The Encyclopedia of Life has been keenly interested in content management systems and social networking phenomena, especially relating to how well these might be of benefit to practicing taxonomists who are under pressure to get online. So, we have been getting serious about Drupal and want to make a stab at hosting sites called “LifeDesks” that as a start will focus on particular groups of organisms and will be similar to Scratchpads, a most amazing collection of Drupal-based sites hosted at the Natural History Museum in London, England. LifeDesks would sit just to the side of EOL, but will have the advantage of providing some extra, distinct visibility for participants while still feeling part of the EOL dream. A bit of work needs to be done on Drupal to make this work and we’re interested in sharing developments with the wider Drupal community.

So, although it’s short notice, we’re going to host a Drupal code sprint August 11-14 in Chicago, Illinois to kick-off our relationship with Drupal. Please visit http://sprint.eol.org to see what we have in store and please also spread the word to any Drupal developers you know.

Outside of the Field Museum, Rick attended the Consortium for the Barcode of Life meeting in San Diego the week of June 23rd, specifically to go to a session on data visualization, presenting BioSynC’s efforts to develop interactive tools with Adobe.

Mark and Darolyn left the Evolution meeting (previous post) in Minneapolis on the 23rd to travel to Keelung, Taiwan for an organism-focused synthesis meeting on Decapods (shrimps, crabs, crayfish and lobsters) from the  25th to the 29th. This meeting was an exceptional example of the power of organism-focused meetings to bring together key scientists focused on a megadiverse group to develop great taxonomic, phylogenetic, and conservation resources for the broader community on a scale not previously seen. Hosted by Professor Tin Yam Chan, the meeting developed ties between the US decapod crustacean biologists working on the Decapod Tree of Life project with their counterparts in Australasia. These groups have exceptionally complementary talents and resources, and combining their efforts proved very productive. It could be said that they made a quick and effective leap forward in the fundamental understanding of decapod diversity. The meeting involved around 24 specialists and six students from 9 countries, with the goal of among other things, creating the first comprehensive species list for decapod crustaceans, no small feat given that there are over 15,000 known species. Darolyn will be posting in greater detail about how the meeting went really soon.

Staff Update

Here is a group photo of our staff and summer interns (we always look this good), unfortunately all the postdocs were out that day, from left to right: Alta Buden, Kate Harney, Nick Lilly, Krista Larson, Audrey Aronowsky, Darolyn Striley, Mark Westneat, and Rick Ree

On June 9th our new summer interns started! Three of them are from the BitMap program, which means they are trained in bioinformatics, (Krista Larson, Scott Bradley and Pratima Maiti) and two others hail from the University of Chicago (Kate Harney) and Princeton (Nicholas Lilly).

Here is a little bit about each of them and some photos (that may or may not be photoshoped) we took with the Olmec head at the Field Museum:

Krista Larson

Krista is a graduate student in computer science with interests in biology and bioinformatics.  Her work history is diverse, starting with working in the pharmaceutical industry, moving on to IT consulting, and then as IT support for an investment consulting firm until she finally realized what she wanted to do when she grew up.  Currently she is working with Rick Ree on an application for grafting and editing phylogenetic trees.  Always up for a new challenge, she also recently worked as a ‘crystal expert’ doing chandelier restoration at a hotel in downtown Chicago.

Scott Bradley

Scott has a degree in Electrical Engineering from Purdue University and is completing a Master’s in Computer Science at DePaul University where he has focused his course work in artificial intelligence and software development for the sciences. Scott has been doing systems and software design and development for over 14 years across many fields, including telecommunications, manufacturing, architecture, and web application development. His most recent work has been on projects for Siemens Corporate Research, and AT&T. Scott’s broad academic background also includes a degree in theology. His research has included theological inquiry into the nature of human creativity, and his current interests include search and discovery and the general application of programming and artificial intelligence to creative and scientific pursuits. He was once called “some sort of academic hippy” in a job interview, and well, he didn’t get that job anyway, but that might be why we like him.

