Project: Benthic Marine Algal Herbarium of Long Island Sound Digital Collection

Submitted by: Shelley Cudiner and Nancy Gillies

Date: 03/28/01

Website: http://www.lib.uconn.edu/rcl/Stamford/Algae/Coversheet.htm

Project Goal 15 points

Goal of the project

To produce an identification database of collected and pressed specimens of algae from the Long Island Sound for teaching purposes while at the same time creating an image archive for UConn’s algal herbarium. At present approximately 75% of the algae found in Long Island Sound are in C. Yarish’s UConn Stamford’s herbarium collection and are readily available for digitization. Most, if not all, of the remaining 25% are available at other herbaria collections, including the Environmental Lab of NE Utilities, Eaton Herbarium at Yale; Brooklyn Botanical Garden Herbarium; New York Botanical Herbarium; Farlow Herbarium at Harvard; Trinity College and Connecticut College. There are approximately 200-300 species found in the Long Island Sound. The pictures will be saved in as bitmap files for archive and jpg files for study and identification. The database will be searchable by keywords and subject headings including the names of algae and taxonomy. Some entries may include brief explanatory notes and credits. Records will display taxonomy and a thumbnail image, with links to jpg and bitmap images.

The structure of the online collection will be flexible enough to allow for expansion and changes to the database in the future.

Objectives of the project

1. Provide public online access to a complete Long Island Sound Benthic Marine Algal Herbarium collection.
2. Create an image archive and compendium documenting all benthic marine macroalgae species in the Long Island Sound.

Value of the collection to the institution

The product will highlight significant research being performed at three of campuses of the University of Connecticut. It will provide quick and universal access to specimens that are currently available only at several different locations. It will preserve unique specimens for future users. It will provide an inventory of all local specimens and will provide surrogate specimens for those missing from local collections. It will offer a complete and searchable database for purposes of research, instruction, and identification. It will offer a unique and valuable resource to the Connecticut virtual library initiative.

Value of the collection to the intended audience

The product will provide faculty and students with a complete inventory of alga specimens from the Long Island Sound. It will provide viewable specimens of each species. It will provide a searchable database for identification and teaching purposes. It will be accessible anywhere at anytime.

Ownership of the reproduction rights

Will work with UConn General Attorney to write memo of copyright agreements.

Collaboration and partnerships

Ecology and Evolutionary Biology Department (Charlie Yarish, Louise Lewis)
Marine Science Department (George McManus, Bob Whitlatch)
Environmental Lab of NE Utilities (Milan Keser)
National Museum of Natural History, Smithsonian Institution (James N. Norris)
Northeast Algal Society (James Sears)

Additional possible contacts

Trinity College (Craig Schneider)
Connecticut College (Pete Siver)
Eaton Herbarium at Yale
Brooklyn Botanical Garden Herbarium
New York Botanical Herbarium
Farlow Herbarium at Harvard

Collection Description 15 points

Description of the collection

Definitions

Algae – Any of various primitive, chiefly aquatic, one-celled or multicellular organisms that lack true stems, roots, and leaves but usually contain chlorophyll. (Bottom line: includes seaweeds)

Benthic – Referring to organisms which live on or attached to the bottom of aquatic habitats.

Herbarium – A collection of dried and pressed specimens (e.g. algae and plants) systematically arranged and labeled; used for taxonomic studies.

Macroalgae – Freshwater or marine algae that are visible to the naked eye.

Phycology – Study of algae. Synonym for algology.

Taxonomy – a system of arranging organisms into natural, related groups based on some factor common to each, as structure, embryology or biochemistry: the basic taxa now in use are, in descending order from most inclusive, kingdom, division, class, order, family, genus, and species.

Approximately 500-600 samples of pressed algae on herbaria paper, including some taxonomy. Sizes vary from about 8"x10" to 12"x16" and some pressings are cut and continued on consecutive pages. The condition of the collection from the past twenty-five years is good, though some of the samples are coming up from the pages and need conservation before scanning.

Yarish also has some books of pressed algae specimens dating back as far as 1860. While these may not be integral to this project, if we already have current samples, they may require attention and could be scanned and added to the database as a historical component.

How the collection relates to other collections

The product will create a virtual collection whose original artifacts reside in separate locations around the state. It will augment the phycology monograph collections at the Avery Point, Stamford, and Storrs campuses. It carries the potential for enhancing the current knowledge base through submission of new data by students, faculty, and researchers.

Database creation

The Marine Algal Herbarium database will be hosted on a UConn library server with open access from the WWW, unrestricted by domain. CD-ROM and/or DVD collections could be created for smaller subsets of the database for in-class teaching materials (because the web can load too slowly for online demonstrations). The cataloging form that will be used will conform to the Dublin Core metadata standard for description of data files. The project team looked into whether it was necessary to catalog each image using MARC description and felt that using Dublin Core was sufficient. A record will be created in OCLC for the herbarium collection and holdings for Stamford added. The record will include an 856 field with the URL of the Herbarium database’s web page.

