Resources and sites of interest and related to MetNet

Source material Other links of interest

Reference-material

MetNet collects and integrates biological interaction networks and annotations from various data sources. This website was built based on and incorporating the following data sources:

Database	Citation	Format	Information retrieved
AraCyc	Zhang et al, 2005	Plain text files organized according to frame data model	Pathways, interactions and biomolecules participated in. Name, synonyms, references, comments. The majority of Arabidopsis metabolic pathways in MetNetDB come from AraCyc
AGRIS	Palaniswamy et al, 2006	Plain text files organized according to simple graph model	Transcription network, references and binding sites of individual transcriptional factors
YeastCyc		Plain text files organized according to frame data model	Pathways, interactions and biomolecules participated in. Name, synonyms, references, comments. The majority of Yeast biochemical pathways in MetNetDB come from YeastCyc
YeastRact	Pedro T. Monteriro et al, 2008	Plain text files organized according to simple graph model	Regulations between transcription factors and genes, references
ChlamyCyc	May P et al, 2009	Plain text files organized according to frame data model	Pathways, interactions and biomolecules participated in. Name, synonyms, references, comments. The majority of Chlamydomonas reinhardtii metabolic pathways in MetNetDB come from ChlamyCyc
GO	Harris et al, 2004	MySQL dump files organized according to acyclic directed graph data model	The whole copy of gene ontology database
TAIR	Swarbreck et al, 2008	Plain text files (Tabular data)	Affymetrix array elements and their corresponding LocusID mapping, Unitprot ID, TargetP location of polypeptides, loci of each AraCyc pathway
MapMan	Thimm et al, 2004	Excel files (Tabular data)	Gene annotation, MapMan BIN ID, gene function category
BioCyc open chemical compound database	Kanehisa et al, 2006	Plain text files organized according to frame data model	UNQUE-ID, synonyms
ChEBI	NAR mol.db.coll.	MySQL dump organized according to directed graph data model	ChEBI ID, formula, molecular weight, IUPAC, SMILES
PubChem	Wheeler et al, 2007	XML files organized according to object data model	PubChem CID, synonyms
NCI	Sitzmann et al, 2008	Structure data format according to object data model	Synonyms, CAS registry number
KEGG	Kanehisa et al, 2004	Plain text files (for compounds) organized according to object data model	Synonyms
SUBA	Heazlewood et al, 2007	Excel file	Protein subcellular location including experiment verified and software predicted
PPDB	Sun et al, 2009	Tabular data	Curated protein subcellular location, especially those in plastid
AMPDB	Heazlewood and Millar AH, 2005	Tabular data	Mitochondrion proteins, the subcellular location comes from computational prediction
AtNoPDB	Brown et al, 2005	Tabular data	Nucleolar proteins, subcellular location comes from prediction and experiments
AraPerox	Reumann, 2004	Plain text	Putative proteins in peroxisomes. Subcellular location comes from literature and computational prediction
plprot	Kleffmann et al, 2006	Plain text files organized according to object data model	Subcellular location comes from TargetP prediction
BRENDA	Scheer et al, 2011	Plain text files organized according to object data model	Enzyme’s interaction, substrate, product, activator, inhibitor, synonyms, metal ions, references
MetNet curator	free software	Manually curation	All, with focus on signal transduction information
AtPID	Li et al, 2011	Excel spreadsheet	Protein-Protein interaction data
EcoCyc	Keseler et al, 2011	Plain text files organized according to frame data model	Pathways, interactions and biomolecules participated in. Name, synonyms, references, comments.
VitisNet	Grimplet et al, 2009	Plain text files organized according to frame data model	Pathways, interactions and biomolecules participated in. Name, synonyms, references, comments.