Introdução aos Scratchpads: Aproveitando melhor seus dados Brazil November, 2012 Laurence Livermore Natural History Museum, London l.livermore@nhm.ac.uk

O que é Scratchpads? Sítios prontos para dados de biodiversidade, com apoio institucional Plataforma virtual para pesquisa e publicação Acesso livre, fonte livre Modular e flexível What are Scratchpads? They are hosted websites for biodiversity data, but the specifics and the kind of data are entirely up to the user. Scratchpads are designed to be a virtual research and publication platform, a place where you should be able to store, save, publish and reuse your work. They are completely open access, open source and free to use. They are modular and flexible. It is possible for other developers to work with us to write modules for specific functions or communities.

O que Scratchpads não é! Um banco de dados unitário de biodiversidade Restringido por tema, geografia ou táxon Uma ferramenta excluisiva aos taxonomistas What are Scratchpads? Scratchpads are not a single biodiversity database and each site is “owned” by its community, not the Scratchpad project. It is possible for you to host your own site under your own URL, although we provide all the hosting services for free. There is no restriction to the scope of a Scratchpad, they can focus on whatever aspect of biodiversity you want. Scratchpads are not just for taxonomists, but can and are used by citizen scientists and societies.

De onde vêm os recursos financeiros? 2007 2011 2014 ViBRANT Virtual Biodiversity Research & How is Scratchpads Funded? Scratchpads was initially funded by EDIT (2007-2011), so the project has been running for almost 5 years. This followed with joint funding from ViBRANT, a large EU biodiversity project and eMonocot. I am here in Brazil because of eMonocot, which is working closely with taxonomic communities around the world to produce a consensus classification for monocot plants. From 2014 onwards, The Natural History Museum has committed to sustaining the project by providing hosting and a full-time developer.

Exemplos de utilização: Taxa (Classificações, pérfis de táxons, espécimes, literatura, imagens, mapas, conjuntos de dados do fenótipo, genótipo, de morfometria, chaves, filogenias) Projetos Conservação Regiões Sociedades Examples of use: Most Scratchpads are used for primarily for taxa and are based around a biological classification. They contain a mixture of data, such as taxon descriptions, specimen records, literature, images, distribution maps, character datasets, keys and phylogenies. Other Scratchpads do not focus primarily on specific taxonomic groups and can cover conservation, projects (like PhD studies), whole regions (multiple taxonomic groups) or societies (where the focus is on users and communicating with them). The modular nature of Scratchpads means you can do all this in one site, although typically a site will focus on only a few of these activities.

Quem usa Scratchpads? Users Sites Pesquisadores profissionais ViBRANT SP 2 Pesquisadores profissionais Naturalistas amadores Cientistas cidadão Indivídos, grupos e sociedades No. total de sítios: 400+ No. total de usuários: 7,000+ Usários ativos: 5,500+ (273 w / 759 m) Contéudo : 430,000+ (nodos) Who uses Scratchpads? Our user community is rich and diverse, composed of professional scientists, amateur naturalists and citizen scientists. They work alone, in small groups or as large 100+ user societies. We now have over 400+ sites, with over 5,500 active users who have generated over 430,000 “nodes” of content.

eMonocot Scratchpads 15 sítios e crescendo 40+ usuários internacionais Scratchpads / eMonocot Portal online! eMonocot Scratchpads In the eMonocot project we have 15 eMonocot Scratchpads which have over 40 international users. The eMonocot Scratchpads cover over 11 families with more planned for additional workshops which will take place this year and in 2013. The Scratchpad to eMonocot Portal link is now active and soon the public will be able to use the portal to browse all the Scratchpad data combined with other external monocot resources. Listagem dos sítios: http://about.e-monocot.org/list-emonocot-scratchpads

Por que Scratchpads? A Ciência é global Precisa de padronização global Workflows globais Cooperação de institutos e organizações de grande porte Why Scratchpads? Science is global Collaborative projects require global workflows, where we can follow the same method and produce data that can be reused. It requires international cooperation between institutes and individuals.

