Wichita State University’s Herbarium: Filling a Critical Gap

Presented by Mary Liz Jameson and Susan MatveyevaWith collaboration from F. Leland Russell, Sai Deng, and Stephen Scott

Great Plains Plant Systematics MeetingKonza Conference Center

October 8, 2010

The Wichita State University Herbarium The Wichita State University Herbarium is one of the nine Kansas Herbariais one of the nine Kansas Herbaria

The Wichita State University Herbarium The Wichita State University Herbarium is one of the nine Kansas Herbariais 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 The Wichita State University Herbarium fills a critical gap in our understanding of Great Plains flora in our understanding of Great Plains flora

• Our herbarium contains many specimens from south-central Kansas and regions that are poorly represented in collections

Data from http://www.konza.ksu.edu/herbmap/

Lespedeza cuneata

Helianthus maximiliani

Asclepias syriaca

Bouteloua hirsuta

The Wichita State University Herbarium fills a critical gap The Wichita State University Herbarium fills a critical gap in our understanding of Great Plains flora 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

Entire Collection Electronically DatabasedEntire 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 HerbariumThe 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 SpecimensDigitizing 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 GoalsLong-Term Goals

• Provide on-line access to biodiversity data and

- ecological modeling - specimen/species mapping

http://herbarium.uvu.edu/Virtual/

Long-Term GoalsLong-Term Goals

•Radius search provides a checklist• Key to plants in a region by pick boxes

• Provide on-line access to biodiversity data and

- ecological modeling - specimen/species mapping - tools for identification - checklists for selected regions

Long-Term GoalsLong-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

- collaborative research tools - phylogenetic tools (BLAST, Cypress) - integration of data from GBIF and NCBI - phenology - predictive modeling (endangered species, invasive species)

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.

Up-load data with your mobile

device

Query the database repository based on locality, taxon name, date,

sequence data, etc.

Query by RSS (e.g., an un-

named image of floral or fauna)

Use web-based tools on Biofinity

to examine evolutionary relationships.

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 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 HerbariumSOAR as a publishing / archiving platform for WSU Herbarium

SOAR as a publishing / archiving platform for WSU HerbariumSOAR 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 HerbariumSOAR 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 HerbariumSOAR 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 HerbariumSOAR 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

Data Flow DiagramData Flow DiagramData Flow DiagramData Flow Diagram

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.

Metadata in Spreadsheet

Image Folder

Data cleanup Java

Program

Data normalization

Program customization

darwin_core.xml

dublin_core.xml

contents (list)

Data Packages

…

Tomcat Server

DSpace batch import Web Browser

Herbarium Data FieldsHerbarium 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)Herbarium Data Fields (Continued)

Original data field Dublin Core Darwin Core Sample data

type image

subject Poaceae; Agropyron smithii Rydb.; Western wheat-grass

subjectClassification PASM

Introduced/Native 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 SiteExternal Zoom Site

Site created by using Zoomify EZ.

What is next? What is next? Development of Research Digital EnvironmentDevelopment 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!!Thank you!!

Any questions?