Scratchpads are an easy to use, social networking application that enable communities of researchers to manage, share and publish taxonomic data online. Sites are hosted at the Natural History Museum London, and offered free to any scientist that completes an online registration form. Key features of the Scratchpads (see also Scratchpad feature list) include tools to manage:

	Classifications		Phylogenies
	Bibliographies		Documents
	Images		Matrices & custom data
	Specimen records		Maps

Users control who has access to content, which is published on the site under Creative Commons (by-nc-sa) license.

Data added to a Scratchpad are automatically classified and grouped around a taxonomy that is supplied by the users or imported from EOL. This is optionally supplemented with information from high quality web accessible databases, to automatic construct content rich web pages about any documented taxon. Currently these sources include Genbank, Morphbank, GBIF, Biodiversity Heritage Library, Yahoo! Images, flickr, Google Scholar and Wikipedia.

A summary of the Scratchpad usage for the months May-Oct 2009 is shown below. See our statistics page for current data.

Scratchpad users include societies, journals, scientists, students and amateurs. Any group with an interest in natural history is eligible for a site and you do not have to have an academic affiliation, or any professional qualification. All you need is time, some information you would like to share, and a little experience using the web. You don't need to be a member of a group, some of the best sites are developed by single users. The best way to start is to explore the current sites and see what other users are doing (see Live examples blog and site list). Site applicants are referred to as the site maintainer. Maintainers assume responsibility for the site's additional users and content. New users can be invited to join by the site maintainer and are assigned different roles (editor, contributor and authenticated user) that control the level of access to site content and functions. In practice the best sites usually have at least two maintainers, at least one of whom has some experience with web development as site maintainers control all aspect of what the site looks like and how it functions. With a little experience the Scratchpads are very easy to use. However, this will take some time initially, especially for those with no or minimal experience of building content on the web.

The rise in the number of Scratchpad sites and registered users over the period of the EDIT project (2006-2011) is shown in the graph below.

Taxonomic information is dispersed across vast specimen collections in a myriad of institutions, a fragmented literature spanning 250 years, and a handful of living experts who have specialist knowledge about particular species. As the volume of taxonomic data has grown, and the number of taxonomic experts has fallen, researchers have increasingly struggled to find, access, and even publish taxonomic works. The Scratchpad project was developed as a means to address these problems. The Scratchpads provide a space on the web that allows communities to bring taxonomic information together without the limitations of traditional paper based publications. Harnessing to the collective efforts of specialists worldwide, Scratchpad users can collaborate on projects that individually might have taken a lifetime to complete. Their sites provide the open access that traditional publishers cannot afford. More importantly, web systems and content can be developed and updated in minutes, living in a state of 'perpetual beta', that reflects the latest knowledge of a particular group.

Origins of the Scratchpads

The premise for the Scratchpads has its origins with the BioCorder project. BioCorder (derived from the name "Biological Recorder") was an NSF funded project conceived by Vince Smith as a distributed web accessible database supporting biodiversity scientists. With the web technology available at the time, BioCorder was arguably not possible to deliver¹. However, it paved the way for the Scratchpad project. The original schema for the BioCorder project as conceived in 2004 is shown below:

1. The BioCorder project morphed into a centralized lab management system for molecular data and is still in use today by David Reed and colleagues at the University of Florida.

We have funding through the ViBRANT, a grant of the European Commission Framework Seven program, until late 2013. This is in addition to matching staff time committed by the Natural History Museum (NHM), London. The NHM has also committed to keeping two posts associated with Scratchpads as well as keeping the server infrastructure hosting the Scratchpads accessible until 2016. Additional funds to support the Scratchpads have been provided by the Global Biodiversity Information Facility (GBIF) and from core funding within the NHM. We are also receiving funding through the Natural Environment Research Council funded e-monocot project, in partnership with the Royal Botanic Gardens Kew and the University of Oxford. Finally we are working with Biodiversity Informatics Group (BIG) of the Encyclopedia of Life project who is supported by $50 million USD worth of funding. This team have similar ambitions to develop a Scratchpad-like infrastructure as part of the Encyclopedia of Life project and the Scratchpad team are working closely with BIG to assist in this process.

Ultimately the longevity of the Scratchpads will be dependent upon whether they remain useful. Without community support for both the infrastructure and the content, the Scratchpad project will be short lived. However, every indication is that the Scratchpads are proving very popular with users. For example, collectively the sites have attracted about 1600 registered users in the projects first 3.5 years. 650 of these users have logged in during the last 12 months. Arguably, because the Scratchpads rely on the Drupal Content Management System, they have greater potential for longevity than other similar projects. This is because they are not dependent upon the taxonomic community to sustain and develop the underlying software. Conceivably anybody with some knowledge of databases and web development could rebuild a Scratchpad. Thus even if the Scratchpad project fails, the content can live on so long as there is the community support for it to do so.

