Piana

From Icbwiki

The icb maintains 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.

Configuration and setup

The piana installation uses python 2.5 from softlib. At the present time, the required python modules for piana are only available on machines that are running the 64-bit version or RedHat Enterprise Linux 5. Descartes, rodin and piana are machines known to work with piana.

A bash script file is available will define environment variables and appropriated paths for using python with piana. The script is located at ~piana/bin/piana-setup.sh. When sourced, the following variables are added to your environment:

 PIANA_DIR - Directory of the piana source distribution
 PIANA_DBHOST - The host of the piana database instance (piana.med.cornell.edu)
 PIANA_DBNAME - The name of the piana database (piana or piana_limited)
 PIANA_DBUSER - Username to use when connecting to the piana database
 PIANA_DBPASS - Password to use when connecting to the piana database

Additionally, the value of PYTHONPATH will be set or modified to include the appropriate python packages required to interface with piana.

Database contents

The following table describes the contents of the piana database as of April 21st, 2008. The "section" column refers to the are in the populate piana documentation. Versions of the raw data sets are shown for both the data loaded by the icb, and the "limited" dataset provided for reference.

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	April 2007	NCBI non-redundant database
4.1.5	ncbi2pdb_pdbaa	April 16 2008	April 09 2007	Correspondence between pdb and gi identifiers (pdbaa)
4.1.6	ncbi2uniprot swissprot	April 16 2008	April 09 2007	Correspondences between uniprot and gi identifiers (swissprot)
4.1.7	pdbsprotec	March 12 2008	January 15 2007	Correspondences between pdb and uniprot identifiers (mapping.txt)
4.1.8	gene	April 18 2008	April 19 2007	Correspondences between NCBI accession number and geneID identifiers (gene2accession)
4.1.9	gene_info	April 18 2008	April 19 2007	Gene NCBI database (gene_info)
4.1.10	refseq	March 13 2008 (release 28)	release 22	NCBI RefSeq Database
4.1.11	cog-myva=gb	September 26 2002	September 26 2002	Cluster of orthologous genes (myva=gb)
4.1.11	cog	March 05 2003	March 05 2003	Cluster of orthologous genes (whog)
4.1.11	kog-kyva=gb	June 06 2003	June 06 2003	Eucariotic Cluster of orthologous genes (kyva=gb)
4.1.11	kog	July 21 2003	July 21 2003	Eucariotic Cluster of orthologous genes (kog)
4.1.12	scop	Release 1.73	Release 1.71	Structural Classification of Proteins (SCOP)
4.1.13	go	April 14 2008	April 2007	Gene Ontology (GO)
4.2.1	dip	April 07 2008	February 19 2007	Database of Interacting Proteins (DIP)
4.2.2	mips	June 01 2004	n/a	The Mammalian Protein-Protein Interaction Database MIPS
4.2.3	hprd	September 01 2007 (Release_7)	n/a	Human Protein Reference Database (HPRD}
4.2.4	bind	April 15 2008	n/a	Biomolecular Interaction Network Database (BOND)
4.2.5	intact	March 29 2008	n/a	IntAct protein-protein interaction database
4.2.6	biogrid	2.0.39	n/a	The BioGRID's curated set of physical and genetic interactions
4.2.7	mint	April 08 2008	n/a	The Molecular INTeraction database (MINT
4.2.8	ori	January 16 2007	January 16 2007	Predicted interactions from distant structure/sequence patterns interact.dat