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Regional Uses of Digitized Herbarium Data in the Pacific Northwest Regional Uses of Digitized Herbarium Data in the Pacific Northwest Ben Legler Consortium.

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Presentation on theme: "Regional Uses of Digitized Herbarium Data in the Pacific Northwest Regional Uses of Digitized Herbarium Data in the Pacific Northwest Ben Legler Consortium."— Presentation transcript:

1 Regional Uses of Digitized Herbarium Data in the Pacific Northwest Regional Uses of Digitized Herbarium Data in the Pacific Northwest Ben Legler Consortium of Pacific Northwest Herbaria University of Washington

2 About PNW Herbaria A short history of PNW Herbaria Started in 2007 to provide a single access point to herbarium specimen data for the Pacific Northwest and to promote collaboration among herbaria. Our first web site hosted 700,000 specimen records from three herbaria (ALA, OSC, WTU).

3 About PNW Herbaria A short history of PNW Herbaria Subsequently, a 3-year NSF grant (2010-2013) enabled us to digitize additional herbaria and rapidly expand the PNW Herbaria web site. Captured 317,000 specimen images from 13 herbaria (primarily smaller herbaria) and entered label data for these. Databased 140,000 bryophyte, lichen, and fungi collections from WTU and OSC. Integrated pre-existing specimen data and images from other herbaria. Partnered with separately funded herbaria in Idaho in a TCN/PEN-style arrangement, to host their data and images. Further expanded the PNW Herbaria web site feature set.

4 About PNW Herbaria PNW Herbaria now hosts 2.1 million specimen records and provides access to 595,000 specimen images. Represents 52% of all specimens in all herbaria in the region. 27 herbaria now share data through PNW Herbaria. (out of 58 herbaria total) Includes specimen data from all herbaria in the region with >30,000 specimens, and many of the smaller herbaria. Map of all Pacific Northwest herbaria Geographic distribution of all georeferenced specimens

5 About PNW Herbaria Software & Workflows Specimen imaging. Databasing software. Web site design and source code. Android apps for collecting label data in the field.

6 Specimen Imaging: Lightbox and digital SLR. Programs to rename images and capture basic metadata. Image processing scripts. Image viewer.

7 Databasing software: Built with MySQL, PHP, JavaScript, HTML. Acccessible through web browser. Functions like a database. Used by 17 herbaria to manage 637,000 specimen records.

8 Databasing software: Includes tools for georeferencing (manually or with GeoLocate).

9 Databasing software: Typical database functionality such as searching, sorting, exporting, auto-save, lookups, joins, tables, label printing.



12 Android Apps: Field Notes App to collect hebarium specimen label data in the field. Familiar workflow: create sites then add specimens to sites. List of sites and collections:Create/edit site:Create/edit collection:

13 Android Apps: Speed up data entry with default values and drop-down lists. Upload records to database server over cell network or wifi. Settings:Default and auto-increment values:Upload to database server:








21 About PNW Herbaria Specimen portal design recommendations Taylor the design to meet the interests of your target audience. Think from the point of view of a user. Provide multiple methods of accessing the data, to serve different needs. Allow bulk data downloads. Make it easy and quick to view the data. Minimize the number of clicks and pages one must navigate through to search for and view a specimen record. Include a map view showing the distribution of all specimens matched by a search. Attempt to clean up errors and standardize data for presentation. Solicit user feedback to help correct record errors and improve data quality. Make the data accessible and usable!

22 Data Usage So… how is the data being used?

23 Data Usage is the data being used?

24 Data Usage is the data being used? Average of 50 unique visitors and ~500 page views per day. Most are return users who have been to the site before. 6.5 pages viewed per visit. Bounce rate of 28%.

25 Data Usage Who is using the data? Government agencies: Natural Heritage Programs, Forest Service, BLM, Fish & Wildlife, noxious weed control. Private consultants. Academic research: systematists, taxonomists, field botanists, ecologists. Herbarium personnel: collections managers, staff, volunteers. Higher education: undergraduates, teaching assistants, faculty. Citizen Science Programs: invasive species, rare care. Amateur botanists, native plant enthusiasts, hikers.

