Piana

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Revision as of 19:01, 8 May 2008
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{| class="wikitable" style="margin: 1em auto 1em auto; background:#efefef;" valign="top" align="left" border="1" cellpadding="5" {| 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;" |- valign="bottom" align="left" style="background:#ffdead;"
-! databaseName+! Name
-! databaseVersion+! Version
-! parsed_file+! Data Source
-! date+! Description
-! databaseDescription+
|- |-
| ncbi_taxonomy | ncbi_taxonomy
| April 18 2008 | April 18 2008
-| names.dmp+| [ftp://ftp.ncbi.nih.gov/pub/taxonomy/ names.dmp]
-| 2008-4-18+
| NCBI Species information | NCBI Species information
|- |-
| swissprot | swissprot
| April 08 2008 | April 08 2008
-| uniprot_sprot_rg_rx_oh_pe_deleted.dat+| [ftp://ftp.expasy.org/databases/uniprot/knowledgebase/ uniprot_sprot_rg_rx_oh_pe_deleted.dat]
-| 2008-4-18+
| Uniprot manually curated database | Uniprot manually curated database
|- |-
| trembl | trembl
| April 08 2008 | April 08 2008
-| uniprot_trembl_rg_rx_oh_pe_deleted.dat+| [ftp://ftp.expasy.org/databases/uniprot/knowledgebase/ uniprot_trembl_rg_rx_oh_pe_deleted.dat]
-| 2008-4-18+
| Uniprot complete not manually curated database | Uniprot complete not manually curated database
|- |-
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| April 18 2008 (release 165) | April 18 2008 (release 165)
| rel165.fsa_aa | rel165.fsa_aa
-| 2008-4-19 
| ncbi genbank database | ncbi genbank database
|- |-
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| April 16 2008 | April 16 2008
| nr | nr
-| 2008-4-20 
| non-redundant ncbi database | non-redundant ncbi database
|- |-
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| April 16 2008 | April 16 2008
| pdbaa | pdbaa
-| 2008-4-21 
| correspondence between pdb and gi identifiers | correspondence between pdb and gi identifiers
|- |-
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| April 16 2008 | April 16 2008
| swissprot | swissprot
-| 2008-4-21 
| correspondences between uniprot and gi identifiers | correspondences between uniprot and gi identifiers
|- |-
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| March 12 2008 | March 12 2008
| mapping.txt | mapping.txt
-| 2008-4-21 
| correspondences between pdb and uniprot identifiers | correspondences between pdb and uniprot identifiers
|- |-
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| April 18 2008 | April 18 2008
| gene2accession | gene2accession
-| 2008-4-21 
| correspondences between ncbi accession number and geneID identifiers | correspondences between ncbi accession number and geneID identifiers
|- |-
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| April 18 2008 | April 18 2008
| gene_info | gene_info
-| 2008-4-21 
| Gene NCBI database - gene_info | Gene NCBI database - gene_info
|- |-
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| March 13 2008 (release 28) | March 13 2008 (release 28)
| RefSeq-release28.catalog | RefSeq-release28.catalog
-| 2008-4-21 
| NCBI RefSeq Database | NCBI RefSeq Database
|- |-
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| September 26 2002 | September 26 2002
| myva=gb | myva=gb
-| 2008-4-21 
| Cluster of orthologous genes | Cluster of orthologous genes
|- |-
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| March 05 2003 | March 05 2003
| whog | whog
-| 2008-4-21 
| Cluster of orthologous genes | Cluster of orthologous genes
|- |-
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| June 06 2003 | June 06 2003
| kyva=gb | kyva=gb
-| 2008-4-21 
| Eucariotic Cluster of orthologous genes | Eucariotic Cluster of orthologous genes
|- |-
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| July 21 2003 | July 21 2003
| kog | kog
-| 2008-4-21 
| Eucariotic Cluster of orthologous genes | Eucariotic Cluster of orthologous genes
|- |-
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| Release 1.73 | Release 1.73
| dir.cla.scop.txt_1.73 | dir.cla.scop.txt_1.73
-| 2008-4-21 
| SCOP - Structural Classification of Proteins | SCOP - Structural Classification of Proteins
|- |-
Line 109: Line 92:
| April 14 2008 | April 14 2008
| mysql_database_GO | mysql_database_GO
-| 2008-4-21 
| GO. Gene Ontology | GO. Gene Ontology
|- |-
Line 115: Line 97:
| April 07 2008 | April 07 2008
| dip20080407.txt | dip20080407.txt
-| 2008-4-21 
| DIP (Database of Interacting Proteins) | DIP (Database of Interacting Proteins)
|- |-
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| June 01 2004 | June 01 2004
| temporal_mysql_database | temporal_mysql_database
-| 2008-4-21 
| The MIPS Mammalian Protein-Protein Interaction Database | The MIPS Mammalian Protein-Protein Interaction Database
|- |-
Line 127: Line 107:
| September 01 2007 (Release_7) | September 01 2007 (Release_7)
| HPRD_Release_7_09012007.txt | HPRD_Release_7_09012007.txt
-| 2008-4-21 
| Human Protein Reference Database | Human Protein Reference Database
|- |-
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| April 15 2008 | April 15 2008
| temporal_mysql_database | temporal_mysql_database
-| 2008-4-21 
| Biomolecular Interaction Network Database | Biomolecular Interaction Network Database
|- |-
Line 139: Line 117:
| March 29 2008 | March 29 2008
| intact.txt | intact.txt
-| 2008-4-21 
| IntAct protein-protein interaction database | IntAct protein-protein interaction database
|- |-
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| 2.0.39 | 2.0.39
| BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt | BIOGRID-ALL-SINGLEFILE-2.0.39.tab.txt
-| 2008-4-21 
| The BioGRID's curated set of physical and genetic interactions | The BioGRID's curated set of physical and genetic interactions
|- |-
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| April 08 2008 | April 08 2008
| 2008-04-08-full.mitab25.txt | 2008-04-08-full.mitab25.txt
-| 2008-4-21 
| the Molecular INTeraction database | the Molecular INTeraction database
|- |-
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| January 16 2007 | January 16 2007
| interact.dat | interact.dat
-| 2008-4-21 
| predicted interactions from distant structure/sequence patterns | predicted interactions from distant structure/sequence patterns
|} |}

