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:

DatabaseCitation 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.

Copyright © 2006-2016 Wurtele lab. Copyright refers to the integration and online application, not the data from the various sources.

 

Number of queries executed: 1