25The response of pathophysiological research to emerging epidemics often occurs 26 after the epidemic and, as a consequence, has little to no impact on improving 27 patient outcomes or on developing high-quality evidence to inform clinical 28 management strategies during the epidemic. Rapid and informed guidance of 29 epidemic (research) responses to severe infectious disease outbreaks requires quick 30 compilation and integration of existing pathophysiological knowledge. As a case 31 study we chose the Zika virus (ZIKV) outbreak that started in 2015 to develop a 32 proof-of-concept knowledge repository. To extract data from available sources and 33 build a computationally tractable and comprehensive molecular interaction map we 34 applied generic knowledge management software for literature mining, expert 35 knowledge curation, data integration, reporting and visualisation. A multi-disciplinary 36 team of experts, including clinicians, virologists, bioinformaticians and knowledge 37 management specialists, followed a pre-defined workflow for rapid integration and 38 evaluation of available evidence. While conventional approaches usually require 39 months to comb through the existing literature, the initial ZIKV KnowledgeBase 40 (ZIKA KB) was completed within a few weeks. Recently we updated the ZIKA KB 41 with additional curated data from the large amount of literature published since 2016 42 and made it publicly available through a web interface together with a step-by-step 43 guide to ensure reproducibility of the described use case (S4). In addition, a detailed 44 online user manual is provided to enable the ZIKV research community to generate 45 hypotheses, share knowledge, identify knowledge gaps, and interactively explore 46 and interpret data (S5). A workflow for rapid response during outbreaks was 47 threats. The resulting structured biological knowledge is a helpful tool for 50 computational data analysis and generation of predictive models and opens new 51 avenues for infectious disease research. 52 53 Availability: www.zikaknowledgebase.eu 54 55 Funding 56 European Commission's Seventh Framework Research Programme project 57 PREPARE (FP7-Health n°602525) and ZIKALLIANCE (MK, H2020; No 734548). 58 59 Author summary 60 During the recent ZIKV outbreak there was little information about the interactions 61 between Zika virus and the host, however, the massive research response lead to a 62 steep increase in the number of relevant publications within a very short period of 63 time. At the time, there was no structured and comprehensive database available for 64 integrated molecular and physiological data and knowledge about ZIKV infection. 65through the massive amount of existing literature. In addition to providing 74 background information for research, scientific publications can be processed to 75 transform textual information into complex networks, which can be integrated with 76 existing knowledge resources to suggest novel hypotheses that potentially contribute 77 to innovative infectious disease r...