Wichita State University’s Herbarium: Filling a Critical Gap
Presented by Mary Liz Jameson and Susan Matveyeva
With collaboration from F. Leland Russell, Sai Deng, and Stephen Scott Great Plains Plant Systematics Meeting
Konza Conference Center
October 8, 2010
The Wichita State University Herbarium
is one of the nine Kansas Herbaria
The Wichita State University Herbarium
is one of the nine Kansas Herbaria
• The herbarium and database
contribute to the biological
infrastructure of the state by
making specimen-level
information accessible.
• Active plant population and
community research increases
the need for knowledge of floral
diversity, seasonality and
distributional data.
• Flora associated with WSU
Reserves provide data in
regions that are now primarily
agriculture or ranching.
Leland Russell examining plant specimens
The Wichita State University Herbarium fills a critical gap
in our understanding of Great Plains flora
• Our herbarium contains many specimens from south-central Kansas and regions
that are poorly represented in collections
The Wichita State University Herbarium fills a critical gap
in our understanding of Great Plains flora
• Examples of species represented in our herbarium that are not recorded in Kansas
County Mapper.
• Distributions are important in our understanding endangered and invasive species
Bouteloua
hirsuta
Asclepias
syriaca
Helianthus
maximiliani
Lespedeza
cuneata
Data from http://www.konza.ksu.edu/herbmap/
Entire Collection Electronically Databased
• Data recorded Excel
• Some fields not Darwin Core compliant
• Efforts to retroactively capture geographic data (using BioGeoMancer)
• All new specimens are geo-tagged
The Vision: WSU Virtual Herbarium
• Collaboration with the WSU Library and
Department of Biology
• Training of undergraduate students in field botany
(early season or late season collecting on WSU
Reserves), databasing, digitizing, and curation
• Augmentation of collection with high quality
specimens (geo-tagged specimens, field images)
• Verification of database records
• Georeferenced data allow for on-the-fly maps
• Digitized images are zoomable, thus enabling
examination of fine structures and label data
• Data and images available on WSU Library server
• In-field tools will allow geo-tagging of images and
direct up-load to external database
Digitizing Specimens
• Protocols and standards were UNM Museum of
Southwestern Biology
• Students verified existing database, modified
specific fields
• Image name derived from first two letters of
genus + species name + specimen number
(e.g., AShirtella178 = Asclepias hirtella specimen
number 178)
• For high resolution and zooming, borrowed the
Library’s 12 megapixel camera
• Images taken using a large copy stand
• Images converted for on-line access
Long-Term Goals
• Provide on-line access to biodiversity data and
- ecological modeling
- specimen/species mapping
http://herbarium.uvu.edu/Virtual/
Long-Term Goals
• Provide on-line access to biodiversity data and
- ecological modeling
- specimen/species mapping
- tools for identification
- checklists for selected regions
•Radius search provides a checklist
• Key to plants in a region by pick boxes
Long-Term Goals
• Provide on-line access to biodiversity data and
- ecological modeling
- specimen/species mapping
- tools for identification
- checklists for selected regions
- in-field tools with direct upload to
external database
- citizen science tools
Up-load data
with your mobile
device
- collaborative research tools
- phylogenetic tools (BLAST, Cypress)
- integration of data from GBIF and NCBI
- phenology
- predictive modeling (endangered species,
invasive species)
Query the
database repository
based on locality,
taxon name, date,
sequence data, etc.
Use web-based
tools on Biofinity
to examine
evolutionary
relationships.
The Biofinity iPhone application
automatically tags a photo with
latitude and longitude coordinates,
date, and time. The application
programmer interface (API)
automatically sends data to the
external database.
Query by RSS
(e.g., an unnamed image of
floral or fauna)
Massive amounts of data will
be able to be processed
quickly, inferences will be
able to be drawn, and actions
can be implemented on the
basis of this new knowledge.
When data are federated and
made accessible, biological
research will be conducted in
a manner that is quite unlike
the way that it is done now.
SOAR as a publishing / archiving platform for WSU Herbarium
• SOAR is the institutional
repository of Wichita State Univ.
