Table 1 Data sources of MetNet

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