Por que Scratchpads? Ciência é realizada “locally” Por cientistas do local Em colaboração com infraestruturas locais Com apoio financeiro do local Why Scratchpads? A lot of science is produced locally. It is produced in collaboration with local infrastructures and funding bodies.

Por que Scratchpads? Isso resulta em : Uma paisagem complexa, fragmentada e de navegação difícil Fontes dispersas de dados Dificuldades em coletar informações para pesquisa Why Scratchpads? This results in: A complex, fragmented landscape of literature which is hard to browse and navigate. Data are dispersed, often published in local journals that are hard to find and not indexed. This makes it very difficult for scientists to find data and lowers the amount of work which is reused.

Porque precisa mudar? Problemas com dados publicados pela maneira tradicional: Maioria de descrições sob controle de reprodução (~1923) Acesso Livre limitado Ausência de mecanismo para atualização e correção Ausência (quase) de integração de dados (exceto citações) Ausência de mecanismos para engajar a comunidade Why should we change? The problems with traditional publication: Most taxonomic descriptions and works and under copyright, placing restrictions on how we can access and re-use them. There is still very little open access publications. Solely printed works have no mechanisms for updates and corrections. There is little or no integration of data, with the exception of citations. There is no mechanism for community engagement, like the ability for scientists to discuss data before and after publication.

Porque precisa mudar? Resultado: Grandes quantidades de “conhecimento” taxonômico não publicado Conhecimento não publicado não pode ser mobilisado para fins úteis Impact científico baixo (mas longa meia-vida) Why should we change? This results in: Vast quantities of unpublished taxonomic knowledge. Almost every scientist, from undergraduates to retired professors have unpublished data. Published knowledge which cannot easily be reused or accessed. Low scientific impact - the current methods assessing the impact of published papers poorly serves taxonomists. There are still many useful taxonomic works which are over 100 years old!

O Conceito Scratchpad Um Scratchpad é sítio que abriga dados para voce e sua comunidade The Scratchpad Concept A Scratchpad is a website that holds data for you and your community but can also communicate with other services to share and retrieve data. This principal is used in eMonocot. We retrieve the initial checklists from eMonocot webservices and all eMonocot Scratchpads feed data like taxon descriptions, distribution records and keys back into the eMonocot portal. Taxonomy is in perpetual beta with many contributors making varying additions to our global knowledge of biodiversity. Dados externos e serviços Seus dados

O que pode fazer Scratchpads? Páginas de taxon (geradas a partir de conteúdo etiquetado) Mapas de distribuição (a partir de espécimes e regiões TDWG - Brummitt, 2001) Registros de espécimes Matrizes de caracteres So what can Scratchpads do? Over the next few slides I will cover some of the key features, and some of the features which will be coming soon to Scratchpads. Rich taxon pages, generated from multiple pieces of “tagged” content Disitrubtion maps, based on specimen (point localities) and regions (Brummitt, 2001) Specimen records Character matrixes

Example Taxon Page Example Taxon Page It is very easy to create professional looking taxon pages with no knowledge of web design. The taxonomy provides the crucial backbone, linking content together and is easily updateable. On this page you can see the classification browser in the side bar, detailed nomenclatural information, images and a diagnostic summary.

Example regional distribution Distribution Map The distribution maps in Scratchpads combine regions with point data. You can import regional distributions or select them by clicking an interactive map for each species.

