Current Projects

Kepler Workflow

    • Objective: We aim to lower data integration barriers by seamlessly combining workflows using CyVerse Discovery Environment and supporting reproducible research and publication by linking to the Research Object infrastructure (ROHub).
    • Overview: The US NSF-funded Science Across Virtual Institutes (SAVI) project developed a proof-of-concept to lower these barriers for the use of environmental data in collaboration with Expert System, technical partner in the EU H2020 EVER-EST project, which is building a virtual research environment for earth sciences around the notion of ROs. We will create containerized applications and incorporate Kepler workflows that bring together diverse data to specific applications, with an emphasis on lightweight visual analytics. Our approach is informed by stakeholder-based use cases and requirements that catalyze future research, actionable science, and to readily integrate into business/decision-making workflows to assure success. Creating a requirements-based framework from all the identified use-cases will inform future applications and the scalability to other projects, will allow us to fully demonstrate the functionality of our development efforts. http://www.researchobject.org/
    • Current Status: Early last November, some of the team met at San Diego Supercomputer Center to discuss the Kepler/RO project and begin implementing web services. There we discussed project direction and created a specific agenda that came out of the meeting. Below are some of the highlights.
  1. Started out using using Shiny, but limited capabilities for leaflet (map library)
  2. Work to embed the workflow to the Kepler RO. Start with focusing on the Kepler/RO loop in the workflow.
  3. Work to incorporate converted NEON data
  4. Now we have a beta Geoserver exposed externally that can be used to query for GPS stations
  5. Possible end user goal – have possible date range of all the data, overall search for times

Currently, we are working to create a prototype and a proof of concept. We are exploring what works, what doesn’t, what’s scalable and what’s not. Moving forward we plan to show scalability capability and design the scoop of the project with the next phase in mind.

Plant Phenology Ontology (PPO)

    • Objective: To annotate plant phenological data sources using terms from the plant ontology, biological collections ontology and the newly developed plant phenology ontology to create a set of high level data which can be used to answer questions relating to phenological stages and their expression across time and space, and different environments. The output will be coordinated global data-store and mechanisms to access that store, and that can be re-used and sustained into the future.
    • Overview: Plant phenology — the timing of life-cycle events, such as flowering or leafing-out — has cascading effects on multiple levels of biological organization from individuals to ecosystems. Despite the importance of understanding phenology for managing biodiversity and ecosystem services, we are not currently able to address continent and global level responses to anticipated climatic changes. For example, ecosystem productivity models preform fairly well in estimating function, but do poorly in estimating the timing of ecological processes (leaf out, peak productivity, mid summer senescence, etc.). The problem of making phenological data useful to broad research and education communities stems from the fact that disparate groups, including ground-based observations, satellite remote sensing, digital repeat photography, and museum collections, are using non-standardized terminologies and metrics during data collection and data processing. https://www.plantphenology.org/
    • Current Status: Plant Phenology Ontology (PPO) Released!
      1. Our team has annotated plant phenological data from multiple sources (NEON, PEP, NPN) using terms from the plant ontology, biological collections ontology and the newly developed plant phenology ontology to create a set of high level data which can be used to answer questions relating to phenological stages and their expression across time and space, and different environments. The open source and freely available ontology output is coordinated to global data-store and mechanisms to access that store, and that can be re-used and sustained into the future. We are proud to announce our current milestone of all data sources mapped to the ontology. Plant phenology is now available for testing on https://www.plantphenology.org/ . Here you can query phenological traits and narrow search by date range, genus, Specific Epithet and source.