Piana

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The icb maintains a local installations of the Protein Interactions And Network Analysis ([http://sbi.imim.es/piana/ PIANA]) database. The MySQL database resides on piana.med.cornell.edu and contains the sample "limited" data distribution and also a locally populated version. The icb maintains a local installations of the Protein Interactions And Network Analysis ([http://sbi.imim.es/piana/ PIANA]) database. The MySQL database resides on piana.med.cornell.edu and contains the sample "limited" data distribution and also a locally populated version.
 +
 +== Local database contents ==
 +{| border=1 cellspacing=1 cellpadding=0
 +! databaseName
 +! databaseVersion
 +! parsed_file
 +! date
 +! databaseDescription
 +! databaseInteger
 +|-
 +| ncbi_taxonomy
 +| April 18 2008
 +| names.dmp
 +| 2008-4-18
 +| NCBI Species information
 +| 1
 +|-
 +| swissprot
 +| April 08 2008
 +| uniprot_sprot_rg_rx_oh_pe_deleted.dat
 +| 2008-4-18
 +| Uniprot manually curated database
 +| 2
 +|-
 +| trembl
 +| April 08 2008
 +| uniprot_trembl_rg_rx_oh_pe_deleted.dat
 +| 2008-4-18
 +| Uniprot complete not manually curated database
 +| 4
 +|-
 +| genpept
 +| April 18 2008 (release 165)
 +| rel165.fsa_aa
 +| 2008-4-19
 +| ncbi genbank database
 +| 8
 +|-
 +| nr
 +| April 16 2008
 +| nr
 +| 2008-4-20
 +| non-redundant ncbi database
 +| 16
 +|-
 +| ncbi2pdb_pdbaa
 +| April 16 2008
 +| pdbaa
 +| 2008-4-21
 +| correspondence between pdb and gi identifiers
 +| 32
 +|-
 +| ncbi2uniprot swissprot
 +| April 16 2008
 +| swissprot
 +| 2008-4-21
 +| correspondences between uniprot and gi identifiers
 +| 64
 +|-
 +| pdbsprotec
 +| March 12 2008
 +| mapping.txt
 +| 2008-4-21
 +| correspondences between pdb and uniprot identifiers
 +| 128
 +|-
 +| gene
 +| April 18 2008
 +| gene2accession
 +| 2008-4-21
 +| correspondences between ncbi accession number and geneID identifiers
 +| 256
 +|-
 +| gene_info
 +| April 18 2008
 +| gene_info
 +| 2008-4-21
 +| Gene NCBI database - gene_info
 +| 512
 +|-
 +| refseq
 +| March 13 2008 (release 28)
 +| RefSeq-release28.catalog
 +| 2008-4-21
 +| NCBI RefSeq Database
 +| 1024
 +|-
 +| cog-myva=gb
 +| September 26 2002
 +| myva=gb
 +| 2008-4-21
 +| Cluster of orthologous genes
 +| 2048
 +|-
 +| cog
 +| March 05 2003
 +| whog
 +| 2008-4-21
 +| Cluster of orthologous genes
 +| 4096
 +|-
 +| kog-kyva=gb
 +| June 06 2003
 +| kyva=gb
 +| 2008-4-21
 +| Eucariotic Cluster of orthologous genes
 +| 8192
 +|-
 +| kog
 +| July 21 2003
 +| kog
 +| 2008-4-21
 +| Eucariotic Cluster of orthologous genes
 +| 16384
 +|-
 +| scop
 +| Release 1.73
 +| dir.cla.scop.txt_1.73
 +| 2008-4-21
 +| SCOP - Structural Classification of Proteins
 +| 32768
 +|-
 +| go
 +| April 14 2008
 +| mysql_database_GO
 +| 2008-4-21
 +| GO. Gene Ontology
 +| 65536
 +|-
 +| dip
 +| April 07 2008
 +| dip20080407.txt
 +| 2008-4-21
 +| DIP (Database of Interacting Proteins)
 +| 131072
 +|-
 +| mips
 +| June 01 2004
 +| temporal_mysql_database
 +| 2008-4-21
 +| The MIPS Mammalian Protein-Protein Interaction Database
 +| 262144
 +|-
 +| hprd
 +| September 01 2007 (Release_7)
 +| HPRD_Release_7_09012007.txt
 +| 2008-4-21
 +| Human Protein Reference Database
 +| 524288
 +|-
 +| bind
 +| April 15 2008
 +| temporal_mysql_database
 +| 2008-4-21
 +| Biomolecular Interaction Network Database
 +| 1048576
 +|-
 +| intact
 +| March 29 2008
 +| intact.txt
 +| 2008-4-21
 +| IntAct protein-protein interaction database
 +| 2097152
 +|-
 +| biogrid
 +| 2.0.39
 +| BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt
 +| 2008-4-21
 +| The BioGRID's curated set of physical and genetic interactions
 +| 4194304
 +|-
 +| mint
 +| April 08 2008
 +| 2008-04-08-full.mitab25.txt
 +| 2008-4-21
 +| the Molecular INTeraction database
 +| 8388608
 +|-
 +| ori
 +| January 16 2007
 +| interact.dat
 +| 2008-4-21
 +| predicted interactions from distant structure/sequence patterns
 +| 16777216
 +|}

