Encyclopedia of Life & the Fungi
Detailed Summary of August 14, 2008 Group Discussion held at State College, PA after
the 2008 MSA Annual Meeting
Persons Present at the Meeting:
Thomas Bruns (boletus@socrates.berkeley.edu)
Paul Cannon (p.cannon@cabi.org)
David Geiser (dgeiser@psu.edu)
David Hibbet (dhibbett@clarku.edu)
Kathie Hodge (kh11@cornell.edu)
Sabine Huhndorf (huhndorf@fieldmuseum.org)
Paul Kirk (p.kirk@cabi.org)
David Maddison (beetle@ag.arizona.edu)
Nicholas Money (moneynp@muohio.edu)
Greg Mueller (gmueller@fieldmuseum.org)
Cynthia Parr (parrc@si.edu)
David Patterson (dpatterson@mbl.edu)
Donald Pfister (dpfister@oeb.harvard.edu)
Anne Pringle (pringle@oeb.harvard.edu)
Amy Rossman (amy.rossman@ars.usda.gov)
Keith Seifert (seifertk@agr.gc.ca)
Joseph Spatafora (spatafoj@science.oregonstate.edu)
Joost Stalpers (j.stalpers@cbs.knaw.nl)
Rod Tullos (ret@eticomm.net)
Thomas Volk (volk.thom@uwlax.edu)
Nathan Wilson (nathan@collectivesource.com)
Goals of the Meeting:
•Goal 1: Critique the design of EoL fungal pages; make recommendations.
•Goal 2: Identify examples of other currently available fungal pages and web resources.
What data are available for all species, what data can be used for specific target groups?
•Goal 3: Develop a strategy for thinking through choices about species or clades that
should be a priority for EoL, and for assembling fungal species pages.
•Goal 4: Identify mechanisms for the future involvement of the world’s mycological
community.
•Goal 5: Identify mechanisms for EoL to communicate its activities to the world’s
mycologists, and enable feedback.
Summary of Discussion: Goals 1 & 2:
TAXONOMY
Catalogue of Life is the default taxonomy of EoL, but in the future a multiclassification
hierarchy will be enabled. Persons who sign up as curators for specific groups will be
able to offer different classification schemes. At the meeting, Paul Kirk gave the
taxonomy used by the new Dictionary of the Fungi (currently in press) to David
Patterson, and this was uploaded by David and will be used by EoL as of January 2010.
Pages are made up of different data objects (text, images, etc.) and individuals can decide
which objects are associated with each name – in other words, person X can use the name
Amanita occultum (not a real species) and associate a specific description and photo with
that name, and person Y can use the same photo for Amanita arcanus. Created pages will
be associated with the persons who created them; note that one species’ name may then
have more than one page.
In other words, different persons will be able to offer their own taxonomic plans. Users
will be able to personalize EoL to view a preferred taxonomy.
Obviously there is a tension between plurality/inclusivity and authority/centrality; the
consensus classification is and will be a product of back and forth discussion.
A discussion ensued as to whether the community should defer creation of EoL pages
until there is a global taxonomic consensus – the general agreement was that the
community should start creating pages now, and not wait for a global consensus.
Nonetheless, as 1) Catalog of Life is the default taxonomy of EoL, and 2) Species
Fungorum is the route for fungal species into Catalog of Life, and 3) MycoBank serves as
a registration system and respository, SHOULD the community be discussing the general
accepted protocols for developing a consensus on scientific names as new species are
described? MycoBank –>IF -> CoL?
A curator’s scope can be paraphyletic. Persons can sign up as curators now, go to
www.eol.org.
Note that data submission will be facilitated by software created by EoL, available as of
January 2009. “LifeDesk” will allow anyone to submit content and self-identify as expert,
kid, citizen scientist, etc. The goal is to make data submission as easy as possible.
AVAILABLE RESOURCES
EoL acknowledges that a majority of species (fungi, but other groups as well) are known
only from the original species description. For these, limited data are available. A species
page may contain only a name, in fact, there are already stub pages for every species
listed by the Catalogue of Life.
