Cloud-based Semantic Integration and Knowledge Discovery Systems in Precision Medicine.

We have developed a cloud-based (AWS and IBM SoftLayer) knowledge environment for scalable semantic mining of scientific literature and PTM integrative knowledge discovery in precision medicine, building upon our novel natural language processing (NLP) technologies and bioinformatics infrastructure. We provided semantic integration of full-scale PubMed mining results from disparate text mining tools, along with kinase-substrate data from iPTMnet, and PTM proteoforms and their relations from Protein Ontology (PRO). We shared the digital objects of those applications in multiple interoperable formats and have registered them in bioCADDIE using CEDAR. We experimented with multiple system setups using operating system, programming language, web server, or database server that best fits each application. We evaluated the cost effectiveness of cloud computing by only paying for what we use and readily experimenting with additional services. A web portal is available for accessing our cloud-based knowledge environment at https://proteininformationresource.org/cloud/.