Back in 2010 we prepared to release a tool to assist ecologists and botanists in the standardization of their plant names. The tool is the Taxonomic Name Resolution Service – and since that time we have come to depend on it almost every day in the lab and in our various collaborations. In short, the TNRS can resolve many forms of taxonomic semantic heterogeneity, correct spelling errors and eliminate spurious names. As a result, we released the TNRS with the hope that it could aid in the integration of disparate biological datasets.
The TNRS is a community and cross-institution effort. Initiated from discussions and a kick-off workshop and meeting at the Missouri Botanical Garden back in 2009, major contributions include taxonomic information from MBGs TROPICOS, Kew Gardens’ The Plant List, and many others. Further, it has built on important open source efforts – including the Taxamatch Algorithm– Developed by Tony Rees (CSIRO), the Taxamatch Web Service, and the Global Names Index. In stepping back, numerous folks have contributed to its development and helped shepherd a tool from the community for the community. More importantly, development of the TNRS has been guided by Brad Boyle and the development staff of iPlant (now Cyverse). The TNRS has a web front end which you can view and use at http://tnrs.iplantcollaborative.org/TNRSapp.html. However, the TNRS also has an API service and an elaborated API via Phylotastic that have now been used to develop other applications for the community including the Taxize R package by the folks at ROpenSci.
During 2010 we were interviewed for this news piece in Nature. Here is a short blurb that explains the context and the enthusiasm at the time . . .
“Brian Enquist and his collaborators were delighted with their freshly compiled data set of 22.5 million records on the distribution and traits of plants in the Americas. But their delight turned to horror when they realized that the data set contained 611,728 names: nearly twice as many as there are thought to be plant species on Earth. Completed in December 2010, the records were intended to help Enquist and his colleagues to discern trends in how forest trees in a wide variety of environments respond to climate change. But the data were clearly full of bogus names, making it impossible to count the species in a particular area, or their relative abundance. “I started to question our ability even to compare something as basic as species diversity at two sites,” says Enquist, a plant ecologist at the University of Arizona in Tucson.
This month, Enquist’s team will unveil a solution that could help botanists and ecologists worldwide. The Taxonomic Names Resolution Service (TNRS) aims to find and fix the incorrect plant names that plague scientists’ records.”
So how has the TNRS held up? Is it still useful? In short, we have been pleasantly surprised but this tool seems to grow more popular as time goes on . . . I put together some summary stats from google on usage of the TNRS website. Each week and month has seen a steady increase of users – and this is just for the online web only access. This is not including the use of the TNRS API or access via R by R packages such as Taxize.
Overall, the number of new page views continues to increase. Plus, the total number of sessions increases with each year. On average people spend about 2 minutes which is close to what I usually spend when I want to submit a handful of species names for checking.
The TNRS continues to attract new visitors but also a large fraction of users are returning users. Its interesting to note that Brazilians and Spaniards are in the top three TNRS users – followed by the Swiss.
Development of the TNRS stemmed from the urgent need to bring taxonomic expertise to the scientists using biodiversity data. The increasing availability of large, digitized biological datasets, while clearly a boon for biodiversity research, is also leading to an accumulation of incorrect, ambiguous or outdated taxon names, with negative consequences for comparative biological science, policy making, and data discovery. It is clear from the continued growth of use of the TNRS that such services are increasingly a necessary component of biodiversity science. Nonetheless, funding for the TNRS has often been pieced together on shoestring budgets and has relied on the input and good will of many but has been spurred by initial one-time investments from the National Science Foundation (in particular Cyverse).
The Future? In an effort to provide a way forward for the use of the mountain of biodiversity data increasingly availabe the Taxonomic Name Resolution Service or TNRS, is an application for correcting and standardizing taxonomic names with reference to existing sources of high-quality taxonomy. We have many thoughts and plans for the next iteration of the TNRS and are looking forward to input from the community for the next six years.
Interested in learning more about the TNRS? Read our original publication by Boyle et al. 2013 in BMC Informatics. Also, here are some tips from Brad Boyle for using the TNRS like a pro and a guide for more in depth use and scrutiny to use for TNRS results.