We notice that the two compiled domain-domain interaction networks have different properties.
For this purpose, we implement the same validation process based on the large compiled domain-domain interaction network that is composed of all interactions in the DOMINE database and high-confidence interactions in the InterDom database.
The simplest methods relied on dictionaries, sometimes referred to as gazetteers, that are compiled by domain experts.
We establish complexity results for answering conjunctive queries under sticky sets of TGDs, showing, in particular, that queries can be compiled into domain independent first-order (and thus translatable into SQL) queries over the given EDB.
These gene sets are compiled by domain experts and they provide canonical representations of biological processes.
The gene sets from the C2 data base are separated in 2 categories: CP canonical pathways- canonical representations of biological processes compiled by domain experts) and CGP (chemical and genetic perturbations- gene set representing genes induced or repressed by the perturbation) (http://www.broad.mit.edu/gsea/msigdb/collections.jsp C2).jsp C2
We focus on the dataset that represents canonical representations of 633 biological processes compiled by domain experts (c2.cp, version2.5).
These canonical representations of biological pathways or processes have been compiled by domain experts and curated from several online databases (BioCarta, Gene Arrays, BioScience Corp, KEGG, Reactome, Sigma-Aldrich Pathways, Signal Transduction Knowledge Environment, Signaling Gateway).
These gene sets represent well-described biological processes compiled by domain experts, which include gene sets derived mainly from BioCarta pathway database [ 34], KEGG pathway database [ 35], and Reactome pathway database [ 36].
The domain-based predictor scans the query protein sequence (E-value ≤1e-5) and compares its Pfam domains with the domains compiled from the training dataset.
However, numerous individuals and organizations have reacted with anger and shock to the discovery that they have a "terrorism" designation on World-Check's database, which is compiled using public domain sources.
