Writing The Encyclopedia Of Life (not EoL.org)

Vincent S. Smith Writing the Encyclopedia of Life

Background 1 The big picture of biodiversity research Goal…
Inventory the Earth’s species
Document their relationships
Publish & apply these data
Data set…
1.8M described species (10M names)
300M pages (over last 250 years)
1.5-3B specimens
People…
4-6,000 scientists
30-40,000 amateurs
Many more citizen scientists?

Background 2 The process of biodiversity research Parochial…
Specialised
Experts
Fragmented & distributed
How do we integrate the BIG with the small? Methodological…
Communities of practice
Hard to record & update
High output but low impact
Different…
Data
Interpretations
Methods

250 yr progress report
At present rates most species will be
extinct long before we describe them The story so far…
Up to 87% of life on Earth is
still undescribed
6% of biodiversity scientists cover
80% of the worlds biodiversity 250 yrs 1000 yrs!!! ? 1758 2008 3008 Bacteria 9021 Spp Archaebacteria 259 Spp. Plants 260k spp. Animals 1.18 M spp. Other 193k spp. Fungi 101k 250 year and counting!

Taxonomic effort Bacteria 9021 Spp Archaebacteria 259 Spp. Plants 260k spp. Animals 1.18 M spp. Other 193k spp. Fungi 101k 1.8 million species

Taxonomic effort Crusta- ceans 39k Birds 10k Reptiles 7.1k Mammals 5k Amphib .5k Sponges 10k Cnidarians 9k Rotifers 1.8k Flatworms 13.7k Insects 0.82 M spp. Molluscs 117 k Fish 25k Bacteria 9021 Spp Archaebacteria 259 Spp. Plants 260k spp. Animals 1.18 M spp. Other 193k spp. Fungi 101k 1.8 million species

Taxonomic effort Crusta- ceans 39k Birds 10k Reptiles 7.1k Mammals 5k Amphib .5k Sponges 10k Cnidarians 9k Rotifers 1.8k Flatworms 13.7k Insects 0.82 M spp. Molluscs 117 k Fish 25k Bacteria 9021 Spp Archaebacteria 259 Spp. Plants 260k spp. Animals 1.18 M spp. Other 193k spp. Fungi 101k Beetles 370k spp. Flies 85k spp. Butterflies & moths 165k spp. Bees, wasps & ants 198k spp. 0.01 papers per species per year i.e 1 paper every 100 years Birds: 1 paper per species per yr. Mammals: 2 papers per species per yr. Elephants: 47 papers per species per yr. 1.8 million species

1,000’s of journals addressing a common set of questions
What is a species?
How many species are there?
Where are species distributed?
How have species distributions changed?
How are species related?
How have species characters changed?
To what extent is are species relationships predictive?
DATA “ Paper minds” Traditional publication

1,000’s of journals addressing a common set of questions Mol. Phyl. Evol. 21,964 pp. since 2000
What is a species?
“ Paper minds” Traditional publication Menopon gallinae Numidicola antennatus Amyrsidea ventralis Somaphantus lusius Menacanthus stramineus Colimenopon urocolius Trinoton anserinum Meromenopon meropis Gruimenopon longum Hoazineus armiferus Copocephalum zebra Comatomenopon elbeli/elongatum Psittacomenopon poicephalus Odoriphila clayae/phoeniculi Ardeiphilus trochioxus Cuculiphilus fasciatus Ciconiphilus quadripustulatus Eomenopon denticulatum Piagetiella bursaepelecani Osborniella crotophagae Hohorstiella lata Neomenopon pteroclurus Machaerilaemus laticorpus/latifrons Austromenopon crocatum Eidmanniella pellucida Holomenopon brevithoracicum Dennyus hirundinis Myrsidea victrix Ancistrona vagelli Pseudomenopon pilosum Bonomiella columbae Chapinia robusta Plegadiphilus threskiornis Actornithophilus uniseriatus MEGAMENOPON Rediella mirabilis Latumcephalum lesouefi/macropus Paraboopia flava Paraheterodoxus insignis Boopia tarsata Therodoxus oweni Laemobothrion maximum Ricinus fringillae Trochiliphagus abdominalis Trochiloecetes rupununi Liposcelis bostrychophilus

1,000’s of journals addressing a common set of questions
What is a species?
“ Species Name” The universal linker “ Paper minds” Traditional publication RAW DATA > Logically interconnected but presently fragmented by the publication process Other problems…
Time & money
Audience mismatch
Findability & reusability

