BIEN Project Charter, December 15, 2009

Project Title

BIEN - The Botanical Inventory and Ecology Network

Start Date

Jan 1^st, 2010

End Date

Dec 31^st, 2011

Project Justification

With seed funding from the National Center for Ecological Analysis and Synthesis (NCEAS), the BIEN team is working to assemble a demonstration project that includes most of the premier plant biodiversity databases for the Americas (sources listed below). By the end of 2011 we will have produced a single resource giving species names, locations, and often abundances, for about 25 million species occurrence records. Our ultimate goal is to unite an ever-growing pool of plant distributional data with information on plant co-occurrence, ecology, traits and phylogeny. This requires that we address the fundamental problem of comparative research at iPlant - the taxonomic impediment. We find that even in the most reliable sources, when taxonomic data are reported in the literature, more than 15% of Latin binomials are either misspelled or are ambiguous, and many more are out of date. Unfortunately, for plant trait and ecological field data, error and ambiguity approaches 25 to 35 %. This taxonomic resolution problem is perhaps the largest barrier remaining to conducting comparative biodiversity science. A system for taxonomic disambiguation is critical and central for data integration.

Project Objectives

We propose to collaborate partner with the Missouri Botanical Garden (MBG) and other biodiversity information providers on the following cyberinfrastructural tasks: (i) assemble a standardized Plant Observation Database (POD) combining information on plant distributions and ecological traits from across the Americas; (ii) closely collaborate with MBG's Tropicos to develop a botanical Taxonomic Name Resolution Service (TNRS) and check list for the Americas for correcting and harmonizing taxa names; (iii) work with iPToL to provide the cyberinfrastructure and phylogenetic information for linking with BIEN data as well as providing an accessible and web-enabled cyberinfrastructure to enable access to objectives i and ii.

Overview of Deliverables

We identify five deliverables:

1. Generate an Americas-wide checklist of plant names and synonyms, using existing monographic and regional taxonomic information within the TROPICOS database
2. A Taxonomic Name Resolution (web) Service (TNRS) will allow multiple taxonomic perspectives to be rendered and explicitly mapped as interested data providers and taxonomists submit names for consideration. Automated and assisted taxonomic standardization will use two operations:
   1. Taxon Matching- Recover validly-published names using exact and fuzzy algorithm to check submitted names and authors against the Tropicos names database returning the canonical spelling of each name or suggestions based on available information.
3. Synonym Correction - Inspect taxonomic status of validly-published names and convert synonyms to accepted names, based on the Americas-wide checklist from (1) above.. Simple synonyms (A = B) are converted automatically and pro parte synonyms (A = B in part + C in part) are flagged for assisted inspection.
4. A Plant Observation Database (POD) which will employ the TNRS to unite georeferenced occurrence data from herbarium specimens and ecological inventories within a single model. Herbarium specimens will supply large samples of presence data needed for modeling species distributions and ranges sizes; ecological inventories will provide data on co-occurrence, diversity, and demography and traits needed to build mechanistic models of the determinants and evolution of species/clade distributions and the geography of traits.
5. An attribute database for the taxa in the checklist including distributional models, phylogenetic status, and trait information for New World plant species. For distributions we will do this by by automating existing ecological niche modeling techniques such as MaxEnt. We will also develop enhancements such as using the large sample of aggregate occurrences within the POD as a tool for distinguishing between true and false absences.
6. Several prominent science publications that focus on questions at the nexus of integrating distribution, abundance, traits, and phylogeny. As a proof of concept for the above four goals we have already outlined these manuscripts at our 2009 working group meeting.

Approach

We will develop cyberinfrastructure by working through successive approximations. We will work toward developing a workable TNRS in the short-term, and an improved TNRS service for the longer term, and then something that works better in a year for uniting existing sources of expert taxonomic knowledge. Specifically, we will partner with the MBG's Tropicos initiative so that names will be corrected against a single authoritative nomenclatural list (a names database accessed as a web service). Ambiguities will be resolved or explicitly identified by the successive application of synonymies from monographs and regional floras (such as Tropicos country checklists; Some of us have used this checklist approach successfully in a recent publication (e.g., (Weiser et al. 2007)) and are eager to develop it as an automated, online service, and with expanded geographic coverage). Finally, we will develop a taxon concept resolution service that exploits explicit taxon concept mappings where available (e.g., the SE floristic atlas), and otherwise uses existing taxon synonomy).

Success Criteria

• Achievement of our primary goals: development of a TNRS webservice, a standardized checklist, a searchable database for at least 20 million observation records for the Americas, and the associated distribution maps, traits, and phylogenetic information for the species list we generate for the Americas.
• Technical goals: (i) A webservice that is usable by any person interested in basictaxon resolution; (ii) an accessible, robust database on distribution, abundance, and traits for the Americas.
• The ability for any user to use the value added and accumulated information in the BIEN database in new and value-added ways.
• Adoption of APWEB's teaching and data resources by the current and newuser communities

Key Assumptions

• Access to the computing and software development staff at iPlant.
• The ability to develop collaborative ties with iPToL. For example, for the standardized species list for the Americas, the BIEN group would like to collaborate with iPToL to generate a phylogenetic tree of the highest resolution possible for these taxa with their associated functional traits, distributions, and information on commonness and rarity.
• Access to an IT testing environment and development web server (iPlant)

Roles and Responsibilities

Signatures - The following people agree that the above information is accurate:

Project team members:
Project sponsor and/or authorizing manager(s):
Notes/Comments – Below we identify the database sources for the POD that will be used to assess the TNRS and quantify the effectiveness of the TNRS. These sources have already been identified and offered for inclusion into the POD. Critical personnel are listed (other BIEN participants and sources):
 
Collection records and taxon occurrence records

• Tropicos, Missouri Botanical Garden (P.M. Jørgensen, C. Freeland),
• The Virtual Herbarium New York Botanical Garden (B. Thiers)
• GBIF (not a primary source, but a collection of other herbarium databases; N. King)
• U. Arizona herbarium (M. Sanderson {iPToL}, B. Boyle)
• U.S. National Herbarium, Smithsonian (W. Wagner to R. Peet)
• SERNEC participant collection s (e.g. NCU, NCSC, UNCC (R. Peet)

Vegetation plots with co-occurrence records

• CTFS-Smithsonian plots (R. Condit)
• RAINFOR (Amazon; O. Phillips, Y. Malhi,)
• ATDN plots (Amazon; H. ter Steege)
• SALVIAS plots (Summarized collection of vegetation inventories; B. Enquist, B. Boyle)
• VEGBANK plots (North American vegetation; R. Peet)
• MBG plots (plots from Ecuador, Peru, and Bolivia; P.M. Jørgensen)
• USFS-FIA plots (North American trees)
• USFS-Landfire plot database (not a primary source, but a compilation of North American vegetation plots; to R.Peet)
• Heritage program plots from various states (e.g. , VA, WV; R. Peet)

Botanical trait and ecological information

• TRAITNET and TRY (B. Enquist, C. Voille, A. Zanne , M. Schildhauer, NCEAS and J. Cavender-Barres)

Literature Cited
Weiser M.D., B. J. Enquist, B. Boyle, T. J. Killeen, P. M. Jørgensen, G. Fonseca, M. Jennings, A. J. Kerkhoff, T. E. Lacher Jr., A. Monteagudo, M.P. Núñez Vargas, O. L. Phillips, N. G. Swenson & Martínez. R.V. (2007). Range size distributions and the latitudinal gradient in New World woody plant species richness. Global Ecology and Biogeography, 16, 679-688.