Our other BitMap intern Pratima Maiti will be posted soon.

Nick Lilly

Last year Nick graduated from Princeton University where he majored Ecology & Evolutionary Biology and minored in Creative Writing and Environmental Studies. For his thesis, he wrote a novel centered around green sea turtle conservation and based on his own field research at the green turtle nesting beaches of Tortuguero, Costa Rica.  In the future, he hopes to publish his book and to continue to combine his interests in biology and creative writing. Nick is currently working on research for a virtual coral reef project. He is also going help us out this summer by getting together information to contribute to EoL turtle pages as well as helping to translate science speak on some of the EOL fish pages. He spends much of his free time both in and out of the BioSynC either eating or preparing baked goods (as do many of us here). Among the many places on Earth he enjoys, he feels particularly attached to the tent he slept in while studying in Kenya, to Rome, to Fassi souks and medersas, to Costa Rican sea turtle nesting beaches and cloud forests, to the Field Museum and Brookfield Zoo, and to his home in the Midwestern United States.

Kate Harney

Kate is entering her fourth year at the University of Chicago majoring in the biological sciences and mathematics. She spent the past semester studying tropical ecology in Ecuador where she spent a month in the rainforest and also traveled to the mountains, coast, and Galapagos Islands. At the UofC Kate is a member of the women’s ice hockey team, something one would not suspect from her calm demeanor.  At BioSynC she is working on background research for a virtual coral reef project and learning Drupal with Alta in order to help redesign our website.

We also have one of our new post-docs starting this month:

Jim Parham

Jim, our second Postdoctoral Research Associate, is a broadly trained herpetologist (although clearly he is into turtles). He is arriving in Chicago from California, where he recently completed a postdoc in molecular systematics at the Joint Genome Institute following his PhD work in paleontology at U.C. Berkeley. Before that he studied geology at the University of Rhode Island. He is primarily interested in how human activities impact our ability to reconstruct natural patterns of reptile diversity (through extinction), distribution (through extirpation and exotic introduction), and phylogenetic relationships (through genetic pollution). He also studies the evolution of major turtle lineages by integrating paleontology with molecular systematics.

That said, as the Director of the Species Pages Group, my primary companions will be the global scientific community. Our goal of 1.8 million species pages in ten years can only be met with intense, coordinated effort. We need to prioritize sharing of digital information already in databases, and target key areas where little information exists online. We need to enrich species pages with knowledge from specialists such as ecologists and physiologists, with observations from museum collections and citizen scientists, and with excellent images and video.

My group works with prospective data partners and will administer a new EOL Fellows program. We’ll be building a curatorial network that will help authenticate contributions from the general public.

How did I get here? My doctoral work in biology at University of Michigan was on the social behavior and communication of crows (Corvus brachyrhynchos) and I’’ve studied the evolution of magpies (Pica) using DNA sequence and behavior. For the past ten years I’’ve worked on a variety of informatics projects. With the Animal Diversity Web I led the development of species pages by college students, negotiated licensing, and developed software for children observing diversity in their schoolyards. At the Human Computer Interaction Lab at University of Maryland we explored ways to visualize biological trees and food webs. More recently, at both University of Maryland at College Park and at Baltimore County, I’’ve worked on semantic web and social technology for scientists (particularly moth and butterfly experts) and for citizens (ecoblogging). In my spare time, I’m a Flickr fan and a geocacher.

Discerning readers will note a trend. – I resist narrow research bins and just want to find the best ways to build and share knowledge about biological diversity. That’’s my passion, and that’’s why I’’m now with the Encyclopedia of Life.

As I work on the human connections that will build the content of the Encyclopedia of Life I welcome your ideas. You can leave them as comments here, or send me a message via the Contact Us form.

