Piana
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| Revision as of 20:29, 8 May 2008 Marko (Talk | contribs) (→Local database contents) ← Previous diff |
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| | gene_info | | gene_info | ||
| | April 18 2008 | | April 18 2008 | ||
| - | | [ftp://ftp.ncbi.nih.gov/gene/ gene_info] | + | | April 19 2007 |
| - | | Gene NCBI database - gene_info | + | | Gene NCBI database ([ftp://ftp.ncbi.nih.gov/gene/ gene_info]) |
| |- | |- | ||
| | 4.1.10 | | 4.1.10 | ||
| | refseq | | refseq | ||
| | March 13 2008 (release 28) | | March 13 2008 (release 28) | ||
| - | | [ftp://ftp.ncbi.nih.gov/refseq/release/release-catalog/ RefSeq-release28.catalog] | + | | March 13 2008 (release 22) |
| - | | NCBI RefSeq Database | + | | [ftp://ftp.ncbi.nih.gov/refseq/release/release-catalog/ NCBI RefSeq] Database |
| |- | |- | ||
| | 4.1.11 | | 4.1.11 | ||
| | cog-myva=gb | | cog-myva=gb | ||
| | September 26 2002 | | September 26 2002 | ||
| - | | [ftp://ftp.ncbi.nih.gov/pub/COG/COG/ myva=gb] | + | | September 26 2002 |
| - | | Cluster of orthologous genes | + | | Cluster of orthologous genes ([ftp://ftp.ncbi.nih.gov/pub/COG/COG/ myva=gb]) |
| |- | |- | ||
| | 4.1.11 | | 4.1.11 | ||
| | cog | | cog | ||
| | March 05 2003 | | March 05 2003 | ||
| - | | [ftp://ftp.ncbi.nih.gov/pub/COG/COG/ whog] | + | | March 05 2003 |
| - | | Cluster of orthologous genes | + | | Cluster of orthologous genes ([ftp://ftp.ncbi.nih.gov/pub/COG/COG/ whog]) |
| |- | |- | ||
| | 4.1.11 | | 4.1.11 | ||
| | kog-kyva=gb | | kog-kyva=gb | ||
| | June 06 2003 | | June 06 2003 | ||
| - | | [ftp://ftp.ncbi.nih.gov/pub/COG/KOG/ kyva=gb] | + | | June 06 2003 |
| - | | Eucariotic Cluster of orthologous genes | + | | Eucariotic Cluster of orthologous genes ([ftp://ftp.ncbi.nih.gov/pub/COG/KOG/ kyva=gb]) |
| |- | |- | ||
| | 4.1.11 | | 4.1.11 | ||
| | kog | | kog | ||
| | July 21 2003 | | July 21 2003 | ||
| - | | [ftp://ftp.ncbi.nih.gov/pub/COG/KOG/ kog] | + | | July 21 2003 |
| - | | Eucariotic Cluster of orthologous genes | + | | Eucariotic Cluster of orthologous genes ([ftp://ftp.ncbi.nih.gov/pub/COG/KOG/ kog]) |
| |- | |- | ||
| | 4.1.12 | | 4.1.12 | ||
| | scop | | scop | ||
| | Release 1.73 | | Release 1.73 | ||
| - | | [http://scop.mrc-lmb.cam.ac.uk/scop/parse/ dir.cla.scop.txt_1.73] | + | | Release 1.71 |
| - | | SCOP - Structural Classification of Proteins | + | | Structural Classification of Proteins ([http://scop.mrc-lmb.cam.ac.uk/scop/parse/ SCOP]) |
| |- | |- | ||
| | 4.1.13 | | 4.1.13 | ||
| | go | | go | ||
| | April 14 2008 | | April 14 2008 | ||
| - | | [ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest/ mysql_database_GO] | + | | April 2007 |
| - | | GO. Gene Ontology | + | | Gene Ontology ([ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest/ GO]) |
| |- | |- | ||
| | 4.2.1 | | 4.2.1 | ||
| | dip | | dip | ||
| | April 07 2008 | | April 07 2008 | ||
| - | | [http://dip.doe-mbi.ucla.edu/ dip20080407.txt] | + | | February 19 2007 |
| - | | DIP (Database of Interacting Proteins) | + | | Database of Interacting Proteins ([http://dip.doe-mbi.ucla.edu/ DIP]) |
| |- | |- | ||
| | 4.2.2 | | 4.2.2 | ||
| | mips | | mips | ||
| | June 01 2004 | | June 01 2004 | ||
| - | | [http://mips.gsf.de/proj/ppi/ temporal_mysql_database] | + | | n/a |
| - | | The MIPS Mammalian Protein-Protein Interaction Database | + | | The Mammalian Protein-Protein Interaction Database [http://mips.gsf.de/proj/ppi/ MIPS] |