In recent years there has been an explosion of interest in the field of biodiversity informatics. However, there are no projects (yet) that directly compare with the Scratchpads. Here are a few notes on major informatics initiatives, some of which are related to or used by the Scratchpads:

	Biodiversity Heritage Library (BHL) BHL is an ambitious project to digitize the contents of the world’s ten largest Natural History libraries. The projects focus is on out of copyright works, although where possible, efforts are being made to include in copyright material. The Scratchpads use BHL content as part of their taxon pages feature.
	Catalogue of Life (CoL) CoL is attempting to compile a single unified classification for all 1.8 million known species. As of 2010, CoL has 1.26 million species records and is engaged in projects to complete the database. We have no formal relationship with CoL, although the Natural History Museum is a partner in the project. Scratchpad users can use parts of the CoL classification which forms the backbone of the Encyclopedia of Life (EOL) within their own sites.
	CATE Creating a Taxonomic e-Science (CATE) was a project funded under the UK's Natural Environment Research Council e-science initiative. The project was a partnership between the University of Oxford, the Natural History Museum and the Royal Botanic Gardens Kew to test the feasibility of creating a web-based, consensus taxonomy for Hawk moths and the plant group Araceae. The CATE Araceae group uses a Scratchpad and a proposed related project to CATE will use the Scratchpads to support satellite research communities.
	Encyclopedia of Life (EOL) EOL is a $50 million dollar initiative to establish a web page (or more accurately a web site) for every species. This ten-year program includes a component called LifeDesk that is very similar to the Scratchpads. The Scratchpad team is working with the LifeDesk group in the development of this tool. Vince Smith is also a member of the Informatics Advisory Group (IAG) for EOL.
	European Distributed Institute of Taxonomy (EDIT) The Scratchpad project is mainly supported by EDIT, although it was not conceived as part of the original EDIT project. One of the aims of EDIT is to bring revisionary taxonomy online. The IT infrastructure for EDIT is being managed by a group based in Berlin, and the Scratchpad team are working with these developers to produce intuitive and sustainable web applications for the taxonomic and systematic community.
	Global Biodiversity Information Facility (GBIF) As a broker for all types of taxonomic data GBIF has a seminal role in the field of Biodiversity Informatics. GBIF have supported the Scratchpads directly by funding an embedded Scratchpad developed at the Natural History Museum, London. GBIF also use the Scratchpads to deliver various restricted vocabularies as web services for other taxonomists, and Scratchpad users benefit from GBIF web services in their own sites as part of the Scratchpad taxon pages feature.
IISE	International Institute for Species Exploration This is a new institute established by Quentin Wheeler at Arizona State University. IISE primarily has an advocacy role for biodiversity science, but in due course will develop a more active cybertaxonomy research program.
	Plazi.org The 100+ million pages of scientific literature containing species descriptions are inaccessible to most people because of copyright restrictions. Plazi is an association supporting and promoting open access to taxonomic literature by extracting and representing the factual components of species descriptions that are not subject to copyright.
	Rod Page Rod is a one-man informatics initiative that is behind many of the most substantive ideas in the field. He was the PhD advisor to Vince Smith and an MSc advisor to Simon Rycroft, both of whom work on the Scratchpad project. Rod has indirectly contributed to the Scratchpad project through development of a web-based application that intuitively displays very large phylogenetic trees and through his BioGUID OpenURL resolver to connect literature references to full text articles.
	Species File This is a web based Content Management System for taxonomists. Managed by David Eades and colleagues at the University of Illinois this software is use by communities to provide and online checklist and nomenclatural database for several taxa including Stick insects, Orthoptera and Cockroaches.
	Taxonomic Database Working Group (TDWG) The body has recently been renamed Biodiversity Information Standards to more accurately reflect its role within the field of biodiversity informatics. We selectively use some TDWG standards to support certain data types within the Scratchpads.
	Tree of Life We have no formal relationship with the ToL project, although Vince Smith is a contributor to the ToL website and is an advisory group member for ToL. Arguably, ToL seeded many of the ideas and concepts that led to the Encyclopedia of Life project and related biodiversity informatics initiatives. Despite being one of the oldest web based initiatives supporting biodiversity science, ToL remains an influential and substantial resource about biodiversity on the web.
	ZooKeys & ZooTaxa These are rapid publication journals for zoological taxonomists. Both journals structure content so that it can be reused. We are working together with ZooKeys on streamlining publishing taxonomic papers and we are working on doing the same with Zootaxa. Zootaxa currently uses a Scratchpad to support certain editorial functions, and in due course would like to expand their sites functionality to accept journal submissions and assist with the peer review process. This is beyond the current scope of the Scratchpad project but may be possible as the Scratchpad project grows and expands.