Pages for sequence groups will also be possible, in other words, if a species is identified
from sequence data only that species can have its own EoL page. Molecular species
pages could be a great aid to molecular ecologists, and Tom Bruns and Joost Stalpers
have started a discussion about how to give these molecular species MycoBank numbers.
Otherwise, the following resources and criteria are essential:
 High resolution images. These are crucial for identification.
 The ability to move across pages. Many sections of EoL pages are applicable to
all fungi, others to certain paraphyletic groups e.g. the mycorrhizal fungi. Data
objects should be linkable back to clades if they are apomorphies, and to the
various tips if they are paraphyletic features.
 The literature resources should be sortable, e.g. by date. This may be an issue for
the BHL and not EoL.
What is the taxonomic scope of “fungi” in EOL? Should we try to think about
mycetozoa, stramenopiles, etc.? General consensus is YES, e.g. Phytophthora should be
included. A database for Phytophthora already exists.
Resources currently available for every fungal page in EoL:
 Nomenclatural history as given by Index Fungorum (= taxonomic authority and
place of publication; this information provides the capacity to link to the BHL)
 Biodiversity Heritage Library resources
For some (most) pages in EOL:
 GBIF data
 GenBank records, although these are known to contain ca. 27% errors
 Barcode of Life records
 Some images, especially from BioPix and the New York Botanical Garden (e.g.
images of types, herbarium labels)/ Greg Mueller is the contact
 Plant Host Index; Fungi on Plants and Plant Products, USDA, Beltsville
 Culture collection information e.g. CABI, Japan World Federation of Culture
Collections, CBS, American Type Culture Collection, etc., etc./ Joost Stalpers is
the contact
Missing but would like to have it:
 Information about interactions with other species, including hosts.
Who is the priority audience for EoL? (unresolved; of course, there are multiple
audiences). For the general population, core requirements for a page should be a 200
word description plus an image.
MANY pages on fungal biodiversity already exist, however, if they are flat HTML the
information may not be easily extracted. EoL needs to create LifeDesk modules to allow
translation of content into EoL.
In this vein, we need a mycological IT committee to help website developers learn how to
make sites EoL compatible/ minable. Nathan Wilson is the contact.
Other resources to think about mining for fungal pages:
 Redlists for conservation status
 Quarantine lists from all countries (e.g., USDA for USA)
 Pathogenicity, biosafety lists--every country should have these lists
 Fungi Canadensis--now available as PDF, only, but could be shifted to more
accessible form
 CABI Crop Protection Compendium (a commercial product)
 CMI descriptions (a commercial product)
 Mycetozoa, Eumycetozoan project (images, species lists, etc)
 PubMed
 Publication abstracts
 Google Scholar
 GOLD genomes database
Many other different pages on many different species of fungi were also discussed, e.g.
pages on Trichomycetes and the Xylariaceae
Summary of Discussion: Goals 2 & 3:
What are the short-term objectives of the EoL fungal community? To create exemplar
pages?
Three kinds of pages could be created:
1. A set of pages focused on diversity across the fungal tree of life
2. A set of pages focused on a single region
3. A set of pages focused on a target genus
Exemplar pages (1.) would be useful for the general public to learn about fungal
diversity:
 exemplars may promote contributions from the general public, e.g. images
 exemplars may not be a scalable effort and may not be an effective use of effort
 exemplars could be based on already available databases for groups—and not
focus on individual species pages – this strategy may be more effective than
asking people to create exemplars from scratch. If these pages are flat HTML (e.g.
Tom Volk’s FOTM) energy should be put into developing tools to mine the pages
After exemplars are deployed, the community will need to be opportunistic, and track
enthusiasm/ activity, and move in those directions where there is activity.
