Biodiversity Data Journal 2: e1079
doi: 10.3897/BDJ.2.e1079
Software description 
The Encyclopedia of Life v2: Providing Global
Access to Knowledge About Life on Earth
Cynthia S. Parr , Nathan Wilson , Patrick Leary , Katja S. Schulz , Kristen Lans , Lisa Walley , 
Jennifer A. Hammock , Anthony Goddard , Jeremy Rice , Marie Studer , Jeffrey T. G. Holmes , Robert
J. Corrigan, Jr.
† National Museum of Natural History, Smithsonian Institution, Washington DC, United States of America
‡ Marine Biological Laboratory, Woods Hole, MA, United States of America
§ Smithsonian Institution, Washington, DC, United States of America
| Harvard University, Cambridge, MA, United States of America
Corresponding author: Cynthia S. Parr (parrc@si.edu)
Academic editor: Ed Baker
Received: 19 Mar 2014 | Accepted: 24 Apr 2014 | Published: 29 Apr 2014
Citation: Parr C, Wilson N, Leary P, Schulz K, Lans K, Walley L, Hammock J, Goddard A, Rice J, Studer M,
Holmes J, Corrigan Jr. R (2014) The Encyclopedia of Life v2: Providing Global Access to Knowledge About Life
on Earth. Biodiversity Data Journal 2: e1079. doi: 10.3897/BDJ.2.e1079
Abstract
The Encyclopedia of Life (EOL, http://eol.org) aims to provide unprecedented global
access to a broad range of information about life on Earth. It currently contains 3.5 million
distinct pages for taxa and provides content for 1.3 million of those pages. The content is
primarily contributed by EOL content partners (providers) that have a more limited
geographic, taxonomic or topical scope. EOL aggregates these data and automatically
integrates them based on associated scientific names and other classification information.
EOL also provides interfaces for curation and direct content addition. All materials in EOL
are either in the public domain or licensed under a Creative Commons license. In addition
to the web interface, EOL is also accessible through an Application Programming Interface.
In this paper, we review recent developments added for Version 2 of the web site and
subsequent releases through Version 2.2, which have made EOL more engaging,
personal, accessible and internationalizable. We outline the core features and technical
architecture of the system. We summarize milestones achieved so far by EOL to present
results of the current system implementation and establish benchmarks upon which to
judge future improvements.
† ‡ ‡ § ‡ ‡
§ ‡ ‡ | |
§
© Parr C et al. This is an open access article distributed under the terms of the Creative Commons Attribution License (CC BY
4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are
credited.
We have shown that it is possible to successfully integrate large amounts of descriptive
biodiversity data from diverse sources into a robust, standards-based, dynamic, and
scalable infrastructure. Increasing global participation and the emergence of EOL-powered
applications demonstrate that EOL is becoming a significant resource for anyone
interested in biological diversity.
Introduction
Biodiversity science has produced hundreds, if not thousands, of isolated database
resources (Chavan and Ingwersen 2009, Page 2009, Lapp et al. 2011) in addition to a
markedly diverse landscape of journals (Krell 2002). Though a growing number of projects
recognize the value of and help connect their resources to global hubs (e.g. Gaiji et al.
2013, Roskov et al. 2014, Smith et al. 2011) many do not (Parr et al. 2012). Moreover, the
value of open access, management of information overload, and engagement of the public
is increasingly recognised (Wilson 2003, Goddard et al. 2011, Wheeler et al. 2012,
Patterson et al. 2014).
The Encyclopedia of Life (EOL, eol.org) is an online database aiming to document all life
on Earth. Globally and taxonomically comprehensive, EOL serves descriptive information
and media (images, videos, sounds, maps) about biological organisms. While the modern
concept of EOL was proposed by E. O. Wilson (Wilson 2003), it leverages earlier efforts
such as the Tree of Life Web project (Maddison et al. 2007) and All Species Foundation
(Blackmore 2006). The Smithsonian Institution leads EOL’s international consortium, which
includes academic, government, and non-governmental institutions (Encyclopedia of Life
2012). Harvard University and the Marine Biological Laboratory host the Learning +
Education (L + E) and Bioinformatics working groups, respectively.
EOL’s focus on description and illustration complements several related global efforts. The
Catalogue of Life Partnership (CoL, Roskov et al. 2014) focuses on a comprehensive
hierarchy of biological names. Global Biodiversity Information Facility (GBIF, Gaiji et al.
2013), focuses on primary biodiversity data – information on museum specimens, field
observations, and results from experiments. The International Nucleotide Sequence
Database Collaboration (INSDC, Benson et al. 2013), focuses on molecular genetic data.
Like these initiatives, EOL was conceived in response to increasing demands for
biodiversity information from scientists, policy makers, educators, formal and informal
learners, and the general public. EOL integrates content from many sources but accepts
and serves only materials in the public domain or explicitly licensed for re-use under
Creative Commons licenses. EOL shares all content it collects with other projects by
making it available for download through an Application Programming Interface (API). All
new software developed for the project is open source and is supported by an open source
software stack.
The task of documenting all life is vast, perhaps too vast for the relatively small community
of formally-trained biodiversity experts (Wilson 2003, Wheeler et al. 2012). EOL has
therefore put a strong emphasis on providing a platform for the collaboration of those
2 Parr C et al.
experts and biodiversity enthusiasts without formal training. EOL is a Content Curation
Community (Rotman et al. 2012a) rather than a wiki, as it combines aggregation, direct
contribution, and curation processes. The integrity of individual contributions is always
preserved, and attribution to original sources as well as information about review status are
prominently featured in both the human and the machine interfaces to the site.
