Developing bioinformatics tools for conservation science and education

Edward O. Wilson, a retired Harvard professor, in “The Future of Life," writes that "to conserve biological diversity is an investment in immortality," as it serves as a survival mechanism for our species and ourselves. But he predicts that at current rates, half of the Earth's plant and animal species will cease to exist by the end of the century, taking with them their genetic legacy and potential benefits to the world.

At the World Summit on Sustainable Development in 2002, nearly all countries of the world promised to “achieve by 2010 a significant reduction in the current rate of loss of biological diversity.” An army of scientists, conservationists and organizations are working to measure and communicate the state of biodiversity to help drive effective decision-making in support of conservation, similar to recent successes in moving data on climate change into global policymaking.

UMass Boston’s Robert Morris, Department of Computer Science and Robert Stevenson, Department of Biology, are among them. With multi-year National Science Foundation support, Morris and Stevenson have developed software tools that help scientists identify species and manage their data in a collaborative environment. Their electronic field guides greatly accelerate the production of new field guides for species identification. In contrast to traditional methods, which can take years, their software automatically produces many forms of online or publishable field guides. The resulting guides leverage the ease with which high quality digital photography helps support comparing a specimen to an image, thus easing the identification task and helping avoid confusion with species similar to the correct one.

Nonspecialists, especially teachers and students, can also use or develop their own guides. “Field guides are a way for people to connect with the environment,” Morris says. He and Stevenson want to mobilize "citizen science" to help make the case for biodiversity conservation. Their electronic field guides were in use at the Maria Mitchell Institute on Nantucket which last month sponsored Nantucket Biodiversity Initiative Week.

(Their key-building and guide-making software was designed to apply to any science or non-scientific disciplines and can be used for example to build a guide to the world's soccer teams or to your local restaurants.)

The biggest challenge to biodiversity monitoring, however, is open access to species descriptions. Species descriptions are hidden in thousands of journals and books, and access to new descriptions is increasingly restricted by an ever more proprietary copyright environment. The irony is that researchers in developing countries — where most biodiversity is found — cannot access information about their nations' species. Morris has been at the forefront in international organizations such as Biodiversity Information Standards/Taxonomic Databases Working Group and the Global Biodiversity Information Facility promoting common standards for and open access to biodiversity data, especially related to descriptive data and images.

Open access is a lively debate among scientists, librarians, publishers and other stakeholders. Even Wilson, a prominent biologist and an outspoken environmentalist, is questioned in Nature for writing a book which includes 624 descriptions of ants that cannot be readily integrated into the worldwide biodiversity knowledge base as the book is copyrighted. “It is a pity that Wilson, with his ingenuity and access to resources, did not grasp the opportunity to present these important data in a more novel and useful way.”

The winds of change, though, are sweeping through how scientists work and publish. New business models are being tested by publishers, including open access, in which the author pays and content is free to the user.

Technology is propelling this change. Scanning, markup, encoding, searching, retrieving and archiving tools have been developed which recognize, extract and store descriptions of species in scientific publications. Associations have sprung up that distribute these tools and archive the processed documents, resulting in a dynamic database linked to references, maps and the like.

Recently, the Biodiversity Heritage Library launched a large-scale operation to digitize this biodiversity literature. Currently, it includes major US and UK natural history libraries, with the ultimate goal of including the entire global literature. These publications will be openly accessible to the public, unless they are copyrighted -- thus most publications since 1925 are still out of reach.

"Digital library technologies can widen the access to scientific literature, especially to out-of-copyright publications that may be found only in large research libraries," says Morris.

There are well over 100 million pages of scientific publications to which every year more than 20,000 are added. Even with new technology, it would take hundreds of years to process all known species descriptions. That is why Morris and his colleagues advocate for journal production systems with underlying markup templates to facilitate machine reading and sharing of the structured species data.

The vision of openly accessible digital taxonomic literature is based on an interpretation that taxonomic descriptions cannot be copyrighted because they are factual descriptions, and should be open access.

“Such an open access infrastructure is what publically funded science is about: disseminating results as widely as possible,” Morris says. He adds that efforts to conserve the planet's biodiversity depend on free and open access to information about it.