Invited presentation, given in connection with my 2008 Ebbe Nielsen Prize. Part of the 15th meeting of the Governing Board (GB15) of the Global Biodiversity Information Facility (GBIF), Arusha, Tanzania. November 5, 2008.
Macro taxonomy The big picture
of taxonomic research Goal… • Inventory the Earth’s species •Document their relationships • “Publish” these data Data set… • 1.8 M described spp. (10M names) • 300M pages (over last 250 years) • 1.5-3B specimens People… • 4-6,000 scientists • 30-40,000 “pro-amateurs” • Many more citizen scientists?
Micro taxonomy The practice of
taxonomic research Sociology… • Parochial • Specialized experts • Fragmented & distributed Methodology… • Different (domain specific) • Communities of practice • Non transferable skills Output… • Heterogeneous & scattered • High volume, low impact • Hard to find (use) How do we integrate micro & macro taxonomy for the Web?
Integrating macro & micro taxonomy
Pulling taxonomy and taxonomists together on the Web The traditional approach… • Bespoke central database • Data entry via forms & services • Output via reports, services & tools e.g. GBIF, EOL, CBoL, NCBI, CrossRef, Google Scholar, Species2000 & ITIS Advantages (Macro-centric) Challenges (Micro-centric) • Clear fixed input & output • Hard to repurpose (flexibility & agility) • Top down, multilateral (builds trust) • Build & sustain bottom-up engagement • Infrastructure robust & sustainable • Resource intensive
What can Scratchpads do? In
summary: +Administration +Groups +Specimens -Change your site information -Creating a group -Creating a record -Change you front page -Subscribing to a group -Importing from a spreadsheet -Change your logo +Image -Linking specimen & location records -Activity and access logs -Uploading & basic annotation -Linking specimen & pub. records +Backup -Linking image & location records +Tasks -Backing up your data -Linking image & specimen records -Creating a tasklist -Restoring your data -Linking image & publication records +Taxonomy +Bibliography -Overlay annotations on images -Importing from a spreadsheet -Creating a record +Layout -Importing from ClassificationBank -Importing from a ref. manager -Change your theme -Starting from scratch -Exporting to a reference manager -Menus -Taxonomy manager +Blog -Blocks and sidebars -Displaying a classification -Creating and adding a blog +Locations -Adding names +Custom Content -Creating a record -Deleting names -Defining a CCK -Importing from a spreadsheet -Taxonomy & panels -Importing from a spreadsheet +Pages +Users -Creating a custom view -Creating, editing, cloning & deleting -Your settings +Fileshare -Configuring the panels template -Adding a new user -Creating and using a fileshare +Panels -User roles and permissions +Forum -Adding & configuring content -Adding and editing user profile fields -Altering the forum settings -Creating a new panel -Logging in -Creating a container for a forum -Citing a Panels page +Webform -Creating a new forum +Phylogeny -Creating and using webforms -Creating a new topic inside a forum -Adding a phylogenetic tree
Scratchpad applications A multipurpose, flexible
technology ZOOTAXA A rapid international journal for animal taxonomists ISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition) Societies & Organizations GBIF, Zootaxa, Threatened Plants of the World (Kew), BarCoVer (DNA Barcoding) & more (space for data collection, services, discussion, & organization)
How do Scratchpads work? Getting
a Scratchpad Requirements • Biological focus • Agree to T&C’s (click-thru) • CC license “by-nc-sa” Application http://scratchpads.eu/apply • Maintainer • Scope/Mission/API Keys • (Sub)domain name Content • Unrestricted (overlapping) • No branding (focus on authors) • Value added
How do Scratchpads work? Using
a Scratchpad Management • User categories (maintainer, ed. contrib.) • Public / private content (flexible groups) • Admin. page (site settings & behavior) Data Input • Content types (biblio, maps, “page” etc) • Forms, managers, Excel, EndNote etc • Custom content (add or extend data types) Tagging (indexing) • Taxonomy terms (2M +) • Multiple classifications • Auto-tagging
How do Scratchpads work? Indexing
data to make it findable • Tagged data can be presented differently • For example as part of a traditional bibliography • Or as small windows or “panels” of data
How do Scratchpads work? Integrating
data & “publishing” in a Scratchpad Types of Scratchpad Panel… Built with “tagged data” Personalized Common instructions Bibliographic names literature Taxonomic Files and hierarchies documents Photographs & Specimen illustrations records Customized Phylogenetic content trees
A unified theory of biodiversity?
Scratchpads, EOL and scholarly journals ? ZOOTAXA A rapid international journal for animal taxonomists ISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition) 15% of all new species descriptions Approx. 50 new spp. per week! Encyclopedia Biodiversity of Life Journals
Scratchpad impact “Small pieces loosely
joined” 1. Bringing data together Biodiversity studies are data rich, poorly archived & ever changing 2. Bringing people together Biodiversity researchers are few in number, fragmented & highly distributed 3. Bringing science together Biodiversity science demands a different approach to addressing BIG questions BIG IS DIFFERENT!