EOL’s first phase established a basic content aggregation and curation infrastructure with
the original website launching in 2008 (Schopf et al. 2008). The second phase made
improvements to make EOL more engaging, personal, accessible, and internationalizable.
Version 2 was released in September 2011.
In this paper, we review recent developments added for Version 2 and subsequent
releases through Version 2.2. We outline the core features and technical architecture of the
system. We summarize milestones achieved so far, both to present results of the system
implementation and to establish baselines upon which to judge future improvements and
comparisons with other systems. Finally, we discuss the significance of the Encyclopedia
of Life to the landscape of biodiversity informatics.
Project description
Design description: 
Page redesigns
EOL Version 2 involved a complete redesign of page styles to be more personal and
engaging. In addition to the “March of Life” (a changing set of images linked to selected
EOL pages), the homepage (http://eol.org, Fig. 1) now features recent activity from the site,
better navigational links, and a more prominent search box. “Taxon Pages,” which provide
access to all the information associated with a particular biological taxon (species, genus,
family etc.) were completely revised to follow a tabbed paradigm. The default tab is an
Overview that shows a sample of the kinds of information available on other tabs (Fig. 2).
The Overview highlights a brief text summary (where available) for each taxon as well as a
sample of multimedia: a classification, a map, recent discussions, and a few of the EOL
Communities and collections that include the taxon (see below). The Overview tab
becomes especially important as some pages accumulate not only rich content but also
activity by users and curators.
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 3
Figure 1. 
EOL v2 Homepage.When a member is logged in, the upper right corner of the page features links
to member profile, personalized newsfeeds, and other information. Below the site search box, the
"March of Life" thumbnails provide links to a sample of taxon pages drawn at random from pages
above a minimal richness threshold. Two columns then feature EOL-related news items and an
overview of recent community activity, followed by selected site statistics with a link to more
detailed statistics over time. The site footer provides quick access to gateway pages (see below)
and other site documentation.
Figure 2. 
The Overview tab is the default view of an EOL taxon page. It features a sample of images,
including a map, if available, a taxon hierarchy with links to other pages, a brief introduction to the
taxon (if available), an activity feed, and links to relevant collections and communities.
4 Parr C et al.
Comments and newsfeeds
Commenting by users was available in the first version of EOL, but it has become a more
central feature in EOL Version 2. Comments are now displayed much more prominently
and are incorporated into EOL Newsfeeds, which also aggregate user actions relevant to
the topic of the newsfeed. Newsfeed topics include users, taxa, collections and
communities. EOL members (users who register for accounts on the site) are notified of
responses to their comments and actions, and email notifications from newsfeeds can be
customized in a preferences panel. The new EOL commenting system resulted in a roughly
4-fold increase in the rate of commenting compared to Version 1.
Text and link contributions
With the addition of a WYSIWYG editor to the existing text contribution interface, the
authoring of taxon descriptions in the EOL interface has become easier in Version 2, and
over 7,000 articles have been contributed in this way. In addition, we have introduced a link
object so that contributors can submit well-described links to external resources; these are
found on the Resources tab.
Communities and collections
EOL Version 2 introduced the ability for members to form communities and build collections
(of taxa, of image objects, of other collections, etc.) on EOL, as described more fully below
(Implementation). EOL collections allow users to collaborate on projects and to annotate
and arrange EOL content from a personal point of view. Since the content of collections is
available through the EOL API (see Application Programming Interface section below),
they can be employed to organize EOL content for use by other applications. This
collection-making facility likely is the most powerful new EOL feature; users can add value
to the content by organizing it, and software developers can build on this value.
Hotlists
Most of the 1.9 million species described by science (Chapman 2009) are completely
unknown to all but a handful of specialists. While it is important that these organisms be
adequately represented in EOL, content development efforts focus on taxa that are of
highest interest to EOL target audiences. To inform this content strategy, we compiled a
series of taxon collections (“hotlists”) that cover commercially valued species (food,
medicine, materials), rare and endangered species, invasive species, parasites and
diseases, model organisms, and charismatic species. Content progress is continually
assessed for the comprehensive hotlist comprising more than 90,000 taxa, and work with
content partners is prioritized, in part, based on their potential to enrich pages of hotlist
taxa.
Presentation layer redesign
The EOL Version 2 redesign included a complete rewrite of EOL’s presentation layer with
the goal of delivering content in meaningful ways to the widest possible audience
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 5
regardless of the recipient's device, ability or location. The structure, style and client-side
behavior components of each page were separated and rewritten using progressive
enhancement techniques (Champeon 2003). We adhered to best practices for document
structure semantics (e.g. <h1> for page titles) to improve compatibility across devices such
as screen readers and to lay the foundation for accessibility, search engine optimization,
and internationalization.
Accessibility and search engine optimization
Design and architectural changes meet the World Wide Web Consortium (W3C)
recommended Web Content Accessibility Guidelines (WCAG) 2.0 (Termens et al. 2008).
While some adjustments were made purely for the benefit of accessibility, such as an
extension of the EOL color scheme to include better color contrast ratios, the majority of
accessibility improvements were carried out in conjunction with search engine optimization
due to overlaps between the requirements of screen readers and web crawlers. A Sitemap
was generated to instruct search engines which pages are recommended to be indexed.
The sitemap was intentionally kept small and designed to feature the most useful pages to
maximize the benefit of search engine crawlers. For example, links to Taxon Overview
pages are included in the sitemap, but not links to other Taxon Page tabs. About 4 million
pages are included in the sitemap (instead of more than 60 million if all tabs were
included). This work has had the concrete result of raising the overall Google PageRank of
the site (Page et al. 1998).
