| NSF Org: |
DBI Division of Biological Infrastructure |
| Recipient: |
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| Initial Amendment Date: | April 25, 2018 |
| Latest Amendment Date: | January 26, 2022 |
| Award Number: | 1759846 |
| Award Instrument: | Standard Grant |
| Program Manager: |
Reed Beaman
DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences |
| Start Date: | May 1, 2018 |
| End Date: | April 30, 2024 (Estimated) |
| Total Intended Award Amount: | $435,242.00 |
| Total Awarded Amount to Date: | $488,150.00 |
| Funds Obligated to Date: |
FY 2022 = $52,908.00 |
| History of Investigator: |
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| Recipient Sponsored Research Office: |
5200 N LAKE RD MERCED CA US 95343-5001 (209)201-2039 |
| Sponsor Congressional District: |
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| Primary Place of Performance: |
CA US 95343-5001 |
| 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, Capacity: Cyberinfrastructure |
| Primary Program Source: |
01001819DB NSF RESEARCH & RELATED ACTIVIT |
| Program Reference Code(s): |
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| Program Element Code(s): |
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| Award Agency Code: | 4900 |
| Fund Agency Code: | 4900 |
| Assistance Listing Number(s): | 47.074 |
ABSTRACT
For over 150 years, scientists have been classifying different plants, animals, fungi, and microbes based on how these organisms are related to one another. The Open Tree of Life project created a comprehensive website that summarizes these relationships. This website makes it easier for biologists to find previously discovered knowledge about evolutionary relationships and to obtain the data that underlies this knowledge. Understanding the evolutionary relationships between organisms is crucial to answering questions in all areas of biological research. The website is used in research that improves agriculture, fights diseases, conserves biodiversity, ensures food safety, and improves our understanding of basic processes in biology. The Open Tree of Life website also provides students and teachers with up-to-date biological information across the entire tree of life. This project will add several features to the core of the Open Tree of Life project to make it sustainable and to keep the resource up to date.
The Open Tree of Life project has built and deployed the first comprehensive tree of life. That project is used by individual biologists and by other informatics projects. This project will ensure the sustainability of the Open Tree of Life effort by adding new features to the user interface that motivate data deposition and curation, improving the rate and reliability of automated procedures for incorporating new data into the tree, and fixing several aspects of the core infrastructure to make the site easier to maintain and cheaper to run. The results of this work will be available at the Open Tree of Life site (https://tree.opentreeoflife.org) throughout the project.
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.
The Open Tree of Life project (Open Tree) is a collaboration developing tools to curate and share evolutionary estimates covering the entire tree of life. Open Tree provides a framework for a robust, reproducible, and extensible resource to link biodiversity, genomic, evolutionary, and other biological data. We regularly publish new synthetic trees and new taxonomies (https://tree.opentreeoflife.org). The current synthetic tree comprises 2.4 million tips and incorporates data from 1,239 published phylogenies.
Open Tree provides a phylogenetic information resource, through the synthetic tree itself as well as several of the data resources generated in the process of building the synthetic tree. OpenTree provides programmatic access to both the input and the summary data. We have developed and published python and R packages providing easy access to our data and API tools. Through these tools Open Tree provides an essential information resource for several other NSF funded bioinformatic projects, as well as several public outreach and K-12 teaching resources. All Open Tree software is open source, and all data is shared under a CC0 Open Access license.
In this grant we simplified the software used to develop and share the tree which makes the infrastructure easier to maintain long term. We improved the tree synthesis software to make the tree synthesis much faster and more efficient. We also added several new features. These features include the ability to generate a custom synthesis tree for any set of input studies and taxa, and to translate date information from published studies onto nodes in the complete tree for downstream analyses of dated trees.
This project has constructed the largest and most complete picture of the tree of life to date, and has made that data freely available to anyone around the world.
Last Modified: 09/11/2024
Modified by: Emily Jane Mctavish
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