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Harnessing the Knowledge of Plants, Online

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Botanical gardens are building the first online catalog of every known plant species in the world. It could be a game-changing tool for conservation.

By Tate Williams

Enid A. Haupt Conservatory at The New York Botanical Garden

The iconic Enid A. Haupt Conservatory at The New York Botanical Garden. Credit: ©Robert Benson Photography.

For more than 400 years, humans have been collecting bits of leaf and twig, pressing them flat and dry for safe-keeping and writing about them in journals and books, all to better understand the world’s plants and, more recently, to protect them.

Our knowledge has become exponentially more sophisticated over those years, but the information we’ve accumulated remains scattered all over the world and is often difficult to access. As biologists race to protect biodiversity, there’s an effort underway to change that, a global partnership to build World Flora Online — the first online catalog of the estimated 400,000 vascular plant species of the world.

Once established, World Flora Online would act like a central nervous system — linking up a broader drive to digitize the world’s knowledge of plants — to convert archives of print volumes and millions of dried plant bits into a collection of navigable data. The vision, especially if it’s built out and linked with rich information, is one intuitive, clickable hub that can serve biologists studying the Amazon, land managers defending against invasive species and even native plant gardeners. Such a tool could be a breakthrough for conservation.

“Everything else depends on knowing what we have,” says Andrew Wyatt, vice president of horticulture at Missouri Botanical Garden. “If we don’t know what we have, how on earth can we actually plan to conserve the species or the habitats, or move forward in any way, shape or form?”

In 2012, the Missouri Botanical Garden, the New York Botanical Garden (NYBG), the Royal Botanic Gardens, Kew and the Royal Botanic Garden Edinburgh launched the effort to create an online flora of all known plants by 2020, one step in a global partnership to halt the loss of plant biodiversity. There are now more than 30 partners around the world on board, each sifting through their collective resources and figuring out how to link them all up.

“Information about plant species is hard to get at,” says Wayt Thomas, curator of botany at NYBG, and their lead scientist working on the partnership. “A lot of it is not available online; it’s only available hard copy. And, even if it is available online, it may be distributed, scattered all over the Internet, and some of it is reliable while others less so.”

Thomas, and the team at NYBG, have been among the leaders turning stores of plant information into a more accessible digital form. It’s a daunting task, and to get a sense of the scope of information they’re dealing with, it helps to look at the raw data that forms the foundation of these efforts — preserved plant specimens. The millions of specimens, tiny dried bits of shrub, tree, cactus, etc., collected over the years are the bits of data that form the basis of plant biodiversity research.

At NYBG, for example, tucked away in manila folders, stacked in four floors of climate-controlled cabinets, are 7.8 million dried specimens, forming the second-largest such collection, or herbarium, in the world. Each specimen represents a snapshot, one plant found in one place and time. NYBG’s herbarium has dried plants collected during the explorations of Charles Darwin and Captain James Cook.

cataloged specimen.

Each cataloged specimen represents a snapshot, one plant found in one place and time. Credit: Tate Williams.

NYBG’s herbarium adds up to 40,000 new specimens from around the world each year. Staff meticulously glue them to acid-free paper along with descriptive information, for experts to identify and catalog for study.

The preservation process has been pretty much the same since it was developed in the 16th century, but starting in the 1990s, NYBG began turning its flattened plants into searchable files, logging descriptive information indexed with digital photographs. They’re taking up to 30,000 images a month, both to keep on top of incoming specimens and to digitize their historic collection. So far, they have 2.5 million specimens in their digital database.

“We’ll keep going until as much information as we have locked away can be made available, open access to the world,” says Melissa Tulig, associate director of the herbarium, the technology lead on the digitization effort.

Then, there are the hundreds of volumes of books that are informed by the specimens, the authoritative publications on plant species. Garden staff are simultaneously digitizing their own hard copy publications for use by World Flora Online. One current project that is serving as a test case is converting the 114-volume Flora Neotropica, one of their most revered works — taking scans of the pages and then using character recognition software to turn it into searchable information.

Collective Effort, Substantial Results

With these digitization efforts combined, NYBG is building a cross-referenced database of its collective knowledge. Meanwhile, dozens of partner groups large and small are pursuing similar efforts, whether with their own specimens, books or databases they’ve already built. The goal of World Flora Online is to get these efforts connected, make core elements of their data compatible and then go knocking on doors to fill in the gaps.

World Flora Online is initially aiming to house just the names and descriptions of every known species, not digitized specimens, for example. But, what really excites conservationists and researchers is the opportunity to add in or hyperlink such powerful data to that central hub. You could one day pull up a species of Ash, for example, read a vetted description, then follow links to the publications about it, high-resolution images of individual specimens taken throughout history, conservation status and information about efforts to protect it. It will be a road map to finding digitized plant information, as it becomes available.

That’s when things get interesting for researchers like Robert Naczi, curator of North American botany at NYBG, who works down the hall from the garden’s imaging lab.
Naczi wears multiple hats related to the garden’s work on plants in north America, including an update of a staple text — the Gleason and Cronquist Manual of plants in the Northeastern U.S. and neighboring Canada.

The latest edition is from 1991, and with huge breakthroughs in plant science since then, users are eager for the update. Working closely with the digitization team, he’s releasing batches of chapters annually, in an online version and for use by the World Flora Online.

Native Plant Garden

Springtime in the Native Plant Garden at The New York Botanical Garden. Credit: The New York Botanical Garden.

Also an active researcher in plant identification and conservation, Naczi is well acquainted with the importance of more accessible data. He notes a current research project identifying declines in common species in North America, with one example being the American plum in southern New England and the Mid-Atlantic states. Naczi explored plant specimen records at multiple herbaria, finding evidence of declines in several species. It took weeks of traveling to other collections and perusing hundreds of physical specimens with his specialist’s eye.

“It took a lot of time,” says Naczi. “This is very, very time-intensive work, and this is why no one’s done it before.”

Nothing will replace the value of physical specimens, but when more records are digitized, it can mean the difference between days of work and weeks of work. World Flora Online will provide a one-stop location to search and find links to such digitized data, as it’s available.

“Once it’s digitized, oh, it’s golden,” says Naczi.

With limited resources and expertise available in conservation efforts, such time is precious. With an emerging invasive threat, for example, acting fast is the difference between containment and losing control. Naczi also points out the inherent power in the mere act of “putting it all in one place.”

“By having a comprehensive treatment like we envision for the World Flora Online, then we see where the gaps are,” says Naczi.

A Long Road Ahead

There are still significant scientific and technical hurdles before reaching that vision, and the partnership meets every six months to advance plans. Aligning such a large set of partners is not easy. Funding is always a limiting factor. NYBG’s digitization work relies on grant funding, having recently landed chunks of support from the Sloan Foundation and Google for its World Flora Online contributions.

Robert Naczi

Robert Naczi, curator of North American botany at The New York Botanical Garden. Credit: Tate Williams.

And, in a way, such a project will never be truly finished. There’s still an estimated 10 percent more species out there to be discovered, not to mention thousands of duplicate names, conflicts and corrections that will need to be made. Then, there are the never-ending tech advances to keep up with.

But, for Melissa Tulig of NYBG’s digitization lab, the uncertainty is part of the excitement, especially once researchers, programmers or anyone, can get their hands on these entire data sets:

“I mean, analyses we haven’t even thought of yet, about distribution patterns, weather changes and how climate change is going to affect species distributions — there are so many things that creative scientific researchers can do with these data once they are digitized.”

Tate Williams writes from the Boston area about science, the environment and culture. Read more of his work at and follow on Twitter @tatejw.

February 3rd, 2016|Tags: |