EDIT - European Distributed Institute of Taxonomy -

Reference: Tillier S. (2009) Biodiversity Informatics. What's in it for us? Bulletin of the British Ecological Society 2009 40(3): 39-42.

At the recent e-Biosphere conference (http://www.e-biosphere09.org) the overwhelming feeling of the meeting was that burgeoning field of biodiversity informatics was being led, perhaps dominated, by descriptive taxonomists. This came as something of a surprise to many of the leading players in the field, so here we want to explore how a taxonomic initiative may have real benefits for ecologists.

The European Distributed Institute of Taxonomy (EDIT; http://www.e-taxonomy.eu) is a consortium of 29 natural history institutions in Europe and beyond. It works to provide better, faster and more accountable tools to taxonomists, to significantly accelerate the global production of taxonomic knowledge. We are currently just starting the 4th year of a 5 year project.

We organise year-round All-Taxa Biodiversity Inventory and Monitoring programmes, we develop an Internet Platform for Cybertaxonomy with software for the management of taxonomy and biodiversity data, we create collaborative Scratchpad websites to empower research communities across the globe and we improve the training of next generation’s taxonomists. All this in addition to helping the most powerful taxonomic institutions in the world work better together. In this article we will describe what the ecological community can gain by partnering with the recent developments in computer-aided taxonomy.

EDIT's primary objective is to bring Europe's natural history museums into a coherent network, so much of its work has been associated with the descriptive and nomenclatural end of taxonomy. Ecologists, however, have a wealth of occurrence data that can map onto and make use of those taxonomic tools to the benefit of both sides.

The EDIT ATBI+M Approach (http://www.atbi.eu/wp7)

Project leaders: Christoph Häuser, Juan Carlos Monje, Anke Hoffmann, Jutta Eymann, Alexander Kroupa. Contact: christoph.haeuser@mfn-berlin.de

It's no secret that taxonomic expertise is fragmented, and it has been recently pointed out that flawed taxonomy or lack of taxonomic information can entirely ruin ecological assessments. Working for years to follow a species' population and only finding out later that you'd been confusing three closely-related but different taxa with each other can make your work useless.

But it might be even worse when you realise that expertise on that particular group is very rare, and is encoded into publications and collections that require a significant theoretical background to exploit. That doesn't mean that you should give up, though! It's easy to be discouraged by the current state of taxonomy, but significant improvements and transformations are occurring right now. EDIT can help you find the relevant expert and involve him or her with your project, to make sure that you're working with the right species and specimens from the very start.

EDIT aims to strengthen the input of taxonomic expertise for biodiversity conservation. Therefore we support and organize the participation of taxonomists and experts in biodiversity inventory and monitoring efforts in protected areas.

The mechanism for achieving this objective is the establishment of “All Taxa Biodiversity Inventories + Monitoring” (ATBI+M) sites in selected protected areas. ATBI+Ms are intensive, large- scale efforts to record, identify, and document the entire biodiversity of a given area. EDIT’s ATBI+M sites are different from traditional approaches in their longer-term orientation: from an initial species inventory, they will form the basis for monitoring biodiversity changes over time in a time of global change.

European ATBI+M pilot sites have been established in France, Italy and Slovakia. About 4000 species have been recorded in the Mercantour & Alpi Marittime Natural Parks and in the Gemer area so far. The first non-European ATBI+M site will start this year at the Udzungwa National Park in Tanzania.

Where EDIT shines is in its capacity to gather researchers from across Europe and the rest of the world. The alpine ATBI+M has already gathered more than 100 specialists from across the globe – overall, 734 person/days in 2007 and 2008 where experts gave their full attention to cataloguing the diversity of life. We've arranged for them to constitute task forces which swoop across the landscape to inventory everything they can identify, and describe everything they can't.

These include researchers from the largest taxonomic institutions in the world as well as non-professionals, lichenologists as well as bird specialists, a whole host of irreplaceable expertise which would never have come together without an integrated approach. In fact, this approach has already helped build bridges beyond EDIT's strict membership. There has been significant improvement in engaging people who aren't professional taxonomists. We'd like to improve on this further, and build more bridges with the ecological community.

More than 20000 records, belonging to 3640 species, have already been made across the Mercantour and Alpi Marittime parks, and are now freely available on the web through the Global Biodiversity Information Facility. We only expect this to accelerate in the coming years. To us, it is also an opportunity to improve on our methods: to improve engagement outside the taxonomic community, to improve our research process, and to improve on the necessary technical support.

