| NSF Org: |
DBI Division of Biological Infrastructure |
| Recipient: |
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| Initial Amendment Date: | April 2, 2015 |
| Latest Amendment Date: | April 2, 2015 |
| Award Number: | 1458603 |
| Award Instrument: | Standard Grant |
| Program Manager: |
Peter McCartney
DBI Division of Biological Infrastructure BIO Directorate for Biological Sciences |
| Start Date: | July 1, 2015 |
| End Date: | June 30, 2019 (Estimated) |
| Total Intended Award Amount: | $148,101.00 |
| Total Awarded Amount to Date: | $148,101.00 |
| Funds Obligated to Date: |
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| History of Investigator: |
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| Recipient Sponsored Research Office: |
201 ANDY HOLT TOWER KNOXVILLE TN US 37996-0001 (865)974-3466 |
| Sponsor Congressional District: |
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| Primary Place of Performance: |
1 Circle Park Drive Knoxville TN US 37996-0003 |
| 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): |
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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
Because phylogenies (trees) showing the evolutionary relationships of species are so useful in bioscience and biotechnology, there has been a major worldwide effort to determine trees for various groups of organisms. This information can be knitted together into a single "Tree of Life" (ToL) covering millions of species, though it is often better to think of expert ToL knowledge as a forest of overlapping source-trees. Because this body of knowledge is complex, rapidly changing, and distributed among many online resources, getting the latest knowledge is a challenge. The focus of this project is to get ToL knowledge into the hands of scientists, educators, and the public, by building a distributed system of internet services that work together with existing NSF-sponsored projects to deliver custom trees to users as quickly and easily as they currently get online driving directions. The resulting system will allow a greater range of life-sciences researchers to ask more complex and challenging questions relating to diversity and biological functions. The project will work directly with educators and with educational resources such as the Encyclopedia of Life, making it easy for millions of users to access the latest scientific knowledge of species relationships.
Phylogenetic trees are useful in all areas of biology, both to organize knowledge by guiding classification and for process-based models that allow scientists to make robust inferences from comparisons of evolved entities (genes, species, etc). Phylogenetic knowledge is disseminated today via a very large number of idiosyncratic pathways, most of which are not easily traceable. While experts continue expanding the Tree of Life (ToL) knowledge, addressing gaps and conflicts, our focus is on dissemination, putting ToL knowledge in the hands of researchers, educators, and the public. The goal of this project is to design and develop an open web-service architecture for ToL delivery, with the functionality necessary to integrate into scientific workflows, including name-resolution, tree discovery, subtree extraction, and scaling of trees. The architecture will be designed as a sustainable distributed collection of services and will rely on semantically rich descriptions to facilitate composition of services and to documents the tree discovery and reuse process. The project will cultivate this system as a community resource by (1) involving partners, domain experts, and a broader phyloinformatics community in the design process; (2) partnering with other projects to involve them as service-providers or consumers; (3) developing innovative clients demonstrating quantitatively important use-cases; (4) staging a hackathon for participants to add services or develop clients. Results of the project will be accessible via www.phylotastic.org.
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.
We created a public, accessible website to allow scientists, educators, and the broader public to get access to the tree of life, a family tree of species. We also created software using the free software R to let scientists access this information programmatically. We created different software, and a website, for getting estimates of timing of when different groups originate.
A major effort in this grant was outreach. To that end, we organized a workshop at the University of California Museum of Paleontolgy for educators (mostly at middle or high schools). This resulted in numerous lesson plans and online resources, all available at https://jwiggi18.github.io/phyloEd/. For example, one of these projects was http://historyofearth.net/, a dynamic website that shows how the continents have moved through time, what species looked like, and where and when they appeared. It links out to student-appopriate content such as videos and articles. As a side effect of that one project, additional software was developed and made public to make visualizing contintential drift more available. Another project, https://jwiggi18.github.io/phylogenies_as_models/, done by a public school teacher, postdoc, and tenured faculty member teaches about what a phylogeny means and addresses Next Generation Science Standards; it includes quizzes. Other projects include information on the evolution of the horse, cane toads invading Australia, how to combine student species observations to make a tree, and much more. All this material is free and open for reuse.
Last Modified: 02/06/2020
Modified by: Brian C O'meara
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