Award Abstract # 1062193
ABI Development: Collaborative Research: VertNet, a New Model for Biodiversity Networks

NSF Org: DBI
Division of Biological Infrastructure
Recipient: REGENTS OF THE UNIVERSITY OF CALIFORNIA, THE
Initial Amendment Date: May 6, 2011
Latest Amendment Date: August 22, 2014
Award Number: 1062193
Award Instrument: Continuing Grant
Program Manager: Peter McCartney
DBI
 Division of Biological Infrastructure
BIO
 Directorate for Biological Sciences
Start Date: May 1, 2011
End Date: April 30, 2016 (Estimated)
Total Intended Award Amount: $1,871,968.00
Total Awarded Amount to Date: $2,076,373.00
Funds Obligated to Date: FY 2011 = $584,032.00
FY 2012 = $641,145.00

FY 2013 = $646,791.00

FY 2014 = $204,405.00
History of Investigator:
  • Carla Cicero (Principal Investigator)
    ccicero@berkeley.edu
  • Carol Spencer (Co-Principal Investigator)
Recipient Sponsored Research Office: University of California-Berkeley
1608 4TH ST STE 201
BERKELEY
CA  US  94710-1749
(510)643-3891
Sponsor Congressional District: 12
Primary Place of Performance: University of California-Berkeley
1608 4TH ST STE 201
BERKELEY
CA  US  94710-1749
Primary Place of Performance
Congressional District:
12
Unique Entity Identifier (UEI): GS3YEVSS12N6
Parent UEI:
NSF Program(s): ADVANCES IN BIO INFORMATICS
Primary Program Source: 01001112DB NSF RESEARCH & RELATED ACTIVIT
01001213DB NSF RESEARCH & RELATED ACTIVIT

01001314DB NSF RESEARCH & RELATED ACTIVIT

01001415DB NSF RESEARCH & RELATED ACTIVIT
Program Reference Code(s): 1165, 9178
Program Element Code(s): 116500
Award Agency Code: 4900
Fund Agency Code: 4900
Assistance Listing Number(s): 47.074

ABSTRACT

This collaborative award is made to implement an innovative model for biodiversity networks and data sharing called VertNet (http://vertnet.org). Biodiversity is in a crisis caused by multiple human impacts on the environment, and documentation of spatial and temporal biodiversity changes is immediately and urgently needed in order to address this crisis. The community of vertebrate natural history collections has begun to meet this need by establishing social and technological infrastructures that provide open access to data describing planetary occurrences of biological specimens. Taxon-specific data sharing initiatives such as MaNIS, ORNIS, HerpNET and FishNet 2 currently provide, in total, over 85 million records documenting where vertebrates occur. Together these networks include 171 collections from 12 countries, with an additional 52 collections (20 countries) committed to participation. Already, they are accessed at a rate of nearly 2.5 million records per week. Participation in each of these networks has far exceeded expectations, resulting in growing issues of scalability, performance, sustainability, and ability to incorporate new members. VertNet will solve these impediments by moving to a cloud computing solution in which providers and users synchronize changes to a cloud-based network of vertebrate biodiversity data. Cloud computing is a pay-per-use model utilizing internet-based, third party computing resources that are fast and dynamically scalable. The new VertNet model removes the requirement and cost to contributors to buy or maintain their own servers while leveraging all of the data integrity and replication services provided by the cloud. Under the new model, contributors will use a web-based administrative interface to create a "provider" in the cloud. Subsequent updates will use the same local application to publish differences (additions, changes, deletions) since initial publishing. Data storage in the cloud will contain the primary data published from all contributors as persistently and uniquely available records. In addition, it will contain summary information about data aggregations, and will incorporate data from other sources such as auxiliary data look-ups, user feedback, and data quality assessments. VertNet will provide open access to data with new capabilities for discovery and visualization, and will integrate with several existing biodiversity and collection management applications. Development of VertNet will transform the use of vertebrate biodiversity data for cross-disciplinary research, conservation, and policy-making.

The four predecessor projects (MaNIS, ORNIS, HerpNET, FishNet 2) have built a strong tradition of biodiversity informatics training and community-building. VertNet will continue this tradition, with impacts extending beyond the funded institutions. Specifically, VertNet will engage students from across the United States in two Summer Internships in Biodiversity Informatics and two Workshops in Biodiversity Informatics. In addition, undergraduate students will be offered volunteer apprenticeships through existing programs at UC Berkeley. An additional workshop that involves the broader community will address strategies for long-term sustainability of digitization and data-sharing efforts.