Looking within a paper Data mining publications 2. Extract text (OCR) 3. Find keywords 1. Scan Palma, R.L., and R.L.C. Pilgrim. 2002. A revision of the genus Naubates (Insecta: Phthiraptera: Philopteridae). J. R. Soc. N.Z. 32:7-60.
Taxonomic names
Author names
Citations
Collection data
Morphological data
Descriptions
Identification keys
Illustrations
Photographs

2. Extract text (OCR) 3. Find keywords 1. Scan 4. Index 5. Annotate online Palma, R.L., and R.L.C. Pilgrim. 2002. A revision of the genus Naubates (Insecta: Phthiraptera: Philopteridae). J. R. Soc. N.Z. 32:7-60. Looking within a paper Data mining publications
Taxonomic names
Author names
Citations
Collection data
Morphological data
Descriptions
Identification keys
Illustrations
Photographs

How do we bring this all together?
Technical issues
Social issues
Needs to scale (web)
Needs to be sustainable
People “ Publications” Specimens ?

Technical issues 1 Data standards
TDWG (since 1986)
GBIF
Bridging computer science & biology
Its not science!
“ Standards” can mean many things:
Data exchange standards (e.g. Darwin Core)
Common restricted vocabularies (Sp.2000 classification)
Programming standards
Data quality

Technical issues 2 Platforms
Generic databases with custom interfaces (MySQL, Oracle)
(e.g. Species 2000, IPNI)
Bespoke (usually commercial) databases
(e.g. KeEMU, Biota)
Content Management Systems & blogging platforms
such as Drupal, Plone, Wordpress etc
(e.g. EOL’s LifeDesks, GBIF websites)
Wikis such as Mediawiki, Semantic Mediawiki
(e.g. Wikipedia, iTaxon)

Technology moves fast! Technical issues 2 Platforms

Technical issues 2 Platforms - common design considerations
Need scalable and flexible platforms that support:
large numbers of users as passive readers and active contributors
editorial hierarchies serving individual and community needs
the epistemological richness and diversity of all contributors
flexible data models that can be modified or added by contributors
automated integration of third party content
automated semantic enrichment of contributed and 3rd party content
content workflows and curation tools
content archival and citation
content licensing and a conditions of use framework
web services
ease of use

Technical issues 3 Web services (integration hacks)

Social issues 1 The community
Taxonomy as a team sport
(Community size and the community of one)
Networking effects
(quality, multi-disciplinarity and utility of data)
The rise and rise of the “amateur”
Cost of professionals
Top down and bottom up organization
(how to partition the community)
Bottom up benefits, low transaction costs
(social information flows, motivation and relations self organize the group)
Support epistemological richness
Collaborative output, peer review, credit
(incentives)

Social issues 2 Nationalism / Politics
Convention on Biological Diversity, 1992
Biodiversity does not respect national boundaries
Biodiversity questions do not respect national boundaries
Funding is (usually) national / regional
Benefits are expected to be national
Often don’t match the questions we want to address
Politics amongst researchers and institutions (e.g. EDIT and Lifewatch)
Good politicians and not always good scientists

Social issues 3 Incentives
Article citation (most common method of peer recognition)
Influences authors employment, reputation and research opportunities
Traditional metrics of scholarly activity (no. papers, impact factor, H-Index)
Taxonomy is not usually high impact, but has a long half life
High cost of traditional publication (unaffordable to authors & libraries)
Lessons from Zootaxa (low cost, high volume) and Wikipedia (highly linked)

Social issues 4 Licensing
Mickey mouse, copyright and 1923
Copyright transfer agreements
As of 2009 half of all taxonomic treatments are in copyright
Publications on ants

Social issues 4 Licensing
Who owns your work (your employer?)
Branding and credit
Creative Commons
Open Access
Open Science (making science more accountable)

Social issues 5 Human Computer Interactions

Technical solutions & social models Current options for writing the Encyclopedia of Life
“ New” scholarly publishing (semantic enrichment of publications)
One database to rule them all - the Common Data Model (CDM)
EOL.org, ToL.org & related initiatives
Wikipedia / Wikispecies
Scratchpads / LifeDesks

Encyclopedia of Life (EOL) “ A web page for every species ” http://www.eol.org/
A web page for all 1.8M species
Multi-institution collaboration
$50m funding (5 years)
- MacArthur and Sloan Foundations
Megascience mashup
- Aggregating data from the web
10 years to complete
- First draft 2008, “finished” 2017!
Multiple audiences
- Science & outreach