Many thanks to all of you who have already volunteered to help curate pages, and who are busy collecting information to contribute to species pages once our tools are ready. How many people do you think will ultimately be involved in the effort?

Torsten Dikow, net in hand.

This past weekend (July 27-28) BioSynC post-doc Torsten Dikow, expert on robberflies, was invited to participate in the 2008 Middlefork Savanna Bioblitz. On Saturday, he ventured into Middlefork Savanna, one of the “most important sites for biodiversity in northeastern Illinois” according to Chicago Wilderness, to look for specimens of robber flies. Here is the one he found (it was very windy, not stellar for fly catching).

Bioblitzes are an brilliant way to simultaneously raise public awareness about local biodiversity and to collect scientific data: Torsten will now identify that fly and ad it to his research data. In addition the park preserve now has a better idea of what species live there, and thus how to better look out for them. This bioblitz featured over 100 scientists and many more civilians combing the preserve for 24 hours to attempt to identify as many species as possible. They discovered at least 1054 species and more are still being counted by participating scientists and taxonomists. Check out their blog to see how the event progressed.

Bioblitzes are usually centered around a “Tally Tent” where people bring photographs and specimens for documentation, and where the public can watch scientists at work. These events have exciting implications for the EOL; we hope that in the future the EOL can both serve as a resource for people identifying species in them as well as act as a host for the detailed regional data that they produce. Here is the flickr link to the best photos that they took like the one below of a shy and elusive eastern milk snake (Lampropeltis triangulum triangulaum).

From June 20-24th BioSynC staff members Mark Westneat, Audrey Aronowsky, Darolyn Striley and myself hosted a booth at the 2008 Evolution meeting. The meeting attracts leading phylogeneticists, systematists, and evolutionary biologists from around the world making it an ideal conference to recruit scientists to EOL and also to solicit interest in synthesis meetings. It was held in Minneapolis at the University of Minnesota and had an attendence of about a thousand people. Our booth got lots of attention (we were only ones with candy :)) and we met several people who are going to propose synthesis meetings. Our booth was across from the NEScent booth and we had alot of fun getting to know our fellow synthesis meeting organizers, who, for the record are still leaps ahead of us in terms of booth set-up.

Mark gave a 15 minute talk to a full audience titled: “Phylogenetic visualization tools and phyloinformatics in the Encyclopedia of Life”. In the presentation, Mark used his own fish research ( a phylogenetic dataset) which incorporates systematics, developmental genomics, and biogeography to demonstrate the many kinds of data that EOL will be able to handle and also how the research communities that focus on each of these kids of data could work together using EOL. Here are some pictures of us and the booth in action:

I grew up on Cape Cod and join the EOL Informatics Group as a software developer. My experience is in database and web application development.
I will help ensure that the foundations of the Encyclopedia of Life are as solid as possible while allowing flexibility in the future. I have followed this important project for some time and am thrilled to be contributing to its success. It has the potential to be a great resource for learning about and advancing the conservation of the myriad species on earth.

Vitthal Kudal
Software Developer

I am working as a Software Developer with the informatics group of Encyclopedia of Life. I have Master’s degree in Computer Science from University of Pune, INDIA. I have worked for NCL center for Biodiversity Informatics (NCBI) as a Project Assistant. My dream is to make all species data available over the internet on a single command of user and which is going to fulfill by working with the EOL Group. What it is has been like working at EOL? Interesting, inspiring, insightful, impactful, fun and more such words.

Jeremy Rice
Software Developer

Working with the Encyclopedia of Life is the realization a long-time dream for me. I love being at a university, advancing research. The Encyclopedia’s vision to synthesize all information about life present on Earth… that makes it something really essential for me. I’m joining the team with over ten years of experience developing a variety of applications. What really drives me is turning abstract ideas into working products that people appreciate. There’s an abundance of ideas here, and I hope that we can produce some amazing tools to facilitate them…

Dimitry Mozzherin
Software Developer

I was born in Russia, and from my early school years I wanted to become a biologist and a wild life photographer. I happened to become both later. At some point I started to learn programming languages and after discovering Open Source movement I decided to make programming my profession. And I am now at EOL because here I can express my passion for wild life and passion for development Free Software at the same time!

