Piana

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Revision as of 20:15, 8 May 2008
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(Local database contents)
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Line 19: Line 19:
| swissprot | swissprot
| April 08 2008 | April 08 2008
-| [ftp://ftp.expasy.org/databases/uniprot/knowledgebase/ uniprot_sprot_rg_rx_oh_pe_deleted.dat]+| April 03 2007
-| Uniprot manually curated database+| [ftp://ftp.expasy.org/databases/uniprot/knowledgebase Uniprot] manually curated database
|- |-
| 4.1.2 | 4.1.2
| trembl | trembl
| April 08 2008 | April 08 2008
-| [ftp://ftp.expasy.org/databases/uniprot/knowledgebase/ uniprot_trembl_rg_rx_oh_pe_deleted.dat]+| April 03 2007
-| Uniprot complete not manually curated database+| [ftp://ftp.expasy.org/databases/uniprot/knowledgebase/ Uniprot] complete not manually curated database
|- |-
| 4.1.3 | 4.1.3
| genpept | genpept
| April 18 2008 (release 165) | April 18 2008 (release 165)
-| [ftp://ftp.ncbi.nih.gov/genbank/ rel165.fsa_aa]+| April 2007 (release 158)
-| ncbi genbank database+| [ftp://ftp.ncbi.nih.gov/genbank/ NCBI genbank] database
|- |-
| 4.1.4 | 4.1.4
Line 38: Line 38:
| April 16 2008 | April 16 2008
| [ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ nr] | [ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ nr]
-| non-redundant ncbi database+| NCBI non-redundant database
|- |-
| 4.1.5 | 4.1.5

Revision as of 20:19, 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 nr NCBI non-redundant 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
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