Piana
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| Revision as of 20:08, 8 May 2008 Marko (Talk | contribs) (→Local database contents) ← Previous diff |
Revision as of 20:13, 8 May 2008 Marko (Talk | contribs) (→Local database contents) Next diff → |
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| | IntAct protein-protein interaction database | | IntAct protein-protein interaction database | ||
| |- | |- | ||
| - | | | + | | 4.2.6 |
| | biogrid | | biogrid | ||
| | 2.0.39 | | 2.0.39 | ||
| - | | BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt | + | | [http://www.thebiogrid.org/ BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt] |
| | The BioGRID's curated set of physical and genetic interactions | | The BioGRID's curated set of physical and genetic interactions | ||
| |- | |- | ||
| - | | | + | | 4.2.7 |
| | mint | | mint | ||
| | April 08 2008 | | April 08 2008 | ||
| - | | 2008-04-08-full.mitab25.txt | + | | [ftp://mint.bio.uniroma2.it/pub/release/MITAB/ 2008-04-08-full.mitab25.txt] |
| - | | the Molecular INTeraction database | + | | The Molecular INTeraction database |
| |- | |- | ||
| - | | | + | | 4.2.8 |
| | ori | | ori | ||
| | January 16 2007 | | January 16 2007 | ||
| - | | interact.dat | + | | [http://sbi.imim.es/piana#db interact.dat] |
| | predicted interactions from distant structure/sequence patterns | | predicted interactions from distant structure/sequence patterns | ||
| |} | |} | ||
Revision as of 20:13, 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
| Section | Name | Version | Raw Data Source | Description |
|---|---|---|---|---|
| 4.1.1 | ncbi_taxonomy | April 18 2008 | names.dmp | NCBI Species information |
| 4.1.2 | swissprot | April 08 2008 | uniprot_sprot_rg_rx_oh_pe_deleted.dat | Uniprot manually curated database |
| 4.1.2 | trembl | April 08 2008 | uniprot_trembl_rg_rx_oh_pe_deleted.dat | Uniprot complete not manually curated database |
| 4.1.3 | genpept | April 18 2008 (release 165) | rel165.fsa_aa | ncbi genbank database |
| 4.1.4 | nr | April 16 2008 | nr | non-redundant ncbi database |
| 4.1.5 | ncbi2pdb_pdbaa | April 16 2008 | pdbaa | correspondence between pdb and gi identifiers |
| 4.1.6 | ncbi2uniprot swissprot | April 16 2008 | swissprot | correspondences between uniprot and gi identifiers |
| 4.1.7 | pdbsprotec | March 12 2008 | mapping.txt | correspondences between pdb and uniprot identifiers |
| 4.1.8 | gene | April 18 2008 | gene2accession | correspondences between ncbi accession number and geneID identifiers |
| 4.1.9 | gene_info | April 18 2008 | gene_info | Gene NCBI database - gene_info |
| 4.1.10 | refseq | March 13 2008 (release 28) | RefSeq-release28.catalog | NCBI RefSeq Database |
| 4.1.11 | cog-myva=gb | September 26 2002 | myva=gb | Cluster of orthologous genes |
| 4.1.11 | cog | March 05 2003 | whog | Cluster of orthologous genes |
| 4.1.11 | kog-kyva=gb | June 06 2003 | kyva=gb | Eucariotic Cluster of orthologous genes |
| 4.1.11 | kog | July 21 2003 | kog | Eucariotic Cluster of orthologous genes |
| 4.1.12 | scop | Release 1.73 | dir.cla.scop.txt_1.73 | SCOP - Structural Classification of Proteins |
| 4.1.13 | go | April 14 2008 | mysql_database_GO | GO. Gene Ontology |
| 4.2.1 | dip | April 07 2008 | dip20080407.txt | DIP (Database of Interacting Proteins) |
| 4.2.2 | mips | June 01 2004 | temporal_mysql_database | The MIPS Mammalian Protein-Protein Interaction Database |
| 4.2.3 | hprd | September 01 2007 (Release_7) | HPRD_Release_7_09012007.txt | Human Protein Reference Database |
| 4.2.4 | bind | April 15 2008 | temporal_mysql_database | Biomolecular Interaction Network Database |
| 4.2.5 | intact | March 29 2008 | intact.txt | IntAct protein-protein interaction database |
| 4.2.6 | biogrid | 2.0.39 | BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt | The BioGRID's curated set of physical and genetic interactions |
| 4.2.7 | mint | April 08 2008 | 2008-04-08-full.mitab25.txt | The Molecular INTeraction database |
| 4.2.8 | ori | January 16 2007 | interact.dat | predicted interactions from distant structure/sequence patterns |
