Updates consist of conducting monthly searches of relevant electronic databases, importing results into a bibliographic database management program, screening titles to identify relevant articles, retrieving potentially relevant articles and screening full document versions for inclusion.
The nodes and links used to construct this network database were imported from nine public databases, namely, EntrezGene interaction [16], MINT [17], DIP [18], CTD [19], TTD [20], ChemBank [21], PharmGKB [22], OMIM [23], and GAD [24] (Table 1).
All citations were saved in the PubMed database and imported into the EndNote X6 database.
We collected 1206 enzyme proteins with known catalytic activities from KEGG database and imported them into the eFG database.
STRING uses a variety of methods for predicting protein associations: Genomic Context (like gene fusion, phylogenetic co-occurrence, conserved neighborhood), high-throughput experiments (Y2H), conserved co-expression in different conditions, previous knowledge (database imports and and literature co-occurrence), and observed interaction of orthologous genes in other species.
35 The software package YANAsquare 32 provides a database import tool, the KEGG Browser.
The Ensembl variation database imports variation data (SNPs, CNVs, genotypes, phenotypes, etc).
The main page of the database provides hyperlinks to: Filter Database, Import Gene Set, Download Data, View Database, Submit Study, Documentation, and Contact.
In our study, we used the protein-protein interactions from the STRING database [ 50], which integrates and weighs information from numerous sources, including conserved neighborhood, gene fusions, phylogenetic co-occurrence, co-expression, database imports, large-scale experiments, and literature co-occurrence [ 51].
In this work, we localized the PPI of Arabidopsis thaliana from database STRING (http://string-db.org/) [ 24], which integrates and weights information from numerous sources, including conserved neighborhood, gene fusions, phylogenetic co-occurrence, co-expression, database imports(e.g. MINT, HPRD, BIND, DIP, BioGRID, KEGG and Reactome), large-scale experiments, literature co-occurrence [ 25].
