An overview core functionality of the online HPD software. (a) The HPD home page showing a query protein input box (supports multiple protein search using either gene names or UniProt identifiers). (b) A Web page containing the list of pathways retrieved as a result of a query protein input. Links to obtain pathway-pathway similarity matrix and pathway-protein association matrix and to download query-retrieved pathways were also shown on the Web page. (c) An advanced search page in which users may search pathways using gene name(s), with any term that appears within pathway names or with a list of one or more HPD Pathway IDs. This search retrieves a page similar to in (b). (d) A hyperlinked Web page showing pathway detailed information on molecular entities (Proteins, Complexes and Compounds) within the query pathway. (e) A hyperlinked Web page showing detailed pathway information on pathways similar to the query pathway. (f) A hyperlinked Web page showing detailed pathway information on molecular events (Interaction/Reaction/Regulation) within the query pathway. (g) A hyperlinked Web page showing pathway image link and reference articles.