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 a locally populated version along with the sample "limited" data distribution.
== Local database contents == == Local database contents ==
-{| border=1 cellspacing=1 cellpadding=0 +{| class="wikitable" style="margin: 1em auto 1em auto; background:#efefef;" valign="top" align="left" border="1" cellpadding="5"
 +|- valign="bottom" align="left" style="background:#ffdead;"
! databaseName ! databaseName
! databaseVersion ! databaseVersion
Line 8: Line 9:
! date ! date
! databaseDescription ! databaseDescription
-! databaseInteger 
|- |-
| ncbi_taxonomy | ncbi_taxonomy
Line 15: Line 15:
| 2008-4-18 | 2008-4-18
| NCBI Species information | NCBI Species information
-| 1 
|- |-
| swissprot | swissprot
Line 22: Line 21:
| 2008-4-18 | 2008-4-18
| Uniprot manually curated database | Uniprot manually curated database
-| 2 
|- |-
| trembl | trembl
Line 29: Line 27:
| 2008-4-18 | 2008-4-18
| Uniprot complete not manually curated database | Uniprot complete not manually curated database
-| 4 
|- |-
| genpept | genpept
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| 2008-4-19 | 2008-4-19
| ncbi genbank database | ncbi genbank database
-| 8 
|- |-
| nr | nr
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| 2008-4-20 | 2008-4-20
| non-redundant ncbi database | non-redundant ncbi database
-| 16 
|- |-
| ncbi2pdb_pdbaa | ncbi2pdb_pdbaa
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| 2008-4-21 | 2008-4-21
| correspondence between pdb and gi identifiers | correspondence between pdb and gi identifiers
-| 32 
|- |-
| ncbi2uniprot swissprot | ncbi2uniprot swissprot
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| 2008-4-21 | 2008-4-21
| correspondences between uniprot and gi identifiers | correspondences between uniprot and gi identifiers
-| 64 
|- |-
| pdbsprotec | pdbsprotec
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| 2008-4-21 | 2008-4-21
| correspondences between pdb and uniprot identifiers | correspondences between pdb and uniprot identifiers
-| 128 
|- |-
| gene | gene
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| 2008-4-21 | 2008-4-21
| correspondences between ncbi accession number and geneID identifiers | correspondences between ncbi accession number and geneID identifiers
-| 256 
|- |-
| gene_info | gene_info
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| 2008-4-21 | 2008-4-21
| Gene NCBI database - gene_info | Gene NCBI database - gene_info
-| 512 
|- |-
| refseq | refseq
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| 2008-4-21 | 2008-4-21
| NCBI RefSeq Database | NCBI RefSeq Database
-| 1024 
|- |-
| cog-myva=gb | cog-myva=gb
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| 2008-4-21 | 2008-4-21
| Cluster of orthologous genes | Cluster of orthologous genes
-| 2048 
|- |-
| cog | cog
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| 2008-4-21 | 2008-4-21
| Cluster of orthologous genes | Cluster of orthologous genes
-| 4096 
|- |-
| kog-kyva=gb | kog-kyva=gb
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| 2008-4-21 | 2008-4-21
| Eucariotic Cluster of orthologous genes | Eucariotic Cluster of orthologous genes
-| 8192 
|- |-
| kog | kog
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| 2008-4-21 | 2008-4-21
| Eucariotic Cluster of orthologous genes | Eucariotic Cluster of orthologous genes
-| 16384 
|- |-
| scop | scop
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| 2008-4-21 | 2008-4-21
| SCOP - Structural Classification of Proteins | SCOP - Structural Classification of Proteins
-| 32768 
|- |-
| go | go
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| 2008-4-21 | 2008-4-21
| GO. Gene Ontology | GO. Gene Ontology
-| 65536 
|- |-
| dip | dip
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| 2008-4-21 | 2008-4-21
| DIP (Database of Interacting Proteins) | DIP (Database of Interacting Proteins)
-| 131072 
|- |-
| mips | mips
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| 2008-4-21 | 2008-4-21
| The MIPS Mammalian Protein-Protein Interaction Database | The MIPS Mammalian Protein-Protein Interaction Database
-| 262144 
|- |-
| hprd | hprd
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| 2008-4-21 | 2008-4-21
| Human Protein Reference Database | Human Protein Reference Database
-| 524288 
|- |-
| bind | bind
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| 2008-4-21 | 2008-4-21
| Biomolecular Interaction Network Database | Biomolecular Interaction Network Database
-| 1048576 
|- |-
| intact | intact
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| 2008-4-21 | 2008-4-21
| IntAct protein-protein interaction database | IntAct protein-protein interaction database
-| 2097152 
|- |-
| biogrid | biogrid
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| 2008-4-21 | 2008-4-21
| The BioGRID's curated set of physical and genetic interactions | The BioGRID's curated set of physical and genetic interactions
-| 4194304 
|- |-
| mint | mint
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| 2008-4-21 | 2008-4-21
| the Molecular INTeraction database | the Molecular INTeraction database
-| 8388608 
|- |-
| ori | ori
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| 2008-4-21 | 2008-4-21
| predicted interactions from distant structure/sequence patterns | predicted interactions from distant structure/sequence patterns
-| 16777216 
|} |}

Revision as of 19:01, 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

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