Internationalization and localization
In partnership with Bibliotheca Alexandrina, the EOL interface system (menus, controls,
feedback messages, etc.) was fully internationalized. This work, combined with the
separation of structure and style, has allowed the site to support the right to left layout
needed for some non-Latin languages such as Arabic. Translation of site elements into
specific languages was often accomplished by EOL global partners, e.g. Spanish by Costa
Rica's Instituto Nacional de Biodiversidad and Simplified Chinese by the Chinese Academy
of Sciences. The abstraction of interface strings has also enabled a partnership with the
TranslateWiki platform, which supports interface translation by volunteers into over 120
languages. Once a language reaches a translation threshold of 75%, it is added to the
menu of supported languages on EOL. This process has resulted in support of 16
languages in addition to English, with active development continuing for several more. EOL
currently displays only text object content that matches a user's preferred language setting,
but provides links to content available in other languages. Following these links changes
the language setting. The goal is to avoid rendering multiple languages on the same page.
Gateway pages and podcasts
To better support beginning users, EOL now provides pages on general topics such as
“What is biodiversity?” and introductory pages to major groups of organisms. Some of
these pages are adapted from partner projects such as the Encyclopedia of Earth or the
Animal Diversity Web (Myers et al. 2013). These pages now appear in the footer on every
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EOL page. They provide orientation to a topic and suggest internal and external links. In
addition, the Harvard Museum of Comparative Zoology (http://www.mcz.harvard.edu/)
sponsors the EOL One Species at a Time podcast series. These are five-minute CC-BY
licensed stories for classroom learning hosted at http://podcast.eol.org/podcast and
appearing on relevant EOL pages.
Funding: Support was provided by John D. and Catherine T. MacArthur Foundation
(93466-0 amendment to grant 06-89123-000-GEN), Alfred P. Sloan Foundation
(2009-6-076), Smithsonian Institution, Marine Biological Laboratory, and Harvard
University.
Web location (URIs)
Homepage: http://eol.org
Wiki: http://wiki.eol.org
Blog: http://blog.eol.org
Technical specification
Programming language: Ruby on Rails, PHP
Service endpoint: http://eol.org/api
Repository
Type: Git
Usage rights
Use license: Other
IP rights notes: Third-party content copyright remains with rightsholders. All content is
either in the public domain or licensed for re-use with Creative Commons licenses. All but
non-derivative ND licenses are accepted for third-party content (see EOL Policy). User-
generated content (e.g. comments, annotations in collections) is CC-BY licensed according
to the Community Conditions and Comment policy. All EOL-generated source code is
available under the MIT License.
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 7
Implementation
Implements specification
Core system features
Fig. 3 provides a conceptual overview of how most information on EOL is assembled.
Names infrastructure
Resource documents made available by content partners define the text and multimedia
being provided as well as the taxa to which the content refers, the associations between
content and taxa, and the associations among taxa (i.e. taxonomies). Expert taxonomists
often disagree about the best classification for a given group of organisms, and there is no
universal taxonomy for partners to adhere to (Patterson et al. 2008, Rotman et al. 2012a,
Yoon and Rose 2001). As an aggregator, EOL accepts all taxonomic viewpoints from
partners and attempts to assign them to existing Taxon Pages, or create new Taxon Pages
when necessary. A reconciliation algorithm uses incoming taxon information, previously
indexed data, and assertions from our curators to determine the best aggregation strategy.
This taxonomic reconciliation process involves comparing the preferred scientific names,
synonymy, and taxonomy from an incoming resource document to the same information
from all previously indexed resources. It is designed to merge taxa based on synonymy (for
example when the preferred name of one taxon is in the synonymy of another) and keep
taxa separated that are homonyms (the same scientific name appearing in two distinctly
Figure 3. 
High-level data flow from content partners into EOL. Content partners make available EOL data
transfer documents (resource documents) that are periodically indexed by EOL. These provide
names, name hierarchies, and associated data objects to EOL. EOL aggregates these data and
presents them on Taxon Pages. The content assigned to a Taxon Page can be reviewed, hidden, or
reassigned to other Taxon Pages by EOL Curators.
8 Parr C et al.
different clades like Morus which is a genus of both birds and plants). Rank information is
important to the reconciliation process as it permits the differentiation of cross-rank
homonyms. For example, there is a genus of seaweed known as Vertebrata and the same
name is used for the group of all organisms with backbones. Reconciliation is an
automated process and can make incorrect decisions, so there is a series of operations
EOL curators can perform to manually resolve taxonomic and typographic inconsistencies.
Ultimately, multiple taxonomic views indexed by EOL are displayed in the Names Tab of a
Taxon Page, and EOL curators can choose a preferred taxonomy to display for browsing
on the Overview tab.
Partners can provide common names and synonyms as part of their taxon definitions.
Synonyms are used by EOL to help determine which taxon definitions should be
aggregated into the same Taxon Pages. They are also valuable search keywords that help
users find the pages they are looking for.
Previous studies suggest that common names are often more valuable for search than
scientific names or synonyms (Parr et al. 2004). Common names vary by language and
region and as such are an important component of an internationalized EOL. As a user
changes their browsing language, common names shown throughout the site will change
to match the user’s preferred language. Curators have control over which common names
are shown as preferred for each taxon in each language, and can add new common
names when needed.
Taxon pages
Taxon Pages are the main organizational unit of EOL, presenting a standardized page for
every taxonomic entity that the system recognizes. Each Taxon Page has 9 tabs:
Overview, Details, Media, Maps, Names, Community, Resources, Literature, and Updates,
plus an additional tab for EOL curators, Worklist. The default tab, Overview (Fig. 2), offers
a sample of information available on the other tabs and links to more detailed information.