Revision as of 19:47, 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

Name Version Data Source Description
ncbi_taxonomy April 18 2008 names.dmp NCBI Species information
swissprot April 08 2008 uniprot_sprot_rg_rx_oh_pe_deleted.dat Uniprot manually curated database
trembl April 08 2008 uniprot_trembl_rg_rx_oh_pe_deleted.dat Uniprot complete not manually curated database
genpept April 18 2008 (release 165) rel165.fsa_aa ncbi genbank database
nr April 16 2008 nr non-redundant ncbi database
ncbi2pdb_pdbaa April 16 2008 pdbaa correspondence between pdb and gi identifiers
ncbi2uniprot swissprot April 16 2008 swissprot correspondences between uniprot and gi identifiers
pdbsprotec March 12 2008 mapping.txt correspondences between pdb and uniprot identifiers
gene April 18 2008 gene2accession correspondences between ncbi accession number and geneID identifiers
gene_info April 18 2008 gene_info Gene NCBI database - gene_info
refseq March 13 2008 (release 28) RefSeq-release28.catalog NCBI RefSeq Database
cog-myva=gb September 26 2002 myva=gb Cluster of orthologous genes
cog March 05 2003 whog Cluster of orthologous genes
kog-kyva=gb June 06 2003 kyva=gb Eucariotic Cluster of orthologous genes
kog July 21 2003 kog Eucariotic Cluster of orthologous genes
scop Release 1.73 dir.cla.scop.txt_1.73 SCOP - Structural Classification of Proteins
go April 14 2008 mysql_database_GO GO. Gene Ontology
dip April 07 2008 dip20080407.txt DIP (Database of Interacting Proteins)
mips June 01 2004 temporal_mysql_database The MIPS Mammalian Protein-Protein Interaction Database
hprd September 01 2007 (Release_7) HPRD_Release_7_09012007.txt Human Protein Reference Database
bind April 15 2008 temporal_mysql_database Biomolecular Interaction Network Database
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
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