| |- | |- | ||
| | 4.2.3 | | 4.2.3 | ||
| Line 133: | Line 133: | ||
| | bind | | bind | ||
| | April 15 2008 | | April 15 2008 | ||
| - | | [http://bond.unleashedinformatics.com/ temporal_mysql_database] | + | | n/a |
| - | | Biomolecular Interaction Network Database | + | | Biomolecular Interaction Network Database ([http://bond.unleashedinformatics.com/ BOND]) |
| |- | |- | ||
| | 4.2.5 | | 4.2.5 | ||
| | intact | | intact | ||
| | March 29 2008 | | March 29 2008 | ||
| - | | [ftp://ftp.ebi.ac.uk/pub/databases/intact/current/ intact.txt] | + | | n/a |
| - | | IntAct protein-protein interaction database | + | | [ftp://ftp.ebi.ac.uk/pub/databases/intact/current/ IntAct] protein-protein interaction database |
| |- | |- | ||
| | 4.2.6 | | 4.2.6 | ||
| | biogrid | | biogrid | ||
| | 2.0.39 | | 2.0.39 | ||
| - | | [http://www.thebiogrid.org/ BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt] | + | | n/a |
| - | | The BioGRID's curated set of physical and genetic interactions | + | | The [http://www.thebiogrid.org/ BioGRID]'s curated set of physical and genetic interactions |
| |- | |- | ||
| | 4.2.7 | | 4.2.7 | ||
Revision as of 20:40, 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 | Local Version | Limited Version | Description |
|---|---|---|---|---|
| 4.1.1 | ncbi_taxonomy | April 18 2008 | April 03 2007 | NCBI Species information |
| 4.1.2 | swissprot | April 08 2008 | April 03 2007 | Uniprot manually curated database |
| 4.1.2 | trembl | April 08 2008 | April 03 2007 | Uniprot complete not manually curated database |
| 4.1.3 | genpept | April 18 2008 (release 165) | April 2007 (release 158) | NCBI genbank database |
| 4.1.4 | nr | April 16 2008 | April 2007 | NCBI non-redundant database |
| 4.1.5 | ncbi2pdb_pdbaa | April 16 2008 | April 09 2007 | Correspondence between pdb and gi identifiers (pdbaa) |
| 4.1.6 | ncbi2uniprot swissprot | April 16 2008 | April 09 2007 | Correspondences between uniprot and gi identifiers (swissprot) |
| 4.1.7 | pdbsprotec | March 12 2008 | January 15 2007 | Correspondences between pdb and uniprot identifiers (mapping.txt) |
| 4.1.8 | gene | April 18 2008 | April 19 2007 | Correspondences between NCBI accession number and geneID identifiers (gene2accession) |
| 4.1.9 | gene_info | April 18 2008 | April 19 2007 | Gene NCBI database (gene_info) |
| 4.1.10 | refseq | March 13 2008 (release 28) | March 13 2008 (release 22) | NCBI RefSeq Database |
| 4.1.11 | cog-myva=gb | September 26 2002 | September 26 2002 | Cluster of orthologous genes (myva=gb) |
| 4.1.11 | cog | March 05 2003 | March 05 2003 | Cluster of orthologous genes (whog) |
| 4.1.11 | kog-kyva=gb | June 06 2003 | June 06 2003 | Eucariotic Cluster of orthologous genes (kyva=gb) |
| 4.1.11 | kog | July 21 2003 | July 21 2003 | Eucariotic Cluster of orthologous genes (kog) |
| 4.1.12 | scop | Release 1.73 | Release 1.71 | Structural Classification of Proteins (SCOP) |
| 4.1.13 | go | April 14 2008 | April 2007 | Gene Ontology (GO) |
| 4.2.1 | dip | April 07 2008 | February 19 2007 | Database of Interacting Proteins (DIP) |
| 4.2.2 | mips | June 01 2004 | n/a | The Mammalian Protein-Protein Interaction Database MIPS |
| 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 | n/a | Biomolecular Interaction Network Database (BOND) |
| 4.2.5 | intact | March 29 2008 | n/a | IntAct protein-protein interaction database |
| 4.2.6 | biogrid | 2.0.39 | n/a | 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 |