O que pode fazer Scratchpads? Gerência de bibliografia Imagens, video e som (importação em massa) Importação de planilhas Excel What can Scratchpads do? Bibliography management - manual creation, import functions (DOIs, EndNote, BibTex) Images, sounds and video support (with bulk import and metadata editing) Excel spreadsheet import and export for almost all the Scratchpad data (including custom content data templates)

Example Literature Example literature page

O que pode fazer Scratchpads? Editação de dados em tabela Conteúdo específico ao pedido de usuário Gerenciamento dos usuários Formulários (planilhas) específico ao pedido de usuário Medidas analíticas do uso do sítio. What can Scratchpads do? Tabular data editing, allowing you to make bulk changes Custom content - if you need to record specific data, for example: field recordings, soil pH or any kind of data which isn’t already supported by default, it is very easy to create your own custom content types. All Scratchpads support multiple users, at different access roles. You can have: contributors which can add and edit their own content only; editors which can create content and edit the content of others; maintainers which are site super users, and can edit all aspects of a site including the user roles. Custom webforms, for recording data from other users or the general public. Examples could be congress site up forms or the submission of photographs from the general public. We support a growing amount of in-site analytics and also support Google Analytics which provides very rich metrics for analysing the performance of your site.

Medidas analíticas The is an example page for the international visitors to a site. It shows the number of unique visits, the number of pages per visit and the average duration that visitors spent looking at the site. You can export all these metrics from Google Analytics when writing reports about site use.

O que pode fazer Scratchpads? Exportação de Darwin Core Archive (links a eMonocot Portal e EOL) Importação de dados de EOL (taxonomia, informação sobre espécies) Integração de mapas da GBIF Darwin Core Archive is the lingua franca used by a number of biodiversity tools and programs, ranging from biodiversity aggregation services like Encyclopedia of Life and the eMonocot Portal, to collections databases like Specify. By supporting Darwin Core Archive, the data in your site is much more portable and reusable. We offer users an import service from one of our partners, Encyclopedia of Life (EOL), which provides: media, taxon descriptions and classifications. While eMonocot classifications are provided from Kew, eMonocot Scratchpads can still make use of other EOL content. We provide GBIF map overlays for additional distribution records.

Importação e exportação de dados de Scratchpads Import and Export of Data in Scratchpads

Quais novas funções vêm logo? Chaves baseadas em matrizes (usando projeto de caracteres) Ferramenta para publicação- submeter manuscritos pelo seu site para Phytokeys ou Biodiversity Data Journal (NOVO) Checklists, apoio para linguagens múltiplas, outros! We are constantly developing new features and with a growing development team, we should be able to fix issues and add more functionality at a much faster rate. The Scratchpad Team meets regularly to discuss feature priorities and we will consider any feature requests by our users.

Amostras do protótipo: ferramenta de publicação Manuscript preview Multi-figure plates Plate layout ID Key preview ID Key builder

Apoio In-site Support Wiki Training Courses (12 in 2012) One click help within your site Wiki Training manuals, videos & glossary Training Courses (12 in 2012) UK (6), Sweden, (2) Greece (1), Bulgaria (1), South Africa (1), Brazil (1) Ambassadors Programme Enthusiastic experienced users Local support Embedded Issues Queue Bug reports Feature requests Sandbox Site http://sandbox.scratchpad.eu We have a number of help and support systems built into Scratchpads. Many of the Scratchpad editing screens have inbuilt help and for more comprehensive information, including training manuals, users can visit our help wiki. We regularly run Scratchpad training courses and will have given 12 courses in three continents this year. We are actively developing an ambassadors programme for our experienced users that will let them get involved in the early testing of new features and small grants or support to run training courses in their country. The embedded issues queue makes it easy for users to submit help and issue requests which are responded to directly by the support and development team. We use the issues queue to manage our development which is publicly viewable. The Sandbox is a blank site that anyone can use to try out content or experiment. It gets wiped and reset every day, so you don’t have to worry about breaking it! http://scratchpad.eu/help

Agradecimentos Scratchpad technical development Scratchpad outreach Simon Rycroft, Ben Scott, Ed Baker, Alice Heaton & Katherine Boulton Scratchpad outreach Irina Brake & Dimitris Koureas E-Monocot Paul Wilkin & the Kew team, Charles Godfray & the Oxford team ViBRANT Vince Smith, Dave Roberts & Lucy Reeve Our 7,000+ users