The Details, Media, Maps, Names, Resources, and Literature tabs display aggregated,
topical information about the taxon as provided by EOL partners and members, including
interactive GBIF occurrence maps and references from the Biodiversity Heritage Library,
BHL (Norton 2008). BHL runs TaxonFinder on its documents to find biological name strings
(Wei et al. 2010), which EOL then indexes. Any time the BHL tab is visited on a Taxon
Page the system offers links to all pages in BHL that include any of the scientific (not
common) names of the taxon page.
The Community tab offers information about what EOL Communities and Collections are
interested in the taxon, and who the curators of the taxon have been. The Updates tab lists
all of the comments on the Taxon Page as well as statistics about the content on the page,
including the page’s Richness Score (see Richness score below).
Data objects
Images, text, videos, sound files, and maps provided by content providers and EOL
members are referred to as “Data Objects”. Data Objects are the building blocks of EOL.
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 9
Taxon Pages are populated through the aggregation of relevant Data Objects from multiple
sources. Each Data Object also has its own dedicated page that contains information
about the taxon (or taxa) the Data Object is associated with, license information, all
available source and attribution information, a tool for rating the Data Object, links to other
versions of the Data Object, comments on the Data Object, and, for non-text objects, a text
description (caption) if available. These Data Object Pages are accessible through links
from EOL Taxon Pages and through their own unique URLs (e.g. http://eol.org/
data_objects/21942847). EOL curators have access to tools on the Data Object Page to
control visibility and trusted status, and on image Data Object Pages, tools to crop images
to create versions of thumbnail images that are shown throughout EOL. While curators can
hide a Data Object or indicate its trusted status, the content itself can only be changed or
updated by the provider.
Darwin Core Archive support for content ingestion
Initially, EOL harvested resource documents formatted according to an XML transfer
schema drawing from standards such as Dublin Core, Darwin Core (Wieczorek et al.
2012), and TDWG Species Profile Model (SPM). We also accepted Excel spreadsheets
based on a template incorporating these standards. Beginning in May 2012, EOL began
accepting datasets formatted as Darwin Core Archives (DwC-A), a biodiversity informatics
community standard (Baker et al. 2014). For details of the EOL implementation, see http://
eol.org/info/cp_archives. XML datasets continue to be supported, but we recommend that
all new partners provide DwC-A. Darwin Core Archives are very extensible and flexible,
with a meta.xml file providing information about the elements included in flat tabular files
and instructions on how machines should read them. Providers can design their DwC-A to
suit more than one consumer or to adhere to content standards such as Plinian Core. They
are readily understandable by scientists more comfortable with tabular formats; EOL’s new
spreadsheet template is very similar to a formal DwC-A.
Building the content
Most EOL content is aggregated via content partner tools (designed for projects that have
large amounts of content to share) or added directly to the web site by users. Any EOL
member can add and manage an EOL content partner account through their member
profile (see http://www.eol.org/cp_getting_started). After supplying basic information about
their project, users register one or more resource documents that contain the information
they want to share. Resource documents may be customized exports from a database,
they may be created by programs that parse web pages or call web services, or they may
be manually assembled spreadsheets. Some resources are the result of newly published
marked-up taxonomic treatments (Miller et al. 2012, Penev et al. 2010) while others are
taxonomic treatments from legacy literature (Plazi.org). A resource can be a checklist of
taxon names, or it can be a classification with or without references. Most resource
documents include text objects or point to multimedia objects and provide their associated
metadata. EOL staff members are available to assist in preparing resource documents and
must approve the first publication of the resource on EOL. After that, content may be
harvested and automatically published on a schedule in order to maintain synchrony with
10 Parr C et al.
source databases. Each resource that is harvested generates an automatically updating
EOL collection (see Communities and collections below) as well as a panel of traffic
statistics that are made available to partners.
Currently, EOL members can add text objects, also known as articles, directly to EOL using
the “Add an Article” button on the Details tab. Multimedia objects cannot be uploaded
directly to EOL but must be added through partners such as Flickr, Wikimedia Commons,
iNaturalist, Vimeo, YouTube, and Soundcloud.
Richness score
EOL has developed a Richness Score for taxon pages (Fig. 4) that is inspired by
community ecology’s diversity indices (Peet 1974 among others) which are rooted in
information theory. Ranging from 0-100, the Richness Score combines information on the
number and review status of text and multimedia objects, the number of words and distinct
topics of text objects, and the diversity of sources. These factors are assigned weights and
limits (having 200 images may not make a page much more rich than having 25 images).
To develop the richness algorithm, we sampled dozens of pages and had staff assess
them for their gestalt “richness” based on their own criteria. Then we compared those
scores to scores generated by the algorithm, and iteratively changed weights until we
achieved a set of weights that appeared to reflect human perception of “richness.” The
algorithm may be occasionally adjusted based on user input. The Richness Score and its
components are listed in the Updates tab of each Taxon Page and is also available through
the API. It is used to prioritize pages for display in search results, API calls, and the rotating
‘March of Life’ slideshow on the EOL home page. A page with a score of 40 is currently
considered "rich."
Figure 4. 
The EOL richness score is the sum of three weighted components: breadth, depth, and diversity.
Breadth considers the different media types of information objects (including the number of different
subjects available for text), depth considers both average and total number of words in text objects,
and diversity considers the number of different sources of information, or providers. Normalized
object values are scaled to be between 0 and 1 and put on a log-based scale such that the first
objects counts more than the second up to a chosen limit at which point the value is 1 and
additional objects of that type have no impact on the richness. The final score is multiplied by 100,
so that it ranges from 0 to 100. For more detailed information, see http://eol.org/info/
richness_score.