The Scratchpad project is open to anybody who has biological content of scientific value or interest and would like to develop this on a website. There are NO restrictions as long as users conform to a minimal set of legally binding terms and conditions as outlined below. Site maintainers are compelled to click through this agreement when they first join a site and it is the site maintainer’s responsibility to enforce this agreement on all subsequent registered users. By default new users are also presented with this click through agreement. However, site maintainers can at their discretion alter this agreement for subsequent users to suit their own needs.

A PDF copy of this document is available for download.

1. SCRATCHPADS

   The term 'Scratchpad' represents a publicly accessible web page as described on the Scratchpad web site (http://scratchpads.eu). Your scratchpad will be a discrete implementation of a Content Management System.

2. ACCEPTANCE OF TERMS

   This agreement is between the European Distributed Institute of Taxonomy and its agents (collectively “EDIT”),
   and you and your agents (collectively “you”) regarding the use of your scratchpad (the "Site"). By using the Site, you agree to the Terms and Conditions in this document.

3. OWNERSHIP OF SITE

   The text, graphics, sound and software (collectively "Content"; i.e. material that you have up-loaded) on this Site is owned by you and your agents and you bare sole and ultimate responsibility for this Content. EDIT supports the computer hardware infrastructure and software content management system that provides access to this Content

4. ACCESS TO SERVICES AND TERMINATION OF ACCESS

   You are responsible for all activity logged through your user account and for the activity of other persons or entities you grant access to this Site. You agree to notify EDIT immediately you become aware of any unauthorized use. EDIT may terminate your access privileges and remove Content without notice if EDIT believe you have violated any provision of this Agreement. You agree that termination of your access to the Site shall not result in any liability or other obligation of EDIT to you or any third party in connection with such termination.

5. PURPOSE OF SITE

   The Site is made available to you to foster collaborative research in taxonomy and it must be open to use by any suitably qualified person. At least the top page of the Site must grant public access. The Site must not restricted membership to any single geographical area. Areas of the Site may be restricted to nominated parts of your membership (“private areas”) at your discretion. You agree to manage requests for membership and to allocate appropriate access privilidges.

6. CONTENT

   All Content placed on the Site must be legal, decent and truthful. Through your use of the Site you represent and warrant that you have all the rights necessary to receive, use, transmit and disclose all data that you use in any way with the Site. You agree and acknowledge that you are solely responsible for any liabilities, fines, or penalties occasioned by any such violations or lack of rights and that you are solely responsible for the accuracy and adequacy of information and data furnished on the Site. EDIT will, as part of the provision of the Site, implement a periodic archive of the Content that can be made available to the Maintainer on request. You understand and acknowledge that EDIT assumes no responsibility to screen or review Content and that EDIT shall have the right, but not the obligation, in its sole discretion to review, refuse, monitor, edit or remove any Content. EDIT expressly disclaims all responsibility or liability to you or any other person or entity for the Content and you acknowledge and agree that you assume all risk associated with the use of any and all Content.

7. DISCLAIMER OF WARRANTIES

   The use of the Site is solely at your own risk. The site is provided on an "as is" and "as available" basis and EDIT expressly disclaims all warranties of any kind with respect to the site, whether express or implied. EDIT makes no warranty that the access to the site and/or Content therein will be uninterrupted or secure. Your sole and exclusive remedy with respect to any defect in or dissatisfaction with the Site is to cease using the Site.

8. LIMITATION OF LIABILITY

   You understand and agree that EDIT shall not be liable for any direct, indirect, incidental, special, consequential, or exemplary damages resulting from any matter related to your or other persons use of the site.

The Scratchpads rely on the Content Management System Drupal. This provides the underlying architecture on which all the Scratchpad functionality sits. Without Drupal, the Scratchpad project would not exist. Specifically Drupal enables features such as blogs, collaborative authoring, forums, peer-to-peer networking, newsletters, picture galleries, file uploads and downloads etc.