We considered the use of the Voyager Image Server to enter the data, but were told that we could not create a separate database but could have it accessible only through HOMER as a citation database. Our vision for this project is to produce a web page accessible to instructors, students, and researchers worldwide and therefore chose not to use Endeavor software. The Access database could be accessible though HOMER in the future if the Libraries purchase the Endeavor Encompass product which recognizes all Z39.50 compatible databases.

We plan to set up the Dublin Core elements in an Access database which will store the table. Using Cold Fusion as an interface between the database and the web server, we will design the herbarium page with advanced searching options using the access points drawn from the Dublin Core elements. The Library’s webmaster, Steven Wieda, is a project team member and will help us with the Cold Fusion software.

Awareness of other, similar digital collections or projects

The major similar existing collection that we found is "The Seaweed Database." This is a non-subscription database that stores information on the scientific names of seaweeds (including seagrasses). The European part of it is funded by the European Union via the MAST European Register of Marine Species Project, the aim of which is to list all known marine organisms in European waters. The database is also part of the worldwide Species2000 project, the aim of which is to list the world's known species. More than 16,000 seaweed and seagrass names are listed at present, but more are added each day. It is estimated that over 35,000 names are involved. Most of the entries do not have images.

See attached list of "Existing resources" for other online algal resources and databases.

Characteristics of the source to digitize

The collection consists of samples of various algae from the Long Island Sound that have been pressed and mounted onto paper. Most of the algae in the LIS are represented. The samples vary in age, and are mostly in good condition. Some seaweed pressings need conservation attention before scanning. Some samples have a complete taxonomic synopsis. There are also compendiums of seaweeds in the Long Island Sound that will provide a checkpoint for database coverage (see bibliography).

Plan of Operation 25 points

Methodology for accomplishing project

PHASE I

Part I

1. Learn taxonomy of Long Island Sound algae.
2. Order equipment.
3. Evaluate and select herbaria.
4. Conserve materials and prepare for scanning.

6. Start creating an Access database.
7. Start developing a user-friendly interface in ColdFusion.
8. Determine retrieval options, searchable fields, and limitors using ColdFusion.
9. Organize and divide collection into manageable sections according to taxonomy and availability.
10. Choose pressings which best represent the species (there is more than one pressing for some seaweeds).
11. Set up project room as equipment arrives.
12. Learn how to use digital camera and copy stand.
13. Present update to DCPT.

*teaching collection, a subset of the database of commonly used species which could be retrieved separately and burned onto a CD for teaching purposes.

Part II

1. Scan in herbaria. Tweak or touch up scans as necessary.
2. Work out a system for naming images and save to zip drives and server.
3. Start cataloging collection and input data and images into an Access database. Create a test database of 25 records.
4. Return completed sections of Yarish herbarium located in the Biology Labs at the Stamford Campus.
5. Start evaluating interface with evaluation team (see below under Audience) for usability.
6. Refine database as necessary and continue designing interface.
7. Present update to DCPT.

Part III

1. Determine what species are missing from the UConn collection.
2. Retrieve missing species from herbarium at the Environmental Labs of NE Utilities (with the assistance of Dr. M. Keser) or track down from other institutions.
3. Finish Long Island Sound algae database.
4. Market database and teach faculty how to use it.
5. Present update to DCPT.
6. Complete phase I.

PHASE II (additional funding required)

1. Scan in and index herbaria monographs from the 1800’s.
2. Add photographs of algae to records, particularly in teaching collection.
3. Scan in and catalog herbaria from other Northeast Atlantic locations, starting with Cape Cod, and other Massachusetts locations.

Management and technology plan

(Initials imply responsibility)

1. Collect materials

2. Prepare materials

1. Creating final product

Scan in images (SC and CD)

Catalog images (NG)

Build database (SC, SW and NG)

2. Marketing plan/dissemination (SC, NG and CY)

• Present at Connecticut Library Association’s Annual Conference (April 2001), sponsored by the College and University Section. The theme is: Librarians: Knowledge Professionals for the Next Century. Presentations at the conference will be published on the web as proceedings of the conference.