Encyclopedia of Life (EOL) “ A web page for every species ”
First draft 27 Feb. 2008
- 24 “exemplar” pages - 30,000 detailed pages (fish & amphib.) - 1 million “stubs” (names & links)
Huge interest
- 11.5 million hits in first 5 hours - 500+ press articles - Pages unavailable for first two days! - Growth (needs 1,000 spp. per day)
Much praise but growing criticism
- Quality vs. quantity of information - Authoritative “vetting” process - Credit for “authors”
Eight more years to go
- Get more content online - Better tools to engage more people

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

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

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

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

+Administration -Change your site information -Change you front page -Change your logo -Activity and access logs +Backup -Backing up your data -Restoring your data +Bibliography -Creating a record -Importing from a ref. manager -Exporting to a reference manager +Blog -Creating and adding a blog +Custom Content -Defining a CCK -Importing from a spreadsheet -Creating a custom view +Fileshare -Creating and using a fileshare +Forum -Altering the forum settings -Creating a container for a forum -Creating a new forum -Creating a new topic inside a forum +Groups -Creating a group -Subscribing to a group +Image -Uploading & basic annotation -Linking image & location records -Linking image & specimen records -Linking image & publication records -Overlay annotations on images +Layout -Change your theme -Menus -Blocks and sidebars +Locations -Creating a record -Importing from a spreadsheet +Pages -Creating, editing, cloning & deleting -Configuring the panels template +Panels -Adding & configuring content -Creating a new panel -Citing a Panels page +Phylogeny -Adding a phylogenetic tree +Specimens -Creating a record -Importing from a spreadsheet -Linking specimen & location records -Linking specimen & pub. records +Tasks -Creating a tasklist +Taxonomy -Importing from a spreadsheet -Importing from ClassificationBank -Starting from scratch -Taxonomy manager -Displaying a classification -Adding names -Deleting names -Taxonomy & panels +Users -Your settings -Adding a new user -User roles and permissions -Adding and editing user profile fields -Logging in +Webform -Creating and using webforms What can Scratchpads do? In summary:

What can Scratchpads do? Visual taskguide

Current Scratchpads Ants Bees Beetles Big-headed flies Birds Blackflies Ciliates 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 Termites Triticid grasses Weevils Wood Ferns Sulawesi Ferns Stick insects Sites: 130+ Users: 1500+ Pages: 170k Since March 2007

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

European Mosquito Bulletin (ISSN 1460-6127), Phasmid Studies (ISSN 0966-0011) ( submission, review, & dissemination of articles ) eJournals 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

GBIF, Zootaxa, Threatened Plants of the World (Kew), BarCoVer (DNA Barcoding) & more ( space for data collection, services, discussion, & organization ) Societies & Organizations Scratchpad applications A multipurpose, flexible technology ZOOTAXA A rapid international journal for animal taxonomists ISSN 1175-5326 (Print Edition) & ISSN 1175-5334 (Online Edition)

How do Scratchpads work? Getting a Scratchpad http://scratchpads.eu/apply
Biological focus
Agree to T&C’s (click-thru)
CC license “by-nc-sa”
Requirements
Maintainer
Scope/Mission/API Keys
(Sub)domain name
Application Content
Unrestricted (overlapping)
No branding (focus on authors)
Value added

Using a Scratchpad How do Scratchpads work?
User categories (maintainer, ed. contrib.)
Public / private content (flexible groups)
Admin. page (site settings & behavior)
Management
Content types (biblio, maps, “page” etc)
Forms, managers, Excel, EndNote etc
Custom content (add or extend data types)
Data Input Tagging (indexing)
Taxonomy terms (2M +)
Multiple classifications
Auto-tagging

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

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

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

Indexing data to make it findable How do Scratchpads work?
Tagged data can be
presented differently
For example as part of
a traditional bibliography
Or as small windows
or “panels” of data

Integrating data & “publishing” in a Scratchpad How do Scratchpads work? Types of Scratchpad Panel… Taxonomic hierarchies Files and documents Phylogenetic trees Customized content Specimen records Photographs & illustrations Personalized instructions Common names Bibliographic literature Built with “tagged data”

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

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

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

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

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

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

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

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

Questions?

Scratchpad management Scalable & sustainable technology 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 ) Hardware, software & user support

Writing The Encyclopedia Of Life (not EoL.org)

by Vincent Smith

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