Botanical Information and Ecology Network
Brian J. Enquist
Dept. Ecology and Evolutionary Biology
University of Arizona, Tucson, A.Z.
and
The Santa Fe Institute, Santa Fe, N.M.
Botanical Information
and Ecology Network
(BIEN)
Organizers
Brian J. Enquist, University of Arizona,
Richard Condit, STRI, Panama and CTFS
Robert K. Peet, University of North Carolina at Chapel Hill,
Brad Boyle, University of Arizona,
Steven Dolins, Bradley University,
Mark Schildhauer, NCEAS
CTFS Meeting, Panama
December 2006
Advisory meeting for CTFS plot database
A unique opportunity to do something larger . . . .
BIEN Goals
(1) Specific science questions – Compile the primary sources
of biodversity data at the nexus of merging herbarium, plot
(abundance), and trait data for plants in the Americas.
(2) Technology development goals associated with
answering these questions effectively – as well as to
establish an informatics methodology for continuing to
assemble and integrate relevant observation data for this
and other projects.
(3) Longer-term program development – seek support to
develop a permanent technical solution to the integration
of vegetation/botanical data
Science Goals
- Generate a standardized species list for the Americas
- Generate geographic range maps for all species
within the BIEN database
- Ask basic science questions at the nexus between
abundance, distribution, traits, and diversity across
broad gradients
Justification for Working Group
• The lack of standardized and integrated botanical
information across world’s major biomes is an impediment
to advancing basic ecological understanding.
• In order to do biodiversity science need to document
and develop workflows to integrate and ‘scrub’
botanical data
• Need to clarify how the abundance, distribution, and
diversity of plants vary across broad gradients and
respond to global change
Data Sources
Cyberinfrastructure
Plot and Trait Data
TAXONOMIC
PHYLOGENETIC
INTELLIGENCE
DATA SCRUBBING
CORRECTING,
Data Standardization
Tools
Specimen Data
Exchange
schema
Database BIEN 2.0
Data
Discovery
Confederated resource
BIEN 3.0
Science ! Deliverables
Justification for Working Group
• The lack of integrated botanical information across
world’s major biomes is an impediment to
advancing basic ecological understanding.
• This is especially true in the tropics where biodiversity is
uniquely quite high and patchy.
• Need to clarify exactly how tropical and temperate
floras and communities might differ and how they
vary across gradients and respond to global change
BIEN Proposals
- Jan 2008 - NCEAS BIEN Working Group Proposal
- Feb 2009 - iPlant BIEN Working Group Proposal
- Aug. 2010 - iPlant BIEN GeoSpatial Proposal
Provided support for
- Meetings
- Graduate student support
- Post-doctoral funding (Brad Boyle)
- Technician support (John Donoghue, Aaron Marcuse-Kubitza)
2008
2010
BIEN NCEAS Meetings
2009
Additional sub-meetings
Spring 2010
Development of a Taxonomic Name Resolution Service
Meeting Missouri Botanical Garden
Spring 2011
Development of Geospatial Initiative
Meeting at iPlant, Tucson
The past three years . . . . .
What have we learned?
A large fraction of biodiversity data available is crap!
- Mangled coordinates
- Mis-spelled names, taxa
- Bad taxonomy
- Data corruption from cultivated species
- Heterogeneous sampling
Integrating and using biodiversity data is fraught with
numerous technical issues
Not trivial issues – major impediments to use of biodiversity data
Developed tools and workflows to correct, scrub data,
and remove ‘bad data’
Summary – Major Steps BIEN Data Workflow
Hurtles surpassed in order to integrate and standardize botanical data
- Compilation of herbarium, trait, and ecological plot data
- Formalization of BIEN database 2.0
- Geovalidation of observations
- Taxonomic corrections and synonymy (TNRS!)
- Identifying and removing cultivated specimens, plantation data etc.
- Computational challenge – Scaling up geographic range calculations
http://tnrs.iplantcollaborative.org/
The past three years . . . . .
Science anticipation
Botanical data have enormous problems
Developed a workflow, tools, and scripts to standardize,
clean, and scrub botanical data in order to do science
Now, we are ready . . . . .
BIEN 2.0 Data Sources (post scrubbing)
Plot Data
- CTFS
Herbarium and Observation Data
- GBIF
- FIA
- Madidi plots
- MOBOT
- Vegbank
- NYBG
- TEAM
- SALVIAS
- CRIA (Brazil collections)
- Arizona
Plot# = 329,741
- UNC, NCS etc.
- REMIB (Mexico)
Plant Traits
- Utrecht
- GLOPNET
- Numerous literature sources
Specimen# = 9,345,197
Total Number of Species = 204,929
Total number of observations = 12,171,014
- BIEN researcher data
Traits = 27
Trait observations = 140,285
What we now have available
- A scrubbed species list of all plants in the Americas
- Summary data for all species in BIEN
- mean abundance, max abundnce, total #plots observed in
- latitudinal range
- mean trait values and trait variation
- mean dbh, max dbh
- habit information (tree, shrub, liana, etc.)?
- Summary data for all species in BIEN ?
- Conservation Status (IUCN Red List)
-Geographic Range maps (Convex Hull, MaxEnt etc.)
Recent output from High Performance Computing
-A species-level phylogeny for BIEN species (?)
- A website (data soon to be accessible)
http://bien.nceas.ucsb.edu/bien/
What is unique about BIEN2.0?
These are the primary data used for asking questions about
botanical diversity, distribution, and ecology
Computation demands . . .
– No one has modeled ranges for this number of species
- We have a work flow established for large scale calculation of ranges
We have documented a repeatable work flow that any researcher must
use to take species observations and combine them with traits,
ecology, and to put them ‘on a map’.
- this is the most basic work flow that is required in biodiversity science
Meeting goals
Break into subgroups
(1) Do science and write papers
(2) Detail BIEN3.0 database and geospatial tools
Write a major requirements document for NCEAS
(3) Future funding
(4) iPlant/BIEN GeoSpatial planning
NCEAS deliverables
-Species list for new word checklist
-Range maps for all species
- Traits and habit values for a large fraction of BIEN species
-The ability to download and calculate basic stats for taxa and clades
-Data accessible (at least summary data)
GeoSpatial Discovery Proposal to iPlant
NCEAS (other?)
iPlant
User
User Interface
Climate layers
Science User
GeoSpatial Data Discovery
Environment
Applied User
Outreach and
Education
Integrate data
BIEN
Plant Distributions
User contributing data?
- data standardization tools?
What type of science?
What kind of applied
And education demand?
iPlant GeoSpatial Seed Projects
iPlant
cyberinfrastructure
development team
iPlant
Plant Adaptation Group
iPlant Tree of Life
(iPToL)
iPlant
Plant Nutrition
Tree Biology
BIEN
GeoSpatial
Tools
Tree Biology
Data Discovery
NCEAS
McGill et al.
NCEAS
Group
Data Discovery
Environment
Proposed GeoSpatial Tools
Merge BIEN 3.0 with climate and geography layers
Tools for Botanical GeoSpatial Discovery
(1) Click on a map and get a species list
(2) Click on a plant clade and map out its distribution
(3) Click on a plant observation (taxa) and obtain climate/environmental data
Tools to Geoscrub and Correct Botanical Observation Data