A specific project goal is to facilitate accurate semiautomatic georeferencing and recording of date and time in standardized formats as background information. Following this approach of simplifying field data recording, EDIT WP7 undertakes to test and further develop available digital data recording tools and devices with an integrated GPS functionality, especially for inventory field work. In one approach we use Windows Mobile 6 with ArcPad 7.1 from ESRI. This software package may be used with handheld PCs as well as with mobile phones having an integrated GPS.

Of course, all this is in support of local decision-making and area management. But it could also support robust ecological work, if ecologists are willing to build interdisciplinary teams to tackle the current issues in science. This is exactly what EDIT can help you with.

Scratchpads (http://scratchpads.eu)

Project leaders: Simon Rycroft, Dave Roberts, Vince Smith Contact : scratchpad@nhm.ac.uk

Integrating the producers, users and sources of digital information is perhaps the greatest challenge facing biodiversity informatics. Scratchpads address this challenge by blending social, technical and policy developments into a platform supporting collaborative biodiversity research.

This data-publishing framework allows groups of people to create their own social networks supporting their research communities. Scratchpads are flexible and scalable enough to support multiple networks, each with its own choice of features, visual design, and data. Diverse and distributed data can be organised, curated and cited by users around multiple taxonomies. The Scratchpad framework currently serves more than 1,100 registered users across 100 sites, spanning academic, amateur and citizen-science audiences. These contributors have generated almost 160,000 pages of content in the first two years of use. Web services on standardised data elements are available for use by related initiatives such as GBIF, Encyclopedia of Life and the Biodiversity Heritage Library.

Technically, and you really don't need to know this, Scratchpads are an implementation of the Drupal content management system, which means that the actual information is held in a MySQL database and served onto web pages as required. What you do need to know is that to create one, the best place to start is to upload a taxonomy, which is either your own encoded onto a spreadsheet, or can be selected from Catalogue of Life or other on-line sources. Either way, it should be a quick and easy step. Once the taxonomy is in place it becomes the central organiser for everything else. You can upload content from word processor files by cut-and-paste or import from spreadsheets or other databases. You can create data tables to contain any kind of data that you like. You can upload images of course. The key to this is that all information elements are tagged with keywords that allow them to be associated on a page. The default tagging is the taxon name, which is automatic where possible, but other tags, such as locality or habitat can be added as needed. The objective of the Scratchpad project is to make the workflow straightforward and easy.

To encourage community-building, the sites are created empty and unbranded, so that each community can develop its own image. Design and layout are entirely up to you, although there are customisable templates available so that the process can be straightforward and little more than choosing a logo or an iconic image. You provide the content which remain yours, published under a creative commons licence.

The essence of collaboration is data sharing, hence the Creative Commons licence. The maintainer can control who can see what, can establish private groups within the community and can expose as much of this to public view as desired by the community. Public pages are most commonly a composite of various elements related by some tag, say a species name. These elements are arranged into a display and the resulting page can be cited by clicking a button that creates a Chicago-style bibliographic entry containing a url. The authorship is a list of those who have contributed data to the page being cited and the url points to a static archive of the page at the time the button was pressed. This means that if you cite the page in an article, the reader will see exactly the same page that the author saw, not a current view containing the latest data. Clearly, if your page is cited, you collect merit points in the citation statistics but we are also working with GBIF to provide usage statistics that will measure the impact of your on-line data. Finally, by the end of the summer, we will have a publication interface (TAPIR) that will make your data visible to other machines on the web (such as GBIF) in a form that will give you credit for your work.

To apply for a site (http://scratchpads.eu) you will need only to specify the scope, either taxonomic, geographical, habitat or a combination, such as the Lichens of Bermuda. We do not mind what subject you choose, provided it is broadly to do with natural history.

You provide the technical expertise to run the site. This is usually one IT-savvy person within a community who takes responsibility, the maintainer, but controls access and editing rights to all other users, including the ability to give others within the community editorial or even maintainers rights. There are a suite of tutorial videos on the main Scratchpad site, under the Help tab, that describe most of the common tasks involved in maintaining your site.

We provide the infrastructure that keeps the site visible and we back it up. We are a very small team, so we do not offer much direct support, but we do run a forum and we do respond to bug reports and feature requests.

Its free and guaranteed to remain so for at least the next 7 years. You can download and withdraw your entire site content at any time as a MySQL dump, should you wish to migrate your content to another site, for instance, or a meteorite strikes the NHM in London. That is as far into the future as we can see right now. If your interest has been piqued by this, then visit http://scratchpads.eu and try the sandbox. This is a demonstrator site that is re-built every hour, so it is impossible to break. For more than 59 minutes anyway.

If you would like to read a longer article describing the Scratchpads from a taxonomic perspective, see
Roberts, D. et al., 2008. Getting Taxonomy onto the Web. The Systematist, 30, 3-10.