Screenshot of the Cuebee interface after formulation of the query 1, “List the genes that are downregulated in the epimastigote stage and exist in a single metabolic pathway.”

Each row contains triples that are required to formulate the query. The query formulation is initiated by first selecting the server (PE All Datasets). After selecting the dataset, users begin to type in the search field and Cuebee provides suggestions matching the first letters typed in a drop down list. In this case “Microarray Analysis” is selected, and the query was limited to microarray analysis data pertaining to only “epimastigote” lifecycle stage of the parasite using filtering function of Cuebee. The triples are then extended as shown to achieve the desired query. The query uses “Group by” function of Cuebee to group all the epimastigote genes associated with a single metabolic pathway and “Refine” function to identify only those genes from the group that are downregulated; i.e, with log2 ratio less than −1. Specific results show a part of the results that include gene information from microarray lab data and pathway information from KEGG where each pathway ID represents specific pathway in KEGG.