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 11
Communities and collections
EOL Communities provide a way to group users. The primary value of this feature at the
moment is to share the management of different EOL Collections. They also provide a
simple forum through the associated newsfeed. Collections provide a way for users to
organize, annotate, and share the content on the site. Collections may range from species
lists for local areas (e.g. Florida Native Plants) to lists of homonyms (Homonyms on EOL)
to content collections for education or entertainment (e.g., X-ray Vision: Fish Inside Out).
Many different types of items within EOL can be collected including Taxon, Image, Article,
User, Community and even other Collection pages (e.g., a collection of video collections).
Collections can be viewed as a visual gallery, a simple list, or an annotated list and can be
sorted in a variety of ways including by Richness Score. Annotation fields allow Collection
managers to provide notes, references, or sort fields for each item in the collection. By
default, an EOL Collection is managed by the user who creates it. However, any manager
can share management privileges with other EOL members or communities.
Curation
EOL provides curation tools for volunteer data curators. All curators must register under
their real names. To facilitate participation of EOL members with different levels of
expertise, three different curator levels are distinguished. As of April 2014, almost 300 EOL
members have registered as assistant curators and over 1,300 members have been
approved as full or master curators.
The Assistant Curator status requires no qualifications and conveys limited curation
powers. Assistant Curators can add taxon associations to data objects (e.g., to identify
organisms shown in an image), but these associations are marked as "unreviewed" until
confirmed by a Full Curator. Assistant Curators can also add common names, select
preferred common names, select exemplar images and articles, and crop image
thumbnails. They are encouraged to add text and help find problems that Full Curators can
resolve. Full Curators must have credentials (e.g. relevant professional affiliations,
publications, membership in a professional association). In addition to the powers of
Assistant Curators, they can trust or untrust text or multimedia objects and select preferred
classifications for taxon pages. Master Curators can manage taxon concepts (overriding
the automated reconciliation process by merging or splitting classifications featured on a
given taxon page) and delete comments that do not adhere to EOL community policies.
Untrusted content is hidden from public view but still visible to Full and Master Curators for
further review. Curation actions and comments are reported to content providers
(Feedback, in Fig. 3) so that the problem can be resolved at the source. In the case of
multiple curation actions on a single object, name or classification, the current review or
priority status reflects the decision of the most recent curator. The display sequence of data
objects on EOL pages is also affected by user ratings (on a 1 to 5 scale) which can be
submitted by any EOL member. Object ratings are averaged across all raters, with ratings
by curators carrying more weight. Curators can work directly on EOL taxon and data object
pages, or they can use the EOL Worklist tab which provides an interface for to quickly find
12 Parr C et al.
taxon-specific content that is unreviewed or recently added or to filter by particular
providers like Wikipedia or Flickr.
Search
The EOL website search is configured to find scientific names and common names, with
preference in search result ordering given to preferred scientific names (names that have
been manually selected by curators as “preferred” for a taxon) first, followed by preferred
common names, and synonym. EOL search also indexes Communities, Collections, EOL
members, Data Objects, and EOL documentation pages, and search results can be filtered
by these categories. If there is a best result, the system takes the user directly to that taxon
page, with an option to return to the search results page to view other results.
API
The EOL Application Programming Interface (API) allows content indexed by EOL to be
easily accessible to other websites and software developers. Through the API, applications
can search EOL Taxon Pages, fetch page metadata such as names, images and text, and
access hierarchy and collection information. The latest versions of API methods allow data
to be returned in either XML format or the simpler JSON format. Method documentation
has been improved and internationalized, and now includes forms to help users test the
methods and their various parameters by interactively showing the responses. An example
of a website using the EOL API to feature EOL data within their own site is the Smithsonian
National Museum of Natural History’s Species of the Day widget. This widget is created
using the API to draw data from a custom EOL Collection. Other examples include various
games, visualizations, and other sites that re-use EOL content.
Technical architecture
EOL Version 2 provided an opportunity to significantly improve the hardware and software
infrastructure of EOL. The entire software and hardware stack supporting the serving of
eol.org moved to the Research Computing group at Harvard University while remaining
managed by the EOL Operations team at the Marine Biological Laboratory. The new
architecture introduced KVM-based virtual machines to the infrastructure, allowing a more
efficient use of resources and faster deployment of new infrastructure services to support
the hosting of the site (Fig. 5). The open source tools Chef and Capistrano were used to
create a new mechanism for deploying the application based on data stored in Github. 
Resque is used to managed the email notification and download queues.
The EOL technical team uses a modified version of the Scrum software development
framework (Schwaber 2004) to plan, develop, and improve EOL features. More information
about the specific approach that the EOL team uses is available at http://eol.org/info/
development.
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 13
Audience
EOL has a worldwide audience including experts, enthusiasts and casual visitors. About
39% of user sessions originate in the United States and more than 47% of user sessions
originate in countries where English is not an official language. Starting with v2, visitors
registering to become EOL members were invited to select one or more audience
categories to describe themselves. Of 6,410 people who self-identified by 18 April 2014,
47% chose "enthusiast", 36% chose "student", 20% chose "educator", 18% chose "citizen
scientist", and 20% chose "professional scientist". However, this distribution may not reflect
the more than 73,000 current EOL members or the vastly larger number of visitors who
never register or who encounter EOL content primarily via social media channels.
Experts and enthusiasts are encouraged to participate in EOL as content curators. As of
April 2014, almost 300 EOL members have registered as assistant curators and over 1,300
members have been approved as full or master curators.
