Piana

From Icbwiki

(Difference between revisions)
Jump to: navigation, search
Revision as of 19:47, 8 May 2008
Marko (Talk | contribs)
(Local database contents)
← Previous diff
Revision as of 19:51, 8 May 2008
Marko (Talk | contribs)
(Local database contents)
Next diff →
Line 26: Line 26:
| genpept | genpept
| April 18 2008 (release 165) | April 18 2008 (release 165)
-| rel165.fsa_aa+| [ftp://ftp.ncbi.nih.gov/genbank/ rel165.fsa_aa]
| ncbi genbank database | ncbi genbank database
|- |-
| nr | nr
| April 16 2008 | April 16 2008
-| nr+| [ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ nr]
| non-redundant ncbi database | non-redundant ncbi database
|- |-
| ncbi2pdb_pdbaa | ncbi2pdb_pdbaa
| April 16 2008 | April 16 2008
-| pdbaa+| [ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ pdbaa]
| correspondence between pdb and gi identifiers | correspondence between pdb and gi identifiers
|- |-
| ncbi2uniprot swissprot | ncbi2uniprot swissprot
| April 16 2008 | April 16 2008
-| swissprot+| [ftp://ftp.ncbi.nih.gov/blast/db/FASTA/ swissprot]
| correspondences between uniprot and gi identifiers | correspondences between uniprot and gi identifiers
|- |-
-| pdbsprotec+| [http://www.bioinf.org.uk/pdbsprotec/ pdbsprotec]
| March 12 2008 | March 12 2008
| mapping.txt | mapping.txt

Revision as of 19:51, 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
Personal tools