ProSetComp

Abstract

The amount of data available in public bioinformatics resources and the complexity of user interfaces they are served through often challenges appreciation and effective utilization of these valuable resources. While education, documentation and training activities mitigate this problem, there is still a need to develop user interfaces to serve simple day-to-day needs of scientists. To this end, we developed ProSetComp; a simple web-based platform to create and compare protein sets, following a traditional software development process; from requirement analysis to implementation. First, we interviewed and collected user scenarios from wet lab scientists with seniority, research interests and backgrounds. Reviewing the user scenarios, we identified one high impact need that drove the development of ProSetComp; ability to 1) create protein sets by searching databases, 2) compare these protein sets in different dimensions such as functional domains, pathways, molecular functions and biological processes, and 3) visualize results graphically. Next, we collected and integrated necessary data from several bioinformatics resources including UniProt, Reactome, Gene Ontology and PFAM in a local relational database. Finally, we designed user interfaces that facilitate the creation of protein sets by using form-based query generators and exploring the relationship between created protein sets using tabular and graphical representations. The current internal release of the platform contains ~120 million protein entries. The user interface supports >50 search criteria to create up-to four protein sets and comparison of these sets in four dimensions; protein domains, molecular functions, biological processes, and pathways. The commonality and differences between protein sets, along with tables, can be explored using novel user interface components such as Venn and UpSet diagrams. The first public release of ProSetComp (http://ceng.mu.edu.tr/labs/bioinfo/prosetcomp) is targeted for mid-August, 2018 and planned to be updated monthly thereafter. Upon public release, source code ProSetComp will become available through GitHub. The database content and user interface will be expanded as per community needs. The ProSetComp project is supported by The Scientific and Technological Research Council of Turkey (TUBITAK, Grant number: 216Z111).