Digital Plant Research Center
As one of the leading botanical gardens and research institutions in the world, The New York Botanical Garden has a responsibility to make our resources available, useful and relevant. For more than 100 years, we have endeavored to document plant and fungal diversity, and share the insights we have gained with scholars and the general public.
Plants and fungi are fundamental to human life, providing us with oxygen, food, water, shelter, clothing and medicine. Despite two and a half centuries of work, botanical science still has an incomplete knowledge of the breadth of plant and fungal diversity, and of the factors that govern their growth. This is even more important at a time of rising concern about environmental issues such as conservation and climate change.
The goal of the Digital Plant Research Center is to present information about plant and fungal diversity resulting from the collections and research programs of The New York Botanical Garden to a wide audience for the purpose of furthering research and increasing biodiversity literacy among students and the general public. The Digital Plant Research Center will be a system of interconnected digital resources to include the wide range of research endeavors of The New York Botanical Garden, all of which will be searchable through a common interface. The components of the DPRC are the following:
The C. V. Starr Virtual Herbarium
Databasing and imaging of the 7.2 million specimens in the Herbarium began in 1995; to date, approximately 1 million specimens have been cataloged and images have been captured for approximately 120,000 specimens. During the next seven years, our goal is to catalog all specimens acquired and loaned during the course of the planning period, as well as to catalog specimens from areas of current research emphasis such as the Caribbean region, Brazil, and the Intermountain west.
Electronic Floras and Monographs
Through the addition to the Virtual Herbarium of descriptive text, identification keys, digitized photographs, publications, and field observations, staff members will be able to construct electronic floras and monographs as a means of documenting the plants of a given region, or of a particular evolutionary group. These data will be linked to specimen records and images, literature references, gene sequences, and ethnobotanical uses, creating a comprehensive profile for the species that have been studied in depth by NYBG scientists. We will explore development of a mechanism for ordering print on demand, or even assembling customized works (e.g., request a volume with all NYBG publications on a plant family, bound together; or request subsets of publications).
The LuEster T. Mertz Library
It is the goal of the Library to make their renowned, comprehensive print collections available to their users at the same high level of service that is currently provided in print and on-site. The initiatives required to achieve this are 1.)simplifying and connecting all of our disparate electronic resources, 2)make our online catalog a deeper information experience than a simple list of books and journals, and 3)use web tools and technologies to provide a more robust and integrated search interface for library users incorporating web resources, electronic journals, subscription databases, library catalog holdings and digitized materials.
A significant portion of the pre-1923 Mertz Library holdings will be digitized over the next five years in connection with the Biodiversity Heritage Library. This project will not cover oversized and fragile material because the emphasis will be on mass digitization; getting a huge bulk of subject specific material scanned as quickly as possible. Oversized and fragile and rare material will be digitized as separate projects. Additional digitization projects Additional Mertz Library projects will focus on areas of unique strength and include Latin American materials. Additional subject strengths would include titles indexed in the Index of American Botanical Literature, materials that relate to North America particularly North American Flora, the Torrey Archives, the Fruits of New York State by Hedrick, and NYBG archives including the personal papers of 29 scientists who worked at the Garden.
The library materials will be digitized and rendered searchable so that a user could enter a query and receive links to all digitized literature that matches the query. Where the digitized literature cites NYBG specimens, there would be a link to the citation in the Virtual Herbarium. These digitized collections will be joined with the electronic journals and databases in the collection.
Institute of Economic Botany Collections
All collections and artifacts belonging to the Institute of Economic Botany (IEB) will be digitized and to the extent possible (i.e., where in compliance with accepted practices regarding Intellectual Property Rights agreements) the uses of plants by people will be documented on line to some degree of specificity. These could be searchable by plant name, region, cultural group, or use. Collections such as the H.H. Rusby Collection of Economic Products will be photographed and presented in 3-dimensional views on line. Images and videos taken by IEB staff, presenting plant-based cultural practices, habitats, plant products, interviews, and related data will also be available on line, as will publications and field notes.
Collections: The addition of various Lab collections will enhance the DPRC further. Collections ranging from liquid preserved specimens, to microscope slides, to seed collections to DNA and frozen tissue samples will be databased and digitized. Scanning electron micrographs, histology sections, pollen slides and other collections of images from the Lab will also be included. These will be linked to plant name and Herbarium specimen voucher. This will enable the user to create queries based on plant part (e.g., DNA extract, pollen, flowers, etc.) as well as on plant name or collection.
Gene sequences: The most commonly accessed molecular data available through the DPRC will most likely be individual gene sequences and sequence databases. Individual gene sequences will be linked to species name and voucher number. In addition, we will develop searchable databases of sequences including a database of unique plant DNA barcodes. Gene sequences and databases will be searchable by plant name, gene name, or gene sequence and linked to library, herbarium, living collections, systematic research and IEB databases. These sequences will also be deposited in Genbank -- and the Genbank record can include a link to the DPRC -- but the links to other information in the DPRC will be unique and will allow access to a wide range of important information not accessible through standard sequence databases.
In genomics, we will create a database of whole genome sequences (including chloroplast sequences from plant groups such as green algae and monocots studied by NYBG staff) with both raw and finished data. We will also include gene expression datasets such as Expressed Sequence Tags or microarray data derived from NYBG research projects. It would also be possible to host data sets derived from research by colleagues and collaborators, becoming a public repository where such genomic data would be linked through the DRPC to a wide variety of information and literature on the plants. This access to linked information would be unique to the DPRC and is not currently found in any other molecular databases. It will therefore be invaluable to researchers interested in evolution, physiology, ecology, conservation studies and other areas using genomic techniques to answer questions about how plants respond to various factors.
The Lionel Goldfrank III Computerized Catalog of the Living Collections includes information about the age, source, and current location of every plant in the Garden's living collections. Currently, a static version of the catalog is available on-line and we receive regular requests for samples and specimens from a wide range of people. Unfortunately, the current on-line catalog is out of date. Making a live version of the database available to researchers, educators, and the general public will allow the Garden to better serve its research and educational goals. The information in the database could be expanded to include digital photos of plants on the grounds and cultural information specific to the site that would serve the Garden's Home Gardening audiences. It could also include phenological information, which would strengthen the Garden's climate change research program. Staff will be needed to gather and enter this data. A live version of the Computerized Catalog could also be available to visitors, who could print out maps with the locations of plants they would like to see while here. It could be incorporated into state of the art electronic interpretation that would significantly enhance the visitor experience.