PUBLICATIONS PRODUCED AS A RESULT OF THIS RESEARCH

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(Showing: 1 - 10 of 21)
Costello MJ, J Wieczorek (2014). "Best practice for biodiversity data management and publication" Biological Conservation , v.173 , 2014 10.1016/j.biocon.2013.10.018
Deck J, K Barker, R Beaman, PL Buttigieg, G Dröge, R Guralnick, C Miller, ÉÓ Tuama, Z Murrell, C Parr, B Robbins, D Schigel, B Stucky, R Walls, J Wieczorek, N Morrison, J Wooley "Clarifying Concepts and Terms in Biodiversity Informatics" Stand Genomic Sci. , v.8 , 2013 , p.352 10.4056/sigs.3907833
Deck J, K Barker, R Beaman, PL Buttigieg, G Dröge, R Guralnick, C Miller, ÉÓ Tuama, Z Murrell, C Parr, B Robbins, D Schigel, B Stucky, R Walls, J Wieczorek, N Morrison, J Wooley "Clarifying Concepts and Terms in Biodiversity Informatics" Stand Genomic Sci. , v.8 , 2013 , p.352 doi: 10.4056/sigs.3907833
John Deck, Robert Guralnick, Ramona Walls, Stanley Blum, Melissa Haendel, Andréa Matsunaga and John Wieczorek "Meeting Report: Identifying practical applications of ontologies for biodiversity informatics" Standards in Genomic Sciences , v.10 , 2015 10.1186/s40793-015-0014-0
Otegui J, Guralnick RP "The geospatial data quality REST API for primary biodiversity data" Bioinformatics , v.32 , 2016 10.1093/bioinformatics/btw057
Ramona L. Walls , John Deck , Robert Guralnick , Steve Baskauf, Reed Beaman , Stanley Blum, Shawn Bowers, Pier Luigi Buttigieg , Neil Davies, Dag Endresen, Maria Alejandra Gandolfo, Robert Hanner, Alyssa Janning, Leonard Krishtalka, Andréa Matsunaga, Pet "Semantics in Support of Biodiversity Knowledge Discovery: An introduction to the Biological Collections Ontology and Related Ontologies" PLoS One , 2014 doi:10.1371/journal.pone.0089606
Ramona L Walls, Robert Guralnick, John Deck, Adam Buntzman, Pier Luigi Buttigieg, Neil Davies, Michael W Denslow, Rachel E Gallery, J Jacob Parnell, David Osumi-Sutherland, Robert J Robbins, Philippe Rocca-Serra, John Wieczorek, and Jie Zheng "Meeting report: advancing practical applications of biodiversity ontologies" Standards in Genomic Sciences , 2014 doi:10.1186/1944-3277-9-17
Robert P. Guralnick, Nico Cellinese, John Deck, Richard L. Pyle, John Kunze, Lyubomir Penev, Ramona Walls, Gregor Hagedorn, Donat Agosti, John Wieczorek, Terry Catapano, Roderic Page "Community Next Steps for Making Global Unique Identifiers Work for Biocollections Data" Zookeys. doi:10.3897/zookeys.494.9352 , 2015 10.3897/zookeys.494.9352
Robertson T, M Döring, R Guralnick, D Bloom, J Wieczorek, K Braak, J Otegui, L Russell, P Desmet "The GBIF Integrated Publishing Toolkit: Facilitating the efficient publishing of biodiversity data on the Internet" PLoS ONE , v.9 , 2014 , p.e102623 10.1371/journal.pone.0102623
Steven J. Baskauf, John Wieczorek, John Deck, Campbell O. Webb "An RDF Guide for the Darwin Core standard" Semantic Web Journal , 2014 636-1846
Thomer A, Vaidya G, Guralnick R, Bloom D, Russell L "From documents to datasets: A MediaWiki-based method of annotating and extracting species observations in century-old field notebooks" ZooKeys , v.209 , 2012 , p.235 10.3897/zookeys.209.3247
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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 VertNet project was established with four foundational objectives: (1) to facilitate open web access to specimen data from museums, educational institutions, and government repositories; (2) to enhance the value of these specimen collections by making them accessible to the public; (3) to provide services that would permit these collections to focus their resources on curation; and (4) to design a data-sharing network that could be adopted easily by other disciplines with similar needs.

VertNet is a collaboration between four U.S. universities (University of California at Berkeley, University of Colorado at Boulder, University of Kansas, and Tulane University) that built upon the lessons and strengths of four predecessor projects (MaNIS, ORNIS, HerpNet, FishNet 2). As a result, VertNet is a thriving data-sharing community and network of data publishers that links hundreds of biodiversity collections and repositories across the United States and rest of the world. As of June 2016, this network includes 212 institutions representing 696 collections. The VertNet project has made more than 300 million records available to the public via the vertebrate-focused data portal (http://www.vertnet.org) and in support of other major biodiversity projects in the U.S. (https://www.idigbio.org) and abroad (http://www.gbif.org).

Access to data from these biodiversity collections is of critical importance to educators, researchers, scientists, and policy-makers in addressing pressing challenges and questions about global climate change and the associated loss of biodiversity. VertNet has addressed the international demand for quick, reliable access to high quality data that describes biodiversity so that any person or organization, from a seventh-grade teacher in Ohio to the Army Corps of Engineers, can and will have the information available to them to generate lessons plans, monitor changes in the environment, and make informed decisions about human development, energy policy, and national defense.

Intellectual Merit.  The intellectual merit of the VertNet project is threefold. First, VertNet has addressed the critical need for high quality data for biodiversity research, monitoring, and decision-making by providing an integrated, publicly accessible, and cost-effective online data portal for vertebrates. Second, VertNet has developed a new model for making all of these data accessible in a way that makes it easy for anybody to find biodiversity data quickly, and has been emulated by other large-scale biodiversity projects in the U.S. and around the world. This new model has become an essential tool in the efforts of both professionals and hobbyists to better understand the world in which we live. Third, VertNet has transformed how biodiversity science is conducted. Researchers and educators who endeavor to model species distributions, determine overall patterns of global biodiversity, and document biodiversity changes over time now have access to new integrative tools and biodiversity data that increase the quality and usefulness of information contributed by the VertNet community.

Broader Impacts. Perhaps the most enduring result of the VertNet project is its commitment to providing training to people who use biodiversity data. During the funding period, VertNet conducted more than 60 training workshops and webinars to teach members of the community the skills necessary to become successful researchers, educators, and students. Through these workshops, VertNet has extended the benefits of its funding far beyond the four collaborating institutions by training more than 1500 students, educators, museum professionals, researchers, and scientists globally, with considerable...

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