In fact there are two aspects to content development:
1. importing content that exists now
2. promoting updates in the future
An alternative model would be to have EOL generate static html for web sites (e.g. Tom
Volk’s FOTM) based on information deposited at EOL by the current web managers-little enthusiasm for this?
Short-term goals are to harvest information from, e.g.:
 Tom Volk’s Fungal pages
 Rod Tulloss’s Amanita pages
 Xylariaceae pages
 Phytophthora pages
 And others?
By uploading these sites we could showcase the power of EOL to the research
commmunity (in this instance, getting away from viewing general public as the primary
users).
A template for students to create species pages is under development at Berkeley,
Harvard, Penn. State, U. Oregon and U. Wisconsin LaCrosse. The template will be
distributed broadly starting early 2009. Templates will involve MushroomObserver.org,
stay tuned for more information.
Summary of Discussion: Goals 4 & 5:
The plan is for the current group to dispand as news of EoL diffuses through the
community, and EoL becomes a global effort.
Why would individuals participate? Curators will be called editors on EoL pages, which
should enable individuals to receive credit for the pages they coordinate. Curators will
also gain exposure for themselves and their fungi, and be able to spark interest and
disseminate information via EoL.
Access to EoL software may enable persons to organize and present personal data to the
global community, and as more and more data become available EoL may itself become
a source of metadata.
Coordinating EoL and ToL outreach efforts is a priority.
Groups that could be used to communicate about EoL and ToL:
Inoculum/ MSA website
International Mycological Association
Asian Mycological Association
Australasian Mycology group
ISHAM and other medical mycology groups
Lichenologists, ABLS
International Association of Lichenologists
Indoor air quality groups/Aerobiology groups
International Commission on Indoor air fungi--Rob Sampson
Russian Society of Protistology
Mushroom Observer
Meetings/organizations:
Latin American Mycological Congress, Argentina, Nov. 2008
MSA 2009 (with BSA)
Bionet International
NAMA foray (Tom Volk is the contact)
Plant pathology societies--APS mycology committee
EoL could also host a blog about the development of fungal pages, but how to
manage/respond to a blog? What would be the editorial policies?
[A final note: this initial meeting was constrained by the limited funding available for
travel, etc. EoL aims to be an international effort and has established an Institutional
Council to provide advice on reaching the public outside of North America. Members of
the Council include:
Ana Luisa Guzman, CONABIO (Mexico)
Frank Bisby, Catalogue of Life Partnership (UK)
Stefan Claesson, Consortium of European Taxonomic Facilities
(CETAF)(Sweden)
Mark Costello, Ocean Biogeographic Information System (OBIS) (New
Zealand)
Richard Edwards, ARKive/Wildscreen (Bristol, UK)
Gerardo Fragoso, UNEP World Conservation Monitoring Centre
Rodrigo Gamez, Instituto Nacional de Biodivresidad (INBio) (Costa Rica)
Kees Hendriks, Naturalis Museum (Netherlands)
Leslie Honey, NatureServe (USA)
Richard Lane, Natural History Museum (London, UK)
Michael Saunders, Royal Botanical Garden Kew (UK)
Barbara Thiers, New York Botanical Garden (USA)
Simon Tillier, Museum National d'Histoire Naturelle (France)
Chris Anderson, Sapling Foundation (USA)
Joanne Daly, Atlas of Living Australia
John Fitzpatrick, Cornell Lab of Ornithology (USA)
Rainer Froese, FishBase (Germany, Philippines)
Fernando Gast, Humboldt Institute (Colombia)
Le Kang, Chinese Academy of Sciences (China)
John McCarter, Chair (USA)
Erik Moller, Wikipedia Foundation
Michael Novacek, American Museum of Natural History (USA)
Richard O'Grady, American Institute of Biological Sciences (AIBS) (USA)
Sara Oldfield, Botanic Gardens Conservation International (BGCI)
David Penman, Global Biodiversity Information Facility (GBIF) (Denmark)
Gideon Smith, South African National Biodiversity Institute
Simon Stuart, World Conservation Union]