Anne Thessen
Post-doctoral Investigator

I’m working on data mobilization for EOL and the International Census of Marine Microbes. Lots of biological data can be found on the printed page, which must be read to retrieve information. I’m trying to find ways to make this information easier to retrieve and use. Prior to joining the EOL team, I worked on Arctic primary production, toxin-producing diatoms and shellfish grazing.

SOS have also published a list of the “top 10″ species described in 2007.

This list has attracted some comment at The Other 95%, Zooillogix, and Catalogue of Organisms.

These lists have implications for EOL. The report gives us a lower bound on the rate of new species description — EOL will need to be able to add at east 46 species pages a day just to keep pace with new discoveries, never mind what has already been described. It isn’t doing anything like this at present, and hence none of the species in the SOS top ten list are in EOL (most are already in Wikipedia, and all return at least some information in iSpecies).

iNaturalist.org is a place where you can record what you see in nature, meet other nature lovers, and learn about the natural world.

It looks gorgeous (lots of Flickr Creative Commons photos), use of Wikipedia, and the TimeMap Javascript library.

Arguably the species pages are clearer than EOL’s (compare Anolis carolinensis on iNaturalist and EOL).But what makes it especially cool is the way it engages users with the ability to add observations of organisms, and request identifications. I like the emphasis on being

…a fun and efficient way to record, find, and share nature observations.

I think its a great project that could provide useful ideas for the design of EOL’s pages.

Extracting signal from noise is, of course, one of the classic bread-and-butter activities of information science. What’s fascinating here is the Web 2.0 angle. Birdwatchers are famously passionate data collectors who develop reputations among their peers. When they contribute their data to eBird — and thence to the Avian Knowledge Network — those reputations can begin to be measured, and used to tune the analysis of a large body of contributed data.

These are, of course, issues directly relevant to EOL. Jon has long been interested in integrating information (including digital libraries), social networking, and how people interact with technology. His podcast is a mine of useful information. Click this link to subscribe to it in iTunes.

It was my task as chair of the IAG to try and condense the detailed reports given by BIG, and the subsequent discussions, into a written report. That has now been done, and the result presented to BIG. In this post I will summarise two key areas, namely content and vetting. The report also addressed topics such as the site design, globally unique identifiers, and organisational matters, but I think content and vetting are the two that generated the most debate.

Content

Now that EOL is live and people have had a chance to look around, it is striking that 76% percent of visitors don’t return, and 44% of all visitors left in under 10 seconds. After the initial launch where, if anything, EOL was too popular, interest seems to have dropped off markedly. One possible reason for this is the relative lack of content. As I noted elsewhere, for many pages EOL compares unfavourably with other sites, such as David Stang’s ZipcodeZoo, or my own mashup iSpecies. EOL’s current strategy has been to limit its content to “vetted” information from trusted providers. For 24 exemplar taxa EOL provides relatively detailed information, but for the rest of life the content it currently displays is pretty sparse.

The challenge is how to cover all life in reasonable detail. If we take the well-worn estimate of 1,800,000 million described species, and EOL’s 10 year time frame, then BIG needs to add around 500 species pages per day! Doing this without massive automation simply won’t scale. Assembling the 24 exemplar pages required considerable effort, yet simple aggregators such as iSpecies can generate a roughly similar level of detail within seconds. The diagram below compares pages for Anolis carolinensis (EOL exemplar taxa) in EOL (left, or go here) and iSpecies (right, or go here). The iSpecies account is assembled automatically on the fly from sources such as GenBank, GBIF, Google Scholar, Yahoo Images, and Wikipedia.