• Present a poster session at the Phycological Society Association’s 55th Annual Meeting, June 23-28, 2001 at the Estes Park Conference Center in Estes Park, Colorado. (The meeting will consist of daily plenary lectures, organized symposia, and contributed oral/poster papers.)
• Design a one-page color flyer for dissemination at conferences and via mail. (Graphic design on flyer and copies donated by Gateway Graphics)
• Mount on biology liaison pages, and on Avery Point campus’ Marine Science page
• Include in D-Compass
• Inform biology faculty of availability
• Incorporate into WebCT pages of appropriate biology classes
• Develop a list of potentially interested parties, such as Connecticut Sea Grant College Program, Long Island Sound Office of the CT State DEP, Mike Guiry’s Seaweed Database, NE Utilities, Pan American Marine Biotechnology Association, International Phycological Society, and Northeast Algal Society (NEAS). Contact and inform these parties of the availability of the web site and make link available to them.

Realistic timeline for accomplishing project

Phase I

Part I –3 months

Part II – 5 months

Part III – 4 months

Audience, Collaboration, and Key Personnel 15 points

Project Team

• Shelley Cudiner, Reference Librarian and Biology Liaison for Stamford – user side and some developer side knowledge of database capabilities and restraints

• Nancy Gillies, Director of Jeremy Richard Library – in-depth knowledge of cataloging and administrative capabilities

• Carole Dyal, Library Conservator/Preservation Officer – preservationist
  

• Dr. Charlie Yarish, Professor of Ecology and Evolutionary Biology – owner of benthic marine algal herbarium at UConn Stamford, contacts with numerous other seaweed scientists and organizations internationally (letter attached)

• Shirley Quintero, Applications Developer - Cold Fusion programming, Access, HTML

• Steve Wieda, Webmaster/Database Developer – high degree of skill in ColdFusion, Access and HTML, and holds degree in biology

Project Collaborators

• Dr. George McManus, Associate Professor, Marine Science Department, UConn Avery Point – will serve on the evaluation team (letter attached)

• Dr. Raquel Carmona, Marine Sciences Research Assistant at the Marine Biotechnology Labs at the Stamford Campus – will serve on the evaluation team and assist in identification and taxonomy

• Gale Hartch, Biology Teaching Coordinator, UConn Stamford – will serve on evaluation team and assist in identification and taxonomy

• Dr. Milan Keser, Environmental Lab of NE Utilities – has given a verbal commitment to provide open access to the NE Utilities herbaria

• Dr. Dave D’Alessio, Assistant Professor, Communications, UConn Stamford – knowledge of digital photography, scanning and media, also familiar with database interfaces

• Dr. James Sears, Chair of Flora Committee of Northeast Algae Society – will provide access to NEAS Keys to Benthic Marine Algae

• Dr. James N. Norris, Research Scientist and Curator, National Museum of Natural History

• Dr. Robert Whitlatch, Department Head of Marine Sciences, UConn – will serve on evaluation team

• Dr. Scott Kennedy, Research & Information Services Area Head – assist in written documentation and liaison to Connecticut Virtual Library Initiative

Adequacy of Resources 10 points

Need to obtain

• Copystand – a copystand holds a digital camera above an image on a stand

• Digital camera – lens must be high quality for clean imaging

• Server space – for a database of approximately 300 records and bitmap images

• "NEAS Keys to Benthic Marine Algae of the Northeastern Coast of North America from Long Island Sound to the Strait of Belle Isle" book – has listing and taxonomy for all alga species in Northeast
• Zip disks
• 75 watt light bulbs
• Computer with zip drive and CD ROM burner
• 19" monitor

Resources on hand

• Microsoft Access – to construct database
• Adobe Photoshop – ITS
• ColdFusion – software for designing web interface for database
• Dublin Core – metadata-cataloging system
• Space/room for project with desk, table and network connection – available in Stamford library

Budget and Cost Effectiveness 10 points

Evaluation Plan 10 points

Evaluation plan appropriate to the scope of the project

Project is divided into 3 major parts; DCPT will be kept appraised of progress in the form of brief presentations at the conclusion of each part. This will include online demonstrations and the opportunity for suggestions and feedback.

Dr. G. McManus, Dr. R. Carbona, Dr. R. Whitlatch and G. Hartch will serve on an evaluation team to keep Project Team and DCPT appraised of database usability and value. The Evaluation Team will communicate to the Project Team in person, by phone or email, and to the DCPT by email.

DCPT will also receive emails with updates on the accomplishing of milestones, such as the successful trial run of the copystand scanner, number of items preserved, scanned and cataloged, location of website, etc.

Total 100 points

Bibliography

Little, R John. 1980. A Dictionary of Botany. New York: Van Nostrand Reinhold.

Agnes, Michael, editor in chief. 1999. Webster’s New World College Dictionary. Ohio: Macmillan.

Sears, James R. 1998. NEAS Keys to the Benthic Marine Algae of the Northeastern Coast of North

American from Long Island Sound to the Strait of Belle Isle. Dartmouth, MA : Northeast Algal Society.