes | ||
| |- | |- | ||
| Line 91: | Line 77: | ||
| | June 06 2003 | | June 06 2003 | ||
| | kyva=gb | | kyva=gb | ||
| - | | 2008-4-21 | ||
| | Eucariotic Cluster of orthologous genes | | Eucariotic Cluster of orthologous genes | ||
| |- | |- | ||
| Line 97: | Line 82: | ||
| | July 21 2003 | | July 21 2003 | ||
| | kog | | kog | ||
| - | | 2008-4-21 | ||
| | Eucariotic Cluster of orthologous genes | | Eucariotic Cluster of orthologous genes | ||
| |- | |- | ||
| Line 103: | Line 87: | ||
| | Release 1.73 | | Release 1.73 | ||
| | dir.cla.scop.txt_1.73 | | dir.cla.scop.txt_1.73 | ||
| - | | 2008-4-21 | ||
| | SCOP - Structural Classification of Proteins | | SCOP - Structural Classification of Proteins | ||
| |- | |- | ||
| Line 109: | Line 92: | ||
| | April 14 2008 | | April 14 2008 | ||
| | mysql_database_GO | | mysql_database_GO | ||
| - | | 2008-4-21 | ||
| | GO. Gene Ontology | | GO. Gene Ontology | ||
| |- | |- | ||
| Line 115: | Line 97: | ||
| | April 07 2008 | | April 07 2008 | ||
| | dip20080407.txt | | dip20080407.txt | ||
| - | | 2008-4-21 | ||
| | DIP (Database of Interacting Proteins) | | DIP (Database of Interacting Proteins) | ||
| |- | |- | ||
| Line 121: | Line 102: | ||
| | June 01 2004 | | June 01 2004 | ||
| | temporal_mysql_database | | temporal_mysql_database | ||
| - | | 2008-4-21 | ||
| | The MIPS Mammalian Protein-Protein Interaction Database | | The MIPS Mammalian Protein-Protein Interaction Database | ||
| |- | |- | ||
| Line 127: | Line 107: | ||
| | September 01 2007 (Release_7) | | September 01 2007 (Release_7) | ||
| | HPRD_Release_7_09012007.txt | | HPRD_Release_7_09012007.txt | ||
| - | | 2008-4-21 | ||
| | Human Protein Reference Database | | Human Protein Reference Database | ||
| |- | |- | ||
| Line 133: | Line 112: | ||
| | April 15 2008 | | April 15 2008 | ||
| | temporal_mysql_database | | temporal_mysql_database | ||
| - | | 2008-4-21 | ||
| | Biomolecular Interaction Network Database | | Biomolecular Interaction Network Database | ||
| |- | |- | ||
| Line 139: | Line 117: | ||
| | March 29 2008 | | March 29 2008 | ||
| | intact.txt | | intact.txt | ||
| - | | 2008-4-21 | ||
| | IntAct protein-protein interaction database | | IntAct protein-protein interaction database | ||
| |- | |- | ||
| Line 145: | Line 122: | ||
| | 2.0.39 | | 2.0.39 | ||
| | BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt | | BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt | ||
| - | | 2008-4-21 | ||
| | The BioGRID's curated set of physical and genetic interactions | | The BioGRID's curated set of physical and genetic interactions | ||
| |- | |- | ||
| Line 151: | Line 127: | ||
| | April 08 2008 | | April 08 2008 | ||
| | 2008-04-08-full.mitab25.txt | | 2008-04-08-full.mitab25.txt | ||
| - | | 2008-4-21 | ||
| | the Molecular INTeraction database | | the Molecular INTeraction database | ||
| |- | |- | ||
| Line 157: | Line 132: | ||
| | January 16 2007 | | January 16 2007 | ||
| | interact.dat | | interact.dat | ||
| - | | 2008-4-21 | ||
| | predicted interactions from distant structure/sequence patterns | | predicted interactions from distant structure/sequence patterns | ||
| |} | |} | ||
Revision as of 19:47, 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
| Name | Version | Data Source | Description |
|---|---|---|---|
| ncbi_taxonomy | April 18 2008 | names.dmp | NCBI Species information |
| swissprot | April 08 2008 | uniprot_sprot_rg_rx_oh_pe_deleted.dat | Uniprot manually curated database |
| trembl | April 08 2008 | uniprot_trembl_rg_rx_oh_pe_deleted.dat | Uniprot complete not manually curated database |
| genpept | April 18 2008 (release 165) | rel165.fsa_aa | ncbi genbank database |
| nr | April 16 2008 | nr | non-redundant ncbi database |
| ncbi2pdb_pdbaa | April 16 2008 | pdbaa | correspondence between pdb and gi identifiers |
| ncbi2uniprot swissprot | April 16 2008 | swissprot | correspondences between uniprot and gi identifiers |
| pdbsprotec | March 12 2008 | mapping.txt | correspondences between pdb and uniprot identifiers |
| gene | April 18 2008 | gene2accession | correspondences between ncbi accession number and geneID identifiers |
| gene_info | April 18 2008 | gene_info | Gene NCBI database - gene_info |
| refseq | March 13 2008 (release 28) | RefSeq-release28.catalog | NCBI RefSeq Database |
| cog-myva=gb | September 26 2002 | myva=gb | Cluster of orthologous genes |
| cog | March 05 2003 | whog | Cluster of orthologous genes |
| kog-kyva=gb | June 06 2003 | kyva=gb | Eucariotic Cluster of orthologous genes |
| kog | July 21 2003 | kog | Eucariotic Cluster of orthologous genes |
| scop | Release 1.73 | dir.cla.scop.txt_1.73 | SCOP - Structural Classification of Proteins |
| go | April 14 2008 | mysql_database_GO | GO. Gene Ontology |
| dip | April 07 2008 | dip20080407.txt | DIP (Database of Interacting Proteins) |
| mips | June 01 2004 | temporal_mysql_database | The MIPS Mammalian Protein-Protein Interaction Database |
| hprd | September 01 2007 (Release_7) | HPRD_Release_7_09012007.txt | Human Protein Reference Database |
| bind | April 15 2008 | temporal_mysql_database | Biomolecular Interaction Network Database |
| intact | March 29 2008 | intact.txt | IntAct protein-protein interaction database |
| biogrid | 2.0.39 | BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt | The BioGRID's curated set of physical and genetic interactions |
| mint | April 08 2008 | 2008-04-08-full.mitab25.txt | the Molecular INTeraction database |
| ori | January 16 2007 | interact.dat | predicted interactions from distant structure/sequence patterns |