The Scratchpad project is about tweaking Drupal's underlying infrastructure to make it easier to use and better suited to the needs of the taxonomic and systematic community. We do this by developing specific modules that support specific taxonomic data types (e.g. biological specimens and literature), templates for the import and export of data (e.g. taxonomic classifications), and by making web services of other data readily accessible (e.g. Google Scholar, Biodiversity Heritage Library, flickr, NCBI Genbank, Morphbank etc). The Scratchpad project also hosts all this content, making is simpler for users to establish a rich web presence that is supported and built by a community of users.

Yes! Perhaps the simplest thing you can do is switch to using Drupal for your biodiversity informatics projects. This is the Content Management System (CMS) that performs all the underlying functionality for the Scratchpads. Its free, open-source (distributed under the GNU General Public License) and is maintained and developed by a community of thousands of users and developers. This wide user base makes the Scratchpad project much more sustainable than developing purpose built CMS applications for bespoke needs.

Drupal forms the underlying architecture on which the Scratchpad modules, templates and web services sit. By switching to Drupal you can make use of these tools as well and adapt them to your purposes. Anyone with PHP and MySQL experience will pick up Drupal development quickly, and there are some excellent books available to guide you through this process. For some specific Scratchpad resources:

• Take a look at the complete list of the modules we use on the Scratchpads
• Alternatively take a look at our SVN repository to access the full Scratchpad code base

With a few exceptions (notably the way Drupal handles taxonomy) we have not altered the core Drupal code. If you are interested in developing modules for the Scratchpad project, and would like direct access to our SVN repository contact us.

The name "Scratchpad" reflects the fact that taxonomy is in a state of 'perpetual beta', constantly changing and reforming to reflect our current knowledge of a particular group. Working in collaboration, users 'scratch out' their ideas on their sites, which act like a notepad for any and all biological content. Unlike related projects, this content does not have to be structured or standardized.

The name continues to evoke mixed feelings amongst both the developers and users of the Scratchpads. Dave Roberts originally proposed the name, despite mild objection from Vince Smith. Vince has since become a fierce advocate of the name, while Dave has proposed that it be changed on several occasions! It has now (2010) been decided to keep the name 'Scratchpads'. Regardless, Scratchpad users brand their sites with their own names and logos to reflect their sites content and purpose. The majority of users are not even aware of the Scratchpad project. In this sense Vince has christened the Scratchpads as the "anti-brand". The only evidence that people are using or viewing a Scratchpad is in the footer of each page. Arguably, the Scratchpad brands invisibility has been fundamental to the Scratchpads success.

Below are a few papers that reference the Scratchpads and related projects and we also have a Scratchpad leaflet.

• Smith, V.S, Duin, D., Self, D., Brake, I. & Roberts, D. (2010)

  Motivating Online Publication of Scholarly Research Through Social Networking Tools.

  Webcentives: Incentives and Motivation for Web- Based Collaboration . Conference Proceedings paper delivered at COOP2010, The 9th International Conference on the Design of Cooperative Systems on 18 May, 2010 as part of a workshop titled Incentives and Motivation for Web-Based Collaboration. Published in Workshop Proceedings of 9th International Conference on the Design of Cooperative Systems - COOP 2010, Aix-en-Provence, France, May 2010. Volume 7, Issue 10, pp. 329-339.

• Blagoderov, V., Brake, I., Georgiev, T., Penev, L., Roberts, D., Rycroft, S., Scott, B., Agosti, D., Catapano, T., Smith, V. S. (2010)

  Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys.

  ZooKeys 50: 17–28. doi: 10.3897/zookeys.50.539

• Smith. V.S., Rycroft, S.D., Harman, K.T., Scott, B. & Roberts, D. (2009)

  Scratchpads: a data-publishing framework to build, share and manage information on the diversity of life.

BMC Bioinformatics 2009, 10(Suppl 14):S6doi:10.1186/1471-2105-10-S14-S6.

• Smith, V.S, Rycroft,S.D.,Roberts, D. (2008)

  Scratchpads: Getting Biodiversity online, redefining publication.

  Lecture Notes in Computer Science. (Not available)

• Roberts, D. Rycroft, S.D., Brake, I., Harman, K., Scott B. & Smith, V.S. (2008)

  Getting Taxonomy onto the Web.

  The Systematist (newsletter article). (Not available)

• Mayo, S. J., Allkin, R., Baker, W., Blagoderov, V., Brake, I., Clark, B., Govaerts, R., Godfray, C., Haigh, A., Hand, R., Harman, K., Jackson, M., Kilian, N., Kirkup, D.W., Kitching, I., Knapp, S., Lewis, G.P., Malcolm, P., von Raab-Straube, E., Roberts, D.M., Scoble, M., Simpson, D.A., Smith, C., Smith, V.S., Villalba, S., Walley, L., Wilkin, P. (2008)

  Alpha e-taxonomy: responses from the systematics community to the biodiversity crisis.