At least in North America, the formal education audience is an important demographic for
EOL. We see from Google Analytics that there are increases in the use of the site when
most schools are in session. The EOL Learning & Education group also actively posts
information on about 15 listservs, including the National Science Teachers Association
(NSTA), Scuttlebutt (NOAA Marine Education site) and the Ecological Society of America's
EcoLogic Listserv.
Figure 5. 
Software stack for the production EOL web-servers. The vast majority of the code written
specifically for EOL is in Ruby – which handles the website and the API – and PHP, which handles
the content import process and provides some administrative interfaces.
14 Parr C et al.
Additional information
Milestones
EOL’s growth in overall information, provider resources, and membership has steadily
increased (Fig. 6). EOL launched in 2008 with information on approximately 40,000 taxa. In
2012, EOL passed a significant milestone: more than 1 million pages had at least some
text or multimedia content. Based on data through July 31, 2013, these pages now contain
more than 3,192,609 text articles and 1,812,295 image objects, all showing explicit expert
review status (especially important for content from large crowd-sourced partners such as
Wikipedia or Flickr). About 112,000 pages have a Richness score of 40 or higher (out of
100), with 50% of the 90,000 hotlist pages meeting this threshold.
Still, most EOL pages remain without content, i.e., EOL provides nothing but a taxon name,
and in some cases author information and a reference. Overall, EOL has indexed about
3.5 million taxa. This represents most of the 1.9 million extant (Chapman 2009) and
250,000 fossil species (Prothero 2013) described by scientists, as well as higher taxa
(genera, families, orders, etc.), infraspecific taxa (subspecies, varieties, etc.) and hybrids
(mostly in plants and some vertebrates), taxa whose names will eventually turn out to be
synonyms (Alroy 2002, Joppa et al. 2011, Stork 1997), and more than 700,000
provisionally named taxa from molecular genetic data sources like the National Center for
Biotechnology Information (NCBI) and Barcode of Life (BOLD).
Closer examination indicates that EOL has an uneven distribution of content across
languages, licenses, and topics. While EOL has vernacular names in 163 languages (Table
Figure 6. 
Growth in Encyclopedia of Life from 2008-2013. A. Taxon pages with content (at least one text
article, image, map, video, or sound) (Suppl. material 1). B. Published resources (content import
files). A provider may submit more than one resource file, for example when providing different
kinds of content (Suppl. material 2). C. Registered EOL members (Suppl. material 3).
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 15
1), it has text objects in only 17, with the vast majority (97%) still in English (Table 2). While
a significant amount of text content is shared under open licenses as defined by http://
opendefinition.org (44%, public domain, CC-BY, CC-BY-SA), providers of multimedia
content still prefer the more restrictive licenses that EOL permits (Fig. 7). The most
frequent topic of EOL text articles (objects) is “Distribution.” Combined topics that cover
multiple subjects, such as brief summaries and comprehensive descriptions, are also
frequent (Table 3).
Language Common Names
English 690163
Spanish 114579
Chinese 87643
French 85973
German 69945
Japanese 51432
Portuguese 42497
Italian 39264
Czech 37455
Russian 35379
Danish 30775
Dutch 30775
Finnish 29785
Polish 24918
Other 280057
Language Articles
English 3096313
Spanish 58978
Chinese 11678
Arabic 4807
Portuguese 2373
Dutch 1143
Indonesian 173
French 107
Other 10180
Table 1. 
Languages of common (vernacular) names.
Table 2. 
Languages of text articles.
16 Parr C et al.
Subject Articles
Distribution 805503
Molecular Biology 434545
Combined Topics 354322
Type Information 326720
Habitat 292478
Conservation Status 144969
Threats 94140
Morphology 66571
Conservation 65618
Diagnostic Description 61512
Management 57894
Trends 57888
Size 55453
Description 49074
Associations 38677
Taxon Biology 26861
Uses 24458
Trophic Strategy 21563
Population Biology 17767
Taxonomy 16301
Ecology 15060
Reproduction 14996
Notes 14440
Migration 13991
Cyclicity 11880
Life Cycle 9759
Life Expectancy 8875
Behavior 6391
Key 6118
Diseases 4325
Use 4283
Evolution 2158
Risk Statement 2022
Look Alikes 1897
Dispersal 1649
Functional Adaptations 1438
Table 3. 
Subjects of text articles. Combined topics include Wikipedia (n = 223571), Description (n =
49074), General Description (n = 45887), Brief Summary (n = 26862) and Biology (n = 8929).
Subjects with fewer than 100 articles are not shown (Procedures, Legislation, Identification
Resources, Systematics or Phylogenetics, Development).
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 17
Genetics 1000
Growth 785
Barcode 720
Education Resources 646
Physiology 269
Cytology 129
To date, users have created more than 5,000 EOL Collections. Many collections
(approximately 35%) are for specific geographic regions and represent user-generated
checklists that could be useful for refining map queries in areas where occurrence data are
not yet available. Presence of a taxon or object in many user-generated Collections could
be used (by EOL or by others) to sort or filter search results so that they are most relevant
to user needs. Collection statistics, along with traffic statistics, could also help researchers
explore the factors that make an organism or data object more engaging to broad
audiences.
Though there is room for growth in curation activity, EOL is increasingly in a position to
improve data quality across its network of providers. In July 2013, EOL had 1,258
registered curators (250 Assistant, 1,001 Full, 7 Master) of which 163 have been active in
the last 12 months. In comparison, iNaturalist has 94 curators and the World Register of
Marine Species has 826 editors (a thoughtful analysis of curation power across projects
with different models is beyond the scope of this paper). The majority of data objects are
considered trusted (92%), most having been acquired from authoritative sources. An
average of 905 objects per month are being curated. Assistant and Full Curators have
Figure 7. 
