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Wichita State University’s Herbarium: Filling a Critical Gap Presented by Mary Liz Jameson and Susan Matveyeva With collaboration from F. Leland Russell,

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Presentation on theme: "Wichita State University’s Herbarium: Filling a Critical Gap Presented by Mary Liz Jameson and Susan Matveyeva With collaboration from F. Leland Russell,"— Presentation transcript:

1 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

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

3 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

4 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

5 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 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

6 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

7 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

8 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

9 Long-Term Goals Provide on-line access to biodiversity data and - ecological modeling - specimen/species mapping http://herbarium.uvu.edu/Virtual/

10 Long-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

11 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 - 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.

12 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

13 System InformationDSpace 1.4.2DSpace 1.6.2 PlatformJava 1.4.2_17Java-1.6.0-sun-1.6.0.21- 1jpp.2.el5 Software buildingApache Ant 1.6.5Ant-1.6.5-2jpp.2 Apache Maven 2.2.1 (r801777; 2009-08-06 14:16:01-0500) ServerTomcat 4.1.31Tomcat5-5.5.23- 0jpp.7.el5_3.2 DatabasePostgres 8.1.4Postgresql-8.1.21- 1.el5_5.1 *System Information provided by Baseer Khan and Andy Speagle.

14 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?

15 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

16 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

17 Data 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

18 Herbarium Data Fields Original Data FieldDublin CoreDarwin CoreSample Data WSU collection number identifier2294 Species nametitleAgropyron smithii Rydb. [Taxon] Common nametitle.alternativeWestern wheat-grass Specific Locality; country; State; County coverage.spacialNorth America; United States; Kansas; Butler Co.; SW1/4, SW1/4, Sec 34, T28S, R4E Collected bycontributor.authorWinter, Ann [Collector] Identified Bycontributor.authorWinter, Ann [Cataloger] Date collecteddate.created1983-06-14 Date issueddate.issued1983-06-14 FamilyfamilyPoaceae AltitudeverbatimElevation1300' Habitathabitatroadside LatitudeverbatimLatitude LongitudeverbatimLongitude

19 Herbarium Data Fields (Continued) Original data fieldDublin CoreDarwin CoreSample data typeimage subjectPoaceae; Agropyron smithii Rydb.; Western wheat-grass subjectClassificationPASM Introduced/Nativedescription rightsCopyright Wichita State University, 2010 sourceWSU herbarium Identifier.urihttp://library.wichita.edu/techserv /herbarium/browse.asp?id=2294 publisherWichita State University. Dept. of Biological Sciences relationU.S. Dept. of Agriculture Natural Resources Conservation Service relation.urihttp://plants.usda.gov/

20 External Zoom Site Site created by using Zoomify EZ.

21 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!

22 Thank you!! Any questions?

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