SysCID map: a computational knowledge repository for rheumatoid arthritis, systemic lupus erythematosus and inflammatory bowel disease

Chronic inflammatory diseases (CID) is a group of incurable immune system disorders for which no effective treatment options are currently available. Three autoimmune conditions, namely, rheumatoid arthritis (RA), systemic lupus erythematosus (SLE) and inflammatory bowel disease (IBD) are the major forms of CID with a prevalence of over 10% in Europe. Considering this high prevalence and the associated medical and societal burdens, establishing effective treatments for these CID-related conditions is urgently required. However, RA, SLE and IBD all emerge from a complex interplay among proteins, small chemical compounds, environmental factors and a myriad of different types of cells which makes the process of identifying successful druggable targets a formidable challenge for the CID research community. This challenge could be overcome by systems biology approaches as these approaches interrogate complex biological systems through large-scale quantification of numerous biomolecules. Thus, with the aim of facilitating the utilisation of systems biology approaches for the prediction of new druggable targets or even the discovery of new pathways, we built a map, the SysCID map, that encompasses the major molecular and cellular events involved in the onset and progression of RA, SLE and IBD. Encoded in a CellDesigner’s SBML format, the SysCID map contains 1027 reactions and 693 bioentities manually collected from 303 publications. All entities and reactions are well-annotated according to the standards provided by the Minimal Information Requested In the Annotation of Models (MIRIAM). The SysCID map is expected to be both a standardised knowledge repository for the CID research community as well as a hypothesis-generating resource for new discoveries concerning RA, SLE and IBD