26 Data Usage Rare plant conservation Botrychium hesperium “At the Washington Natural Heritage Program we use the Consortium database frequently and extensively. Recently we went through our review list and checked the collections records of each species; for species we have not yet developed data for the consortium provides the best first information on species distribution and abundance.” - WA Natural Heritage Program

27 Data Usage Rare plant conservation “Many of the plants I have suggested to the heritage programs of Oregon and Washington for listing have been a result of my data mining the Consortium Web Site.” - Forest Service “I see a lot of value in finding new locations of our sensitive species that have been collected on federal lands by others, but may have not gone through the local botanist or me for recording in our databases.” - Forest Service



30 Data Usage Exotic and noxious weeds Track the progress and spread of new invasive species. Identify the first records and points of origin for established noxious weeds. EDRR (Early Detection Rapid Response) Citizen Science Program uses the data to educate volunteers on weed distributions, identification, and to encourage them to collect vouchers. Nymphaea odorata “The fact that they can see their data on line I think motivates volunteers to take a greater role and interest in contributing …” - EDRR

31 Data Usage Using specimen data as an identification tool As a virtual herbarium: specimen images can be viewed by individuals without easy access to an herbarium.

32 Data Usage Using specimen data as an identification tool Map-based views make it easy to visualize the distribution of a species. Geographic searches can narrow down the set of potential species for an unknown collection to a few likely ones by consulting what has been collected in that area before.

33 Data Usage Educational uses in the classroom Students use the specimen images to view examples of families and species not represented in their local herbarium, or as an identification aid. Students use the website to develop "monographs" for selected families. Teachers use geographic searches to identify potential locations for field trips. Teach about the use and importance of natural history collections. “My students in plant systematics used the consortium a lot. Initially they were using it to look up species in families we were covering, then checking IDs …” - Boise State University “For me, working at a primarily teaching institution, I would say that the consortium has allowed me to incorporate information into my teaching that would not have been previously possible.” - Linfield College

34 Data Usage Bringing data to the public: field guides and apps

35 Data Usage Bringing data to the public: field guides and apps App is available at Amazon, Google Play, or Apple. (free demo versions are available)

36 Data Usage Bringing data to the public: field guides and apps

37 Data Usage A new Flora of the Pacific Northwest WTU is launching an effort to produce an updated Flora of the Pacific Northwest.

38 Data Usage A new Flora of the Pacific Northwest Use species distributions to help place Flora region boundary. Developed a draft, specimen-based checklist for the Flora region. Determine which species occur in the region. Update species distribution data within keys and treatments. Consult specimen images as a virtual herbarium. Illustrators have remote access to specimen images.

39 Data Usage In support of field work To help plan collecting trips by identifying under-collected areas or sites where species of interest can be found. Use county-level checklists to for targeted collecting of county records. Use species distribution maps to determine if something is unusual, infrequently collected, or unexpected in a particular locale or region. Identify populations and sites for ecological studies, conservation potential, or restoration work. Identify locations for photographing plants. We now have comprehensive information telling us what has been collected where. How can we leverage that to increase effectiveness in the field? Mobile devices open up many possibilities

40 Data Usage In support of field work Pre-compiled datasets allow users to take the PNW Herbaria database into the field for use without a network connection.

41 Data Usage In support of field work

42 Data Usage Targeting county-level records

43 Data Usage Targeting county-level records WTU has been using mobile devices to target collecting in WA since 2002. 6,080 new county records for WTU. Average 26% increase in our taxonomic holdings for each county in WA.

44 Data Usage Data analyses: geographic coverage by herbarium (% of taxa)

45 Data Usage Data analyses: Unique county-level distribution records Small herbaria contain distributional records of species not held by any other herbaria (% of taxa from a county unique to a single herbarium).

46 Data Usage “I have been continually impressed with the feature set, speed, accuracy, and reliability of the pnwherbaria site.” “The CW [Consortium web site] is such a valuable resource to me as an agency botanist I can't even begin to put it into sufficient words – the CW is a total game changer and a phenomenal conservation biology tool.” “I can’t quite imagine my work anymore without these data. I consult it on a near-daily basis for a variety of purposes. Together with internet access to scientific journals, I consider it one of the two information-utilization tools that has most changed how I go about, and think about, my work.” “It is our most often used online tool.” “Having the data in the portal saved a tremendous amount of time (and travel).”

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