Table 1

Data sources of MetNet
Database Format Ref Information retrieved
AraCyc Plain text files organized according to frame data model [14] Pathways, interactions and biomolecules participated in. Name, synonyms, references, comments. Majority metabolic pathways in MetNetDB come from AraCyc
AGRIS Plain text files organized according to simple graph model [15] Transcription network, references and binding sites of individual transcriptional factors
GO MySQL dump files organized according to acyclic directed graph data model [16] The whole copy of gene ontology database
TAIR Plain text files (Tabular data) [18] Affymetrix array elements and their corresponding LocusID mapping, Unitprot ID, TargetP location of polypeptides, loci of each AraCyc pathway
MapMan Excel files (Tabular data) [19] Gene annotation, MapMan BIN ID, gene function category
BioCyc open chemical compound database Plain text files organized according to frame data model [37] UNQUE-ID, synonyms
ChEBI MySQL dump organized according to directed graph data model [38] ChEBI ID, formula, molecular weight, IUPAC, SMILES
PubChem XML files organized according to object data model [39] PubChem CID, synonyms
NCI Structure data format according to object data model [40] Synonyms, CAS registry number
KEGG Plain text files (for compounds) organized according to object data model [41] Synonyms
SUBA Excel file [42] Protein subcellular location including experiment verified and software predicted
PPDB Tabular data [22] Curated protein subcellular location, especially those in plastid
AMPDB Tabular data [24] Mitochondrion proteins, the subcellular location comes from computational prediction
AtNoPDB Tabular data [26] Nucleolar proteins, subcellular location comes from prediction and experiments
AraPerox Plain text [25] Putative proteins in peroxisomes. Subcellular location comes from literature and computational prediction
plprot Plain text files organized according to object data model [23] Subcellular location comes from TargetP prediction
BRENDA Plain text files organized according to object data model [43] Enzyme’s interaction, substrate, product, activator, inhibitor, synonyms, metal ions, references
MetNet curator Manually curation All, with focus on signal transduction information
AtPID Excel spreadsheet [44] Protein-Protein interaction data
EcoCyc Plain text files organized according to frame data model [45] Pathways, interactions and biomolecules participated in. Name, synonyms, references, comments.
VitisNet SBML files made with CellDesigner [46] Manually constructed pathways based on draft genome sequence

Sucaet et al.

Sucaet et al. BMC Bioinformatics 2012 13:267   doi:10.1186/1471-2105-13-267

Open Data