Small pieces loosely joined: a unified theory of biodiversity for the web.

Small pieces loosely joined A unified theory of biodiversity for the web Vincent S. Smith

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

http://Scratchpads.eu

What is a Scratchpad? A website for you & your community 1 2 3 Your data Uploaded & Published & reviewed tagged on your site

What is a Scratchpad? A website for you & your community 1 2 3 Your data Uploaded & Published & reviewed tagged on your site Fast Intuitive Fit for use

What can Scratchpads do? Import, manage, search & browse: Specimens DNA & Phylogenies Literature Images

What can Scratchpads do? Integration & connectivity within & between sites Specimens DNA & Phylogenies Taxonomy Literature Images

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

What can Scratchpads do? Visual taskguide

Current Scratchpads Ants Sites: 70+ Bees Beetles Users: 850+ Big-headed flies Birds Pages: 130k Blackflies Ciliates Since March 2007 Cockroaches Dragon Trees Dung Beetles False Buttonweed Flat worms Flies Foraminifera Fossil Insects Fungus Gnats Holometabola Leaf-miner Flies Lice Lichens of Bermuda Malvaceae Megalastrum ferns Milichiid flies Mosquitoes Mosses Nannotax fossils Nepticuloid moths Palms Pearl oysters Polychaete worms Scaleworms Stick insects Sulawesi Ferns Termites Triticid grasses Weevils Wood Ferns

Scratchpad visitors Tracking visitors across sites Key monthly statistics - 50,000 page views - 6,000 visitors - 8 minutes on site - 50% returning visits (average per month 08’)

Scratchpad applications A multipurpose, flexible technology eBooks 4th Edition Howard & Moore, Birds of the world (fact checking, data compilation, 2010, funding)

Scratchpad applications A multipurpose, flexible technology eJournals European Mosquito Bulletin (ISSN 1460-6127), Phasmid Studies (ISSN 0966-0011) (submission, review, & dissemination of articles)

Scratchpad applications A multipurpose, flexible technology Image galleries Nanno fossils, Cockroaches, Stick insects, Flatworms, Grasses, Lichens & many more… (rapid upload, annotation, & display of images)

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

Autotagging Indexing data to make it findable 1. Create content (e.g. reference) Journal citation 2. Find terms mentions taxon name (Autotag) 3. Submit (Index)

Autotagging Indexing data to make it findable 1. Create content (e.g. reference) 2. Find terms (Autotag) Matches taxonomy term (Drag & Drop) 3. Submit (Index)

Autotagging Indexing data to make it findable 1. Create content (e.g. reference) 2. Find terms (Autotag) 3. Submit Page tagged (indexed) (Index) with taxon name

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

How do Scratchpads work? Integrating data & “publishing” in a Scratchpad Dynamically built species pages

How do Scratchpads work? Integrating data & “publishing” in a Scratchpad Browsed through a taxonomy

How do Scratchpads work? Integrating data & “publishing” in a Scratchpad Including 3rd party content

How do Scratchpads work? Integrating data & “publishing” in a Scratchpad With data curation tools

How do Scratchpads work? Integrating data & “publishing” in a Scratchpad Listing all “authors”

How do Scratchpads work? Integrating data & “publishing” in a Scratchpad Dated, permanent & citable

How do Scratchpads work? Adjusting the panels layout Choose which panels to display

How do Scratchpads work? An example based on the Catalogue of Life classification 2 million taxon pages Open curation at http://catlife.myspecies.info

Biodiversity on the Web The informatics landscape

Biodiversity on the Web Scratchpads are personalizing biodiversity science

Biodiversity on the Web Scratchpads are pulling and pushing biodiversity data TapirLink provides TCS over Tapir can specimens to GBIF provide names and based on Darwincore classifications

A unified theory of biodiversity? Scratchpads, EOL and scholarly journals Encyclopedia Biodiversity of Life Journals

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!

Thanks… Simon Rycroft Dave Roberts Kehan Harman Ben Scott Edward Baker Irina Brake Vladimir Blagoderov

Questions?

Scratchpad management Scalable & sustainable technology Hardware, software & user support Virtual machine, open-source software, self-archiving, backed-up, multi-site configuration (easy to move & upgrade, secure & reliable, citable, screencasts, low admin., low marginal costs)

Small pieces loosely joined: a unified theory of biodiversity for the web.

by Vincent Smith

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