  Kew Bulletin. 63:1-16.

• Roberts, D., Rycroft, S.D., González, M., and Smith, V.S. (2007)

  Scratchpads: what are they?

  European Distributed Institute of Taxonomy News (newsletter article).

Yes! The Scratchpad team has given a number of presentations about the Scratchpads. A selection of these are listed below and more a available in our bibliography. In addition, Vince has made available most of his presentations through his SlideShare account. Asterisks indicate the presenting author:

• Roberts D., King, D., Rycroft, S.D., Morse, D., Penev, L., Agosti, D. & Smith, V.S. (2010)

  Community web sites: small pieces loosely joined

  Fourth Metadata and Semantics Research Conference (MTSR 2010) in the premises of the Faculty of Law at Acala de Henares, Madrid, Spain. 20th October, 2010.

• Brake, I. (2010)

  Scratchpads - A social networking tool to build, share & publish taxonomic information

  7th International Congress of Dipterology. Aug. 8-13th, 2010.

• Blagoderov, V. & Brake, I. (2010)

  Internet or paper: possible solution

  7th International Congress of Dipterology. Aug. 8-13th, 2010.

• Duin, D.*, Self, D., Rycroft, S.D., Roberts D. & Smith, V.S. (2009)

  Online taxonomy: Why do people engage?

  EDIT general meeting, Carvoeiro, Portugal. Dec. 15-17, 2009.

• Smith, VS.* and Rycroft, S. (2009)

  Scratchpads: A standard implementation using Drupal

  Invited. National Biodiversity Network technical conference the Natural History Museum, London, UK. November 19, 2009.

• Harman, K.T., Rycroft, S.D., Scott, B., Roberts, D., Smith, VS. (2009)

  A Matrix based Character Editor for Scratchpads

  Biodiversity Information Standards (TDWG) Annual Conference. Montpellier, France. 9th - 13th November 2009.

• Roberts, D.*, Harman, K., Rycroft, S.D. & Smith, V.S (2009)

  Scratchpads: Building web communities supporting biodiversity science

  Invited.Information Technology in Biodiversity Conservation and in Agriculture organized by the Club of Rome and the EU ICT-ENSURE project, at UNESCO, Paris. January 15th, 2009.

• Roberts, D.*, Harman, K., Rycroft, S.D. & Smith, V.S (2008)

  Scratchpads in the Biodiversity Informatics Landscape

  Invited. Stockholm Biodiversity Informatics Symposium 2008, Swedish Museum of Natural History, Stockholm, Sweden 1-4 December 2008.

• Smith, VS.*, Rycroft, S.D.,Roberts, D. (2008)

  Scratchpads: Getting biodiversity online, redefining publication.

  Invited. The Fourth International Conference on the Comparative Biology of the Monocotyledons - eTaxonomy session. August 15, 2008. (Not yet available)

• Rycroft, S.D.*, Roberts, D., Smith, VS. (2008)

  Scratchpads: Getting biodiversity online, redefining publication.

  Proceedings of BNCOD 2008 "Biodiversity Informatics: challenges in modeling and managing biodiversity knowledge". Cardiff University, UK, 10th July 2008. Officially available online at: http://biodiversity.cs.cf.ac.uk/bncod/SmithEtAl.pdf.

• Smith, VS.*, Rycroft, S.D., Roberts, D. (2008)

  Scratchpads: Getting biodiversity online, redefining publication.

  The International Congress of Entomology, Durban, South Africa. July 5-11, 2008. (Not yet available)

• Smith, VS.* (2008)

  The virtual taxonomist: scholarly communication for the facebook generation.

  Invited. The Virtual Scholar. The second Bloomsbury conference on e-Publishing and e-Publications, UCL Centre for Publishing, University College, London, U.K. June 27, 2008. (Not yet available)

• Smith, VS.*, Rycroft, S.D., & Roberts, D. (2008)

  Scratchpads: Getting biodiversity online, redefining publication.

  EDIT general meeting, Carvoeiro, Portugal. Jan. 24, 2008.

• Roberts, D.*, Smith, VS., Rycroft, S.D. (2007)

  EDIT Scratchpads as a vehicle for community building and outreach.

  Biodiversity Information Standards (TDWG) Annual Conference. Bratislava, Slovakia. Sept. 21, 2007.

• Smith, VS*. (2007)

  Science publishing for the mySpace generation.

  Invited. SciFoo Camp 2007. Googleplex, Mountain View, CA, USA. Aug. 4, 2007.