Distribution of Creative Commons and other licenses for data objects on EOL. CC-BY =
Creative Commons Attribution license; NC = Non-commercial restriction; SA = Share-alike
restrictions. Objects with gnu-gpl/gnu-fdl licenses (3903 images and 21 text articles) are not shown.
Overall, as of July 2013, EOL has 3,192,609 text articles, 1,812,295 images, 806,664 maps, 30,366
sounds, and 10,219 videos (Suppl. material 4).
18 Parr C et al.
different patterns of activity, not surprisingly given their different access to tools (Fig. 8).
Assistant Curators have provided many non-English common names shown in Table 1. Full
Curators tend to have more rigorous rating patterns than either Assistant Curators or non-
curators (Fig. 9). A previous study found evidence that activity by curators increased
commenting activity of non-curators (Ahn et al. 2012).
Figure 8. 
Activity patterns of EOL Assistant Curators compared to Full and Master Curators. Only Full
and Master Curators can select preferred classifications and change the visibility and trust status of
text and multimedia objects. Data Object curation by Assistant Curators is limited to adding
associations between Data Objects and taxa.
Figure 9. 
Data Object rating patterns of EOL members in relation to their curator status. Five stars is
the highest rating, while one star is the lowest rating a member can give a text or multimedia object.
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 19
In the period from August 2012 through July 2013, EOL was visited by 3.7 million unique
users. About 44% of visits are from North America (including Mexico). Thirteen countries
on other continents contributed a significant number of visits.
Discussion
EOL has established its role of improving access to biodiversity information by aggregating
and standardizing descriptive information and multimedia objects currently available across
many otherwise isolated resources. It provides the infrastructure to connect both major
hubs and independent projects (Parr et al. 2012). It is well positioned to provide
connectivity and added visibility to partner projects. Visitor traffic to EOL has increased
steadily since the launch of Version 2 (see Fig. 10) and has averaged 481,000 unique
visitors/month over the past six months. It is natural that EOL should have higher traffic and
visibility than either sites designed for a professional audience (WoRMS, GBIF, BOLD,
OBIS) or sites designed for a less casual, more engaged audience (iNaturalist,
Discoverlife, Project Noah) or sites that are more narrowly focused (Fishbase, ToLweb,
AmphibiaWeb). This is reflected in the Global Rank of alexa.com, (which weighs traffic; Fig.
11) and in the Google Page Rank, (which weighs centrality, i.e., number and quality of links
pointing toward a site; Fig. 12). Successful sites specializing in charismatic fauna (eBird,
Arkive) can show higher traffic, but still have lower centrality. This is why linking back to
content providers at every opportunity is so critical to EOL's mission; the role of a high
visibility node is to connect high value, low visibility nodes to traffic that might not otherwise
find them.
Figure 10. 
Unique visitors to EOL per month, September 2011-January 2014, per Google Analytics.
20 Parr C et al.
EOL complements long-term archives and metadata registries, e.g. DataONE (Michener et
al. 2012) and Dryad (Vision 2010), by focusing on data mobilization – organizing and
providing access for new users and new uses, while maintaining source provenance and
rich attribution. It also plays an important role in aggregating images and type specimen
Figure 11. 
Global Rank for biodiversity web sites per http://www.alexa.com/, 02/26/2014. The rank is
calculated using a combination of average daily visitors to this site and pageviews on this site over
the past 3 months. Lower numbers indicate greater importance, as the site with the highest
combination of visitors and pageviews is ranked #1. Note however that Alexa rankings are known
to be subject to considerable sampling bias since they are largely based on the behavior of users
browsing with an Alexa-compatible toolbar (Lo and Sharma Sedhain 2006).
Figure 12. 
Google PageRank™ of various biodiversity websites, per http://www.prchecker.info/, 02/22/2014.
Larger numbers indicate greater importance, and webpages with a higher PageRank are more
likely to appear at the top of Google search results.
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 21
information from museum collections, essentially leveraging their specimen-level digitation
efforts for biological discovery and education. With a superset of taxa and selected
information from all of its partners, EOL has more breadth than any of its largest sources
(e.g. Gaiji et al. 2013, Costello et al. 2013, Benson et al. 2013). It is likely to be the richest
single source of taxonomically indexed CC-licensed multimedia content about biodiversity.
EOL's CC-licensing requirements have resulted in the application of such licenses to much
content that might otherwise have remained All Rights Reserved (C. Parr personal
observation) and has already fostered re-use of content by third party applications. It will
be interesting to see if the usage of NC licenses, which many find to be problematic
(Hagedorn et al. 2011) decreases or increases over time.
By taking a phased approach (phase 1 of core infrastructure and phase 2 of engagement),
EOL has successfully built a professional, usable platform at a scale appropriate to its task
of serving global biological information to multiple international audiences. Because it is
scalable, as EOL grows, its Richness Scores can be used to assess the availability and
quality of knowledge across the tree of life, especially when extended to structured data.
The scores could also enable assessment of individual contributions and standardization
(Liolios et al. 2012) and direct future investment in data capture and research.