• Implemented & maintained by
University Libraries
• Established in 2007 to provide
secure, stable environment for
digital scholarship created or
curated by WSU authors
• Serves dual function of
publishing platform & digital
archives
• Includes scholarly genres from
e-books and articles, conference
papers, theses & dissertations to
data sets, videos, & web sites
SOAR as a publishing / archiving platform for WSU Herbarium
System Information
DSpace 1.4.2
DSpace 1.6.2
Platform
Java 1.4.2_17
Java‐1.6.0‐sun‐1.6.0.21‐
1jpp.2.el5
Software building
Apache Ant 1.6.5
Ant‐1.6.5‐2jpp.2
Apache Maven 2.2.1 (r801777; 2009‐08‐06 14:16:01‐0500)
Server
Tomcat 4.1.31
Tomcat5‐5.5.23‐
0jpp.7.el5_3.2
Database
Postgres 8.1.4
Postgresql‐8.1.21‐
1.el5_5.1
*System Information provided by Baseer Khan and Andy Speagle. SOAR as a publishing / archiving platform for WSU Herbarium
• Museum collections and data sets
are an important part of SOAR
content
• Lowell D. Holmes Museum of
Anthropology (Pueblo Indian
Pottery, Waconda Lake
archaeological artifacts, Asmat and
Korowai anthropological videos
filmed in Indonesia)
• Library Special Collections
(Kansas towns and cities digital
images)
• Virtual Herbarium – just another
museum collection?
SOAR as a publishing / archiving platform for WSU Herbarium
• Virtual Herbarium is NOT just
another museum collection:
-- multiple specialized
database management
systems (see incomplete &
outdated sample on the right)
-- variety of complex web
sites & portals created by
large universities,
museums & centers
-- subject specific metadata
(Darwin Core)
-- nobody before (at the best
of my knowledge) used
DSpace as front & back
end for Virtual Herbaria
http://www.virtualherbarium.org/vh/othersystems.html
SOAR as a publishing / archiving platform for WSU Herbarium
• Advantages of using SOAR /
DSpace for WSU Herbarium:
– Stable, secure, free, well
maintained, state-of-the-art
system
– WSU biologists have
control over the collection
(collaborative in-house
project)
– As part of multi-subject
environment, herbarium is
open to wider audience
Core values of DwC is preserved:
‐‐ native DwC fields added
‐‐crosswalk DC – DwC created
‐‐ specimen label data is used in records as much as possible ‐‐ metadata enhanced with additional fields to increase collection findability
Data Flow Diagram
Data Packages
Metadata in
Spreadsheet
dublin_core.xml
Data
cleanup
Image Folder
Java
Program
Data
normalization
darwin_core.xml
Program
customization
contents (list)
…
Web Browser
Tomcat
Server
DSpace batch import
Original data and images provided by Biological Sciences Department. The Java program (MetaDataImport) is customized based on Blooma Mohan John’s add on to facilitate DSpace batch import. Program customization by Tse‐Min Wang and Sai Deng. Diagram by Sai Deng.
Herbarium Data Fields
Original Data Field
Dublin Core
Darwin Core
Sample Data
WSU collection number
identifier
2294
Species name
title
Agropyron smithii Rydb. [Taxon]
Common name
title.alternative
Western wheat‐grass
Specific Locality; country;
State; County
coverage.spacial
North America; United States; Kansas; Butler Co.; SW1/4, SW1/4, Sec 34, T28S, R4E
Collected by
contributor.author
Winter, Ann [Collector]
Identified By
contributor.author
Winter, Ann [Cataloger]
Date collected
date.created
1983‐06‐14
Date issued
date.issued
1983‐06‐14
Family
family
Poaceae
Altitude
verbatimElevation
1300'
Habitat
habitat
roadside
Latitude
verbatimLatitude
Longitude
verbatimLongitude
Herbarium Data Fields (Continued)
Original data field
Introduced/Native
Dublin Core
Darwin Core
Sample data
type
image
subject
Poaceae; Agropyron smithii Rydb.; Western wheat‐grass subjectClassification
PASM
description
rights
Copyright Wichita State University, 2010
source
WSU herbarium
Identifier.uri
http://library.wichita.edu/techserv
/herbarium/browse.asp?id=2294
publisher
Wichita State University. Dept. of Biological Sciences
relation
U.S. Dept. of Agriculture Natural Resources Conservation Service
relation.uri
http://plants.usda.gov/
External Zoom Site
Site created by using
Zoomify EZ.
What is next?
Development of Research Digital Environment
•
•
•
•
•
Digital workflow for complete data life cycle:
– from collecting plants (Biofinity, My Labs) to
– adding collections to the updated and enhanced SOAR (internal
image zoom; native DwC metadata; improved search and
indexes)
Reuse data in collaborative projects with other regional herbaria
Integrate tools for investigation and discovery
Federate data from regional collections to increase predictive power
Welcome colleagues to WSU for collecting and collections research!
Thank you!!
Any questions?