Piana
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| | 4.1.7 | | 4.1.7 | ||
| - | | [http://www.bioinf.org.uk/pdbsprotec/ pdbsprotec] | + | | pdbsprotec |
| | March 12 2008 | | March 12 2008 | ||
| - | | mapping.txt | + | | [http://www.bioinf.org.uk/pdbsprotec/ mapping.txt] |
| | correspondences between pdb and uniprot identifiers | | correspondences between pdb and uniprot identifiers | ||
| |- | |- | ||
| - | | | + | | 4.1.8 |
| | gene | | gene | ||
| | April 18 2008 | | April 18 2008 | ||
| - | | gene2accession | + | | [ftp://ftp.ncbi.nih.gov/gene/ gene2accession] |
| | correspondences between ncbi accession number and geneID identifiers | | correspondences between ncbi accession number and geneID identifiers | ||
| |- | |- | ||
| - | | | + | | 4.1.9 |
| | gene_info | | gene_info | ||
| | April 18 2008 | | April 18 2008 | ||
| - | | gene_info | + | | [ftp://ftp.ncbi.nih.gov/gene/ gene_info] |
| | Gene NCBI database - gene_info | | Gene NCBI database - gene_info | ||
| |- | |- | ||
| - | | | + | | 4.1.10 |
| | refseq | | refseq | ||
| | March 13 2008 (release 28) | | March 13 2008 (release 28) | ||
| - | | RefSeq-release28.catalog | + | | [ftp://ftp.ncbi.nih.gov/refseq/release/release-catalog/ RefSeq-release28.catalog] |
| | NCBI RefSeq Database | | NCBI RefSeq Database | ||
| |- | |- | ||
| - | | | + | | 4.1.11 |
| | cog-myva=gb | | cog-myva=gb | ||
| | September 26 2002 | | September 26 2002 | ||
| - | | myva=gb | + | | [ftp://ftp.ncbi.nih.gov/pub/COG/COG/ myva=gb] |
| | Cluster of orthologous genes | | Cluster of orthologous genes | ||
| |- | |- | ||
| - | | | + | | 4.1.11 |
| | cog | | cog | ||
| | March 05 2003 | | March 05 2003 | ||
| - | | whog | + | | [ftp://ftp.ncbi.nih.gov/pub/COG/COG/ whog] |
| | Cluster of orthologous genes | | Cluster of orthologous genes | ||
| |- | |- | ||
| - | | | + | | 4.1.11 |
| | kog-kyva=gb | | kog-kyva=gb | ||
| | June 06 2003 | | June 06 2003 | ||
| - | | kyva=gb | + | | [ftp://ftp.ncbi.nih.gov/pub/COG/KOG/ kyva=gb] |
| | Eucariotic Cluster of orthologous genes | | Eucariotic Cluster of orthologous genes | ||
| |- | |- | ||
| - | | | + | | 4.1.11 |
| | kog | | kog | ||
| | July 21 2003 | | July 21 2003 | ||
| - | | kog | + | | [ftp://ftp.ncbi.nih.gov/pub/COG/KOG/ kog] |
| | Eucariotic Cluster of orthologous genes | | Eucariotic Cluster of orthologous genes | ||
| |- | |- | ||
| - | | | + | | 4.1.12 |
| | scop | | scop | ||
| | Release 1.73 | | Release 1.73 | ||
| - | | dir.cla.scop.txt_1.73 | + | | [http://scop.mrc-lmb.cam.ac.uk/scop/parse/ dir.cla.scop.txt_1.73] |
| | SCOP - Structural Classification of Proteins | | SCOP - Structural Classification of Proteins | ||
| |- | |- | ||
| - | | | + | | 4.1.13 |
| | go | | go | ||
| | April 14 2008 | | April 14 2008 | ||
| - | | mysql_database_GO | + | | [ftp://ftp.geneontology.org/pub/go/godatabase/archive/latest/ mysql_database_GO] |
| | GO. Gene Ontology | | GO. Gene Ontology | ||
| |- | |- | ||
| - | | | + | | 4.2.1 |
| | dip | | dip | ||
| | April 07 2008 | | April 07 2008 | ||
| - | | dip20080407.txt | + | | [http://dip.doe-mbi.ucla.edu/ dip20080407.txt] |
| | DIP (Database of Interacting Proteins) | | DIP (Database of Interacting Proteins) | ||
| |- | |- | ||
| - | | | + | | 4.2.2 |
| | mips | | mips | ||
| | June 01 2004 | | June 01 2004 | ||
| - | | temporal_mysql_database | + | | [http://mips.gsf.de/proj/ppi/ temporal_mysql_database] |
| | The MIPS Mammalian Protein-Protein Interaction Database | | The MIPS Mammalian Protein-Protein Interaction Database | ||
| |- | |- | ||
| - | | | + | | 4.2.3 |
| | hprd | | hprd | ||
| | September 01 2007 (Release_7) | | September 01 2007 (Release_7) | ||
| - | | HPRD_Release_7_09012007.txt | + | | [http://www.hprd.org/download/ HPRD_Release_7_09012007.txt] |
| | Human Protein Reference Database | | Human Protein Reference Database | ||
| |- | |- | ||
| - | | | + | | 4.2.4 |
| | bind | | bind | ||
| | April 15 2008 | | April 15 2008 | ||
| - | | temporal_mysql_database | + | | [http://bond.unleashedinformatics.com/ temporal_mysql_database] |
| | Biomolecular Interaction Network Database | | Biomolecular Interaction Network Database | ||
| |- | |- | ||
| - | | | + | | 4.2.5 |
| | intact | | intact | ||
| | March 29 2008 | | March 29 2008 | ||
| - | | intact.txt | + | | [ftp://ftp.ebi.ac.uk/pub/databases/intact/current/ intact.txt] |
| | IntAct protein-protein interaction database | | IntAct protein-protein interaction database | ||
| |- | |- | ||
Revision as of 20:08, 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 | 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 |
| 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 |