Several challenges remain to be tackled in future phases. While there is some evidence
(growth in collections, emergence of third party applications, curator activity, user traffic) of
effective impact on and engagement by various audiences, tools for community and
curator engagement are not as successful as hoped and so they may require more tailored
experiences and effective feedback (Rotman et al. 2012a, Rotman et al. 2012b). EOL itself
may be too large and diffuse to support effective communities. To satisfy the needs of the
academic community, EOL must continue to seek better ways to provide professional,
quantitative credit for the individuals and institutions who have curated or contributed
content or functionality to the system (Liolios et al. 2012, McDade et al. 2011, Maddison et
al. 2012) we also plan to enable phylogenetic views and access to associated data in
collaboration with the Open Tree of Life project. While taxon names management has been
automated to a large extent, more work is needed to reduce the need for manual curation
and to better integrate EOL systems with relevant systems built by Global Names, i4Life,
and iPlant (Boyle et al. 2013), to name a few. Some of the 3.5 million taxon pages will
represent extinct taxa, subspecies or provisionally named taxa (many of these resulting
from dark taxa shared by GenBank, Parr et al. 2012). Other taxa are likely to be useful for
the Catalogue of Life, which has 1.4 million of the expected 1.9 million described species
(Chapman 2009).
The next phase of EOL moves beyond the limits of encyclopedic text and multimedia to
add the ability to ingest and serve highly structured data (numeric and controlled
vocabulary terms with rich semantics) about the attributes of and relationships among
organisms (Parr et al. in review). In the same way that EOL has helped to bring together
and connect text and media from isolated sources, we aggregate structured data to provide
a broad-scale view of analyzable biodiversity data. EOL’s standardized open access also
facilitates new text mining or crowd-sourcing efforts to extract structured data about
biological diversity, e.g. Thessen and Parr 2014).
22 Parr C et al.
Acknowledgements
Support was provided by John D. and Catherine T. MacArthur Foundation, Alfred P. Sloan
Foundation, Smithsonian Institution, Marine Biological Laboratory, and Harvard University.
The production hardware infrastructure for the EOL website is supported by the Harvard
Faculty of Arts and Sciences (FAS) Sciences Division Research Computing Group. We
thank all of our providers and global partners, Eli Agbayani, Tracy Barbaro, Dana
Campbell, Vitthal Kudal, Erick Mata, David Patterson, and Mark Westneat. Leo Shapiro
and Dawn Field provided helpful comments on the manuscript.
Author contributions
Conceived and designed the experiments: CSP NW BC MS. Coded the software: PL JR
LW AG. Managed data ingestion: JAH, KSS CSP PL. Provided detailed requirements and
tested the software: JAH KSS CSP JTGH MS. Performed analyses: KSS CSP. Wrote the
paper: CSP NW JAH KSS KL PL LW AG.
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Supplementary materials
Suppl. material 1: Taxa with Content
Authors: Cynthia Parr, Nathan Wilson, Patrick Leary, Katja S. Schulz, Kristen Lans, Lisa Walley,
Jennifer A. Hammock, Anthony Goddard, Jeremy Rice, Marie Studer, Jeffrey T. G. Holmes, Robert
J. Corrigan, Jr.
Data type: Comma-Separated-Values
Brief description: Taxon pages with content (at least one text article, image, map, video, or
sound).
Filename: Taxa-with-Content.csv - Download file (231.00 bytes) 
Suppl. material 2: Number of Resources
Authors: Cynthia Parr, Nathan Wilson, Patrick Leary, Katja S. Schulz, Kristen Lans, Lisa Walley,
Jennifer A. Hammock, Anthony Goddard, Jeremy Rice, Marie Studer, Jeffrey T. G. Holmes, Robert
J. Corrigan, Jr.
Data type: Comma-Separated-Values
Brief description: Published resources (content import files). A provider may submit more than
one resource file, for example when providing different kinds of content.
Filename: Number-of-Resources.csv - Download file (81.00 bytes) 
Suppl. material 3: Registered Members
Authors: Cynthia Parr, Nathan Wilson, Patrick Leary, Katja S. Schulz, Kristen Lans, Lisa Walley,
Jennifer A. Hammock, Anthony Goddard, Jeremy Rice, Marie Studer, Jeffrey T. G. Holmes, Robert
J. Corrigan, Jr.
Data type: Comma-Separated-Values
Brief description: Registered EOL members.
Filename: Registered-Members.csv - Download file (100.00 bytes) 
Suppl. material 4: License Distribution
Authors: Cynthia Parr, Nathan Wilson, Patrick Leary, Katja S. Schulz, Kristen Lans, Lisa Walley,
Jennifer A. Hammock, Anthony Goddard, Jeremy Rice, Marie Studer, Jeffrey T. G. Holmes, Robert
J. Corrigan, Jr.
Data type: Comma-Separated-Values
Brief description: Distribution of Creative Commons and other licenses for data objects on EOL.
Filename: License-Distribution.csv - Download file (301.00 bytes) 
Suppl. material 5: Curator Activity
Authors: Cynthia Parr, Nathan Wilson, Patrick Leary, Katja S. Schulz, Kristen Lans, Lisa Walley,
Jennifer A. Hammock, Anthony Goddard, Jeremy Rice, Marie Studer, Jeffrey T. G. Holmes, Robert
J. Corrigan, Jr.
Data type: Comma-Separated-Values
The Encyclopedia of Life v2: Providing Global Access to Knowledge About ... 27
Brief description: Activity patterns of EOL Assistant Curators compared to Full and Master
Curators.
Filename: Curator-Activity.csv - Download file (185.00 bytes) 
Suppl. material 6: Data Object Rating
Authors: Cynthia Parr, Nathan Wilson, Patrick Leary, Katja S. Schulz, Kristen Lans, Lisa Walley,
Jennifer A. Hammock, Anthony Goddard, Jeremy Rice, Marie Studer, Jeffrey T. G. Holmes, Robert
J. Corrigan, Jr.
Data type: Comma-Separated-Values
Brief description: Data Object rating patterns of EOL members in relation to their curator status.
Filename: Data-Object-Rating.csv - Download file (166.00 bytes) 
28 Parr C et al.