Collaborative Proposal: EarthCube Building Blocks: Planet Microbe: Enabling the discovery and integration of oceanographic 'omics, environmental and physiochemical data layers

点击翻译按钮获取中文摘要

Oceanographic research expeditions provide a rich source of data comprised of next generation sequencing, microscopy, and physical/chemical environmental data to explore ocean biodiversity. As collection bottles and chemical sensors emerge from the depths of the ocean, research teams work through the night processing their key component of this oceanographic treasure. Despite careful efforts to share data among collaborators, the moment each sample emerges is often the last time these rich data sources are together. In this project the investigators will develop Planet Microbe, a federated resource of database connections to enable data discovery and open data sharing for historical and on-going oceanography and geobiology sequencing efforts. Planet Microbe will provide the community with a platform that partners -omics data and analyses with any relevant contextual and environmental data available.  To promote the use of Planet Microbe, adoption by the community, and a collaborative research paradigm, the project will leverage and continue development of ECOGEO Research Coordination Network workshop on bioinformatics protocols using open-source web-based Protocols.io software. These protocols will contain multimedia training videos, screenshots, and example datasets in a stepwise format that are cross-linked to specific commands, tools, or outside websites. The investigators will refine and extend these use-cases and protocols in early career workshops. They will adapt the protocols for broader use in high school curriculum in ocean sciences and cyberinfrastructure through an existing collaboration with a technical librarian and science teacher in a high school comprised of 70% minority students. The project will offer undergraduate students research opportunities to design and develop Apps in the existing CyVerse Cyberinfrastructure to address bioinformatic needs from the oceanographic community and participate in protocol development and teaching. Initially, the project will develop a prototype using data from Hawaii Ocean Time-series (HOT) and Bermuda Atlantic Time Series (BATS), both of which produce extensive "-omics" data sets (available via iMicrobe) and oceanographic data (available via the Biological and Chemical Oceanography Data Management Office (BCO-DMO)) and are of great value to the broader science community. Connections between data sets will be derived through automated distance-based algorithms, and refined through collaborative hand-curation. Once the prototype has been validated, additional -omics data sets from two NSF-funded Science and Technology Centers, the Centers for Dark Energy Biosphere Investigations (CDEBI) and Microbial Oceanography Research and Education (CMORE), will be retrieved from disparate -omic repositories (e.g., JGI/IMG, MG-RAST, NCBI, EBI) and queryable through a recommendation algorithm fueled and refined by scientific queries from past users. Finally, data in Planet Microbe will leverage existing EarthCube funded projects to expand beyond BCO-DMO such as: GeoLink, which also includes Rolling Deck to Repository (R2R) and International Ocean Discovery Program (IODP), SeaView to share collected resources and create a "microbe" user scenario, and GeoDeepDive to discover dark data in historical publications. Through this concerted effort, Planet Microbe will become the go-to site for oceanographic data discovery and integration. By reconnecting -omics data with environmental data from oceanographic cruises, Planet Microbe will enable biological inquiry into environmental changes that affect the distribution and abundance of microbes in the sea. Further, algorithms for connecting disparate data types and a robust search interface developed by Planet Microbe will enable the creation of virtual datasets through user-defined oceanographic measurements, features, and thresholds that can be used to synthesize and analyze global datasets in novel ways by the community. In particular, virtual datasets can be used broadly by the geosciences community to refine global ecological models, to inform citizen science efforts, and derive critical information on temporal and spatial data associated with ocean microbes that re important in disaster analysis. Taken together, Planet Microbe will provide a much needed resource for the geosciences community to unite -omics and environmental data toward unforeseen discovery in the Earth system.