We propose a search engine and file retrieval system for all bioinformatics databases worldwide. PubData searches biomedical data in a user-friendly fashion similar to how PubMed searches biomedical literature. PubData is built on novel network programming, natural language processing, and artificial intelligence algorithms that can patch into the file transfer protocol servers of any user-specified bioinformatics database, query its contents, retrieve files for download, and adapt to the user's search preferences. PubData is hosted as a user-friendly, cross-platform graphical user interface program developed using PyQt : http://www.pubdata.bio. The methods are implemented in Python, and are available as part of the PubData project at: https://github.com/Bohdan-Khomtchouk/PubData.