| NSF Org: |
DBI Division of Biological Infrastructure |
| Recipient: |
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| Initial Amendment Date: | June 7, 2018 |
| Latest Amendment Date: | June 7, 2018 |
| Award Number: | 1759965 |
| Award Instrument: | Standard Grant |
| Program Manager: |
Reed Beaman
DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences |
| Start Date: | June 1, 2018 |
| End Date: | May 31, 2023 (Estimated) |
| Total Intended Award Amount: | $283,231.00 |
| Total Awarded Amount to Date: | $283,231.00 |
| Funds Obligated to Date: |
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| History of Investigator: |
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| Recipient Sponsored Research Office: |
1000 OLD MAIN HL LOGAN UT US 84322-1000 (435)797-1226 |
| Sponsor Congressional District: |
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| Primary Place of Performance: |
Logan UT US 84322-1415 |
| Primary Place of
Performance Congressional District: |
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| Unique Entity Identifier (UEI): |
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| Parent UEI: |
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| NSF Program(s): | ADVANCES IN BIO INFORMATICS |
| Primary Program Source: |
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| Program Reference Code(s): | |
| Program Element Code(s): |
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| Award Agency Code: | 4900 |
| Fund Agency Code: | 4900 |
| Assistance Listing Number(s): | 47.074 |
ABSTRACT
Biological collections in the United States have amassed over 500 million specimens but only 14% of these have been digitized; thus we need to greatly expand existing tools and methods to efficiently digitize specimen data. This project addresses this need by transforming Symbiota, one of the most widely used software platforms for mobilizing specimens in US research collections. Symbiota is an online biodiversity data management software platform that integrates data and images from networks of data providers. It has helped mobilize over 37 million specimen records from 766 natural history collections and is one of the most successful platforms for creating large collaborative data communities for sharing and displaying biodiversity data. Symbiota is used by 74% of the projects funded by the NSF Advancing Digitization of Biological Collections program and is thus a key platform to help digitize the estimated 430 million specimens in US collections that have yet to be digitized. Symbiota's success is largely due to its low learning curve and powerful set of tools for documenting species occurrences and integrating them with images and detailed taxonomic descriptions. But its widespread use has yielded significant feedback on how it could be made more effective. To accomplish this and aid its future development, Symbiota needs a fundamental restructuring. This project will transform Symbiota into a new version, Symbiota2, to catalyze contributions, expand research use, enrich education-outreach activities, and increase sustainability. Symbiota2 will enhance our ability to address a broad spectrum of biodiversity-related research questions by facilitating data visualization, linking multiple data sources (e.g., publications), creating better tools for data quality assessment, and monitoring data usage.
The transformation of Symbiota into Symbiota2 will completely refactor its code structure to emphasize modularity and improve usability and accessibility. This transformation will achieve the following goals, derived through direct management of Symbiota data portals and concerted and dedicated interactions with the Symbiota user community: 1) Provide RESTful web services so that data can be easily incorporated into a scientific workflow, 2) Build a plugin architecture to ease the development of new features, 3) Create a database abstraction layer to include a wide variety of backend database management systems, 4) Increase data utility by supporting analytical and visualization tools, 5) Separate the Graphical User Interface (GUI) from other processing so that new GUIs can be used, and 6) Enhance the data collection by making it easier to add new kinds of data and work offline. With these goals met, Symbiota2 will be a powerful biodiversity data management system fulfilling the needs of developers, data providers, researchers, and education professionals, as well as being interoperable with other biodiversity initiatives. Please visit the project's home page at symbiota.org to learn more.
This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.
PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH
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PROJECT OUTCOMES REPORT
Disclaimer
This Project Outcomes Report for the General Public is displayed verbatim as submitted by the Principal Investigator (PI) for this award. Any opinions, findings, and conclusions or recommendations expressed in this Report are those of the PI and do not necessarily reflect the views of the National Science Foundation; NSF has not approved or endorsed its content.
Scientists and collectors collect biological specimens such as plants, insects, and animals. Such collections help document the diversity of life on Earth. Data on the specimens is stored on computers. We developed computer software, called Symbiota2, to help manage the stored biodiversity data. Symbiota2 is a biodiversity data management system available as open-source software at https://gitlab.com/symbiota2. It consists of lots of code, 89,307 lines of Typescript code, 5244 lines of CSS and 7959 lines of HTML and took several years to develop. Though there are other biodiversity management systems, Symbiota2 has some special features. Its user interface is separate from the data management component. The two communicate through the web using services. This separation helps developers write code more quickly and easily. A second feature is that Symbiota2's user interface is available in a variety of languages, making biodiversity data available to non-English speakers. A third feature is that Symbiota2 has special search capabilities provided by a tool (that we did not develop) called Elasticsearch so Symbiota2 sites can quickly and easily add visualizations to showcase biodiversity data. A fourth feature is that Symbiota2 can generate a knowledge graph, which is a special graph with semantic annotations for data exchange and publication. A fifth feature is that Symbiota2 is easy to install and maintain with software already installed on many computers. This helps to free scientists to spend less time maintaining software and more time documenting biodiversity. Symbiota2 also provides tutorials on writing code to ffurther extend Symbiota2 and installation instructions.
Last Modified: 09/29/2023
Modified by: Curtis E Dyreson
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