TRUSTEES OF THE UNIVERSITY OF PENNSYLVANIA, THE

Award purpose

EMPOWERING COLLABORATIVE MALARIA SURVEILLANCE THROUGH A FAIR, SCALABLE PLATFORM FOR HARMONIZING, INTEGRATING, AND INTERROGATING MOLECULAR EPIDEMIOLOGICAL DATA: THE ARTEMISININ RESISTANCE USE CASE - PROJECT SUMMARY/ABSTRACT ARTEMISININ-RESISTANT (ART-R) PLASMODIUM FALCIPARUM HAS RECENTLY EMERGED IN EAST AFRICA, POSING A MAJOR THREAT TO MALARIA CONTROL. NUMEROUS RESEARCH GROUPS ARE GENERATING VALUABLE MOLECULAR SURVEILLANCE AND THERAPEUTIC EFFICACY DATASETS TO TRACK THE EMERGENCE AND SPREAD OF ART-R PARASITES IN AFRICA, YET THESE DATA ARE OFTEN INACCESSIBLE OR LACK ESSENTIAL CONTEXTUAL INFORMATION, MAKING DATASETS DIFFICULT TO INTEGRATE AND SLOWING THE SYNTHESIS OF EVIDENCE NECESSARY FOR INFORMING POLICY RESPONSES TO CONTAIN ART-R SPREAD. THE CLINICAL & EPIDEMIOLOGICAL DATABASE (CLINEPIDB) IS AN OPEN-ACCESS PLATFORM PROVIDING FAIR (FINDABLE, ACCESSIBLE, INTEROPERABLE, REUSABLE) ACCESS TO CLINICAL AND FIELD DATASETS, SUPPORTING INTUITIVE EXPLORATION, VISUAL- IZATION, AND SPATIAL-TEMPORAL INTERROGATION OF EPIDEMIOLOGICAL DATA. CLINEPIDB BUILDS ON THE ROBUST, SCALABLE, AND COST-EFFECTIVE INFRASTRUCTURE UNDERLYING THE VEUPATHDB BIOINFORMATICS RESOURCE CENTER, FACILITATING LONG-TERM PRESERVATION AND REUSE OF INFECTIOUS DISEASE DATASETS. WE PROPOSE TO EXTEND THIS PLATFORM TO BETTER SERVE THE ART-R RESEARCH COMMUNITY BY ENABLING STREAMLINED, CONTRIBUTOR-CONTROLLED SHARING AND INTEGRATED ANALYSIS OF HARMONIZED MOLECULAR AND EPIDEMIOLOGICAL DATASETS, CONSISTENT WITH EMERGING NIH DATA-SHARING POLICIES. IN CONSULTATION WITH A REGIONAL CONSORTIUM OF ART-R RESEARCHERS, WE WILL ESTABLISH AN END-TO-END FRAMEWORK FOR HARMONIZING, INTEGRATING, AND INTERROGATING HETEROGENEOUS MOLECULAR SURVEILLANCE DATASETS. IN AIM 1, WE WILL DEFINE COMMON DATA ELEMENTS AND BUILD CONSENSUS AROUND STANDARDIZED COLLECTION ACROSS RESEARCH GROUPS, USE AI TO ALIGN STUDY-SPECIFIC VARIABLES TO SHARED ONTOLOGIES, AND IMPLEMENT REPRODUCIBLE GALAXY-BASED WORKFLOWS FOR VARIANT CALLING AND METADATA CAPTURE. WE WILL ALSO ENHANCE DO-IT-YOURSELF DATA INGESTION TOOLS TO SUPPORT MULTIPLE FILE TYPES AND METADATA FORMATS, ENABLING SEAMLESS DATASET SUBMISSION BY LOCAL RESEARCH TEAMS. AIM 2 DESCRIBES INTERACTIVE TOOLS TO FACILITATE CROSS-STUDY EXPLORATION OF HARMONIZED DATASETS, INCLUDING BROWSING OF VARIABLE DISTRIBUTIONS, FILTERING AND TRANSFORMING DATA, VISUALIZING GEOSPATIAL AND TEMPORAL TRENDS, AND POPULATING AUTOMATED DASHBOARDS. AIM 3 PROPOSES TO ACCELERATE ETHICAL, TIMELY SHARING OF ART-R DATASETS BY EMBEDDING EARLY GOVERNANCE PLANNING, PROVIDING DEDICATED COORDINATION TO NAVIGATE REGULATORY APPROVALS AND DATA AGREEMENTS, IMPLEMENTING STANDARDIZED FRAMEWORKS FOR CONTRIBUTOR-GOVERNED DATA ACCESS CONTROLS, AND SUPPORTING COMMUNITY-DRIVEN DEVELOPMENT THROUGH TRAINING, OUTREACH, AND CO-DESIGN ACTIVITIES. BY ALIGNING ROBUST INFRASTRUCTURE WITH SCALABLE WORKFLOWS, ONTOLOGY-DRIVEN DATA HARMONIZATION, AND CONTRIBUTOR- GOVERNED SHARING, THIS PROJECT AIMS TO TRANSFORM HOW ART-R SURVEILLANCE DATA ARE SHARED, INTEGRATED AND EXPLORED – ACCELERATING DISCOVERY, IMPROVING REPRODUCIBILITY, AND OFFERING AN EXTENSIBLE MODEL APPLICABLE TO OTHER SURVEILLANCE EFFORTS.