EOL is a long term project, and hence it may seem unfair to judge it so soon after it has been launched (and after Herculean efforts by BIG staff). However, given EOL’s current lack of content, and the existence of other web sites (such as ZipcodeZoo, DiscoverLife, and iSpecies) that already serve a much greater amount of information, my concern is that EOL risks being marginalised. I don’t think that EOL has anything like 10 years in which to prove itself.

How to add content quickly

For the report I prepared a cartoon plotting the cost of obtaining content against the amount of content obtained. “Costs” are in terms of developer time to import data (are they in a standard form, or a format unique to the provider), and time spent negotiating intellectual property agreements (such as how to display credit and attribution information, how the data will look, etc). At the bottom right (1) are large, freely available data sources such as GenBank, GBIF, and Wikipedia. At the left (2) are small sources that require tools to make their content available. In the middle (3) are well-established data providers that can require considerable effort to incorporate into EOL, due to both IPR issues and idiosyncratic data structures. The dotted line is an arbitrary cutoff, above which the effort required to obtain content outweighs the value that content would bring to EOL.

The report recommends going after content in category 1 first. These are sources have massive amounts of data that are freely available, and relatively easy to import. These include PubMed, GenBank, Wikipedia, ITIS, Flickr, and GBIF. As I noted on the iSpecies blog, GenBank records often contain metadata about organismal distribution, habitats, and ecological associations, which could be harvested. There are communities on Flickr building photo libraries of organisms, often tagged with scientific name and geographic location (e.g., Field Guide: Birds of the World). Harvesting these sources will provide considerable initial content for EOL. Of course, not all sources in this category are of comparable quality. GenBank and PubMed are, publicly funded, curated archives of scientific research, Wikipedia and Flickr are not.

Category 2 is next, and this is where we need tools to enable smaller providers to manage their own content, and contribute to EOL at the same time. This content would be targeted by “LifeDesks” (similar to the scratchpads being developed at the Natural History Museum, London).

Content in category 3 may have high scientific value, but in the short term the effort involved in incorporating it may outweigh the value it brings.

It’s perhaps a glib phrase, but I’m reminded of genius of “and” versus the tyranny of “or”. Harvesting resources in category 1 is not an argument against also going after resources in category 2, it’s a question of priorities. In the same way, tools developed for category 2 providers may well facilitate acquiring content from category 3 sources.

Vetting

The issue of “vetting” generated much discussion during the review meeting. It became clear that this term can mean different things:

1. data that is error free (”correct”).
2. data provided by scientific sources (”scientifically authenticated”)
3. data that has been verified by experts

No data source is without error, so EOL will inevitably include erroneous information. Currently the bulk of its data comprise distribution maps from GBIF, which are known to contain errors. For example, some 16% of legume records are incorrect (doi:10.1371/journal.pone.0001124.). The GBIF map below shows numerous, erroneous records of the North American channel catfish (Ictalurus punctatus) in China.

At the scale at which EOL operates (100’s of millions of items of information), manually vetting all information before it is displayed is not feasible, and indeed by displaying GBIF maps EOL tacitly acknowledges this.

Of course, EOL wants to be an authoritative resource (in other words, more than a simple mashup), hence, one of its biggest challenges is to develop methods to catch errors. Innovative methods of annotation will need to be developed. Human Computation (see also Luis von Ahn’s talk at Google) is one approach, recently used by Google’s Image Labeler to annotate web images. BIG will need to develop easy-to-use interfaces so that EOL users can annotate data and flag possible errors. These annotations should be publicly visible, so that users who take the trouble to make annotations get instant feedback, and other users can see which records are contested.

Summary

A project on the scale of EOL is bound to take some time to settle in, and initial expectations were never going to be met, hence the generally under whelmed reaction in the blogosphere (myself included). There is much to do, and the overall theme of the IAG report is that EOL needs more content, fast, and needs to tackle the issue of vetting in a way that will scale.