Revision as of 18:54, 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 the sample "limited" data distribution and also a locally populated version.

Local database contents

databaseName databaseVersion parsed_file date databaseDescription databaseInteger
ncbi_taxonomy April 18 2008 names.dmp 2008-4-18 NCBI Species information 1
swissprot April 08 2008 uniprot_sprot_rg_rx_oh_pe_deleted.dat 2008-4-18 Uniprot manually curated database 2
trembl April 08 2008 uniprot_trembl_rg_rx_oh_pe_deleted.dat 2008-4-18 Uniprot complete not manually curated database 4
genpept April 18 2008 (release 165) rel165.fsa_aa 2008-4-19 ncbi genbank database 8
nr April 16 2008 nr 2008-4-20 non-redundant ncbi database 16
ncbi2pdb_pdbaa April 16 2008 pdbaa 2008-4-21 correspondence between pdb and gi identifiers 32
ncbi2uniprot swissprot April 16 2008 swissprot 2008-4-21 correspondences between uniprot and gi identifiers 64
pdbsprotec March 12 2008 mapping.txt 2008-4-21 correspondences between pdb and uniprot identifiers 128
gene April 18 2008 gene2accession 2008-4-21 correspondences between ncbi accession number and geneID identifiers 256
gene_info April 18 2008 gene_info 2008-4-21 Gene NCBI database - gene_info 512
refseq March 13 2008 (release 28) RefSeq-release28.catalog 2008-4-21 NCBI RefSeq Database 1024
cog-myva=gb September 26 2002 myva=gb 2008-4-21 Cluster of orthologous genes 2048
cog March 05 2003 whog 2008-4-21 Cluster of orthologous genes 4096
kog-kyva=gb June 06 2003 kyva=gb 2008-4-21 Eucariotic Cluster of orthologous genes 8192
kog July 21 2003 kog 2008-4-21 Eucariotic Cluster of orthologous genes 16384
scop Release 1.73 dir.cla.scop.txt_1.73 2008-4-21 SCOP - Structural Classification of Proteins 32768
go April 14 2008 mysql_database_GO 2008-4-21 GO. Gene Ontology 65536
dip April 07 2008 dip20080407.txt 2008-4-21 DIP (Database of Interacting Proteins) 131072
mips June 01 2004 temporal_mysql_database 2008-4-21 The MIPS Mammalian Protein-Protein Interaction Database 262144
hprd September 01 2007 (Release_7) HPRD_Release_7_09012007.txt 2008-4-21 Human Protein Reference Database 524288
bind April 15 2008 temporal_mysql_database 2008-4-21 Biomolecular Interaction Network Database 1048576
intact March 29 2008 intact.txt 2008-4-21 IntAct protein-protein interaction database 2097152
biogrid 2.0.39 BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt 2008-4-21 The BioGRID's curated set of physical and genetic interactions 4194304
mint April 08 2008 2008-04-08-full.mitab25.txt 2008-4-21 the Molecular INTeraction database 8388608
ori January 16 2007 interact.dat 2008-4-21 predicted interactions from distant structure/sequence patterns 16777216
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