Encyclopedia of Life Blog

As e-Biosphere winds down, I wanted to report back on what happened, what I thought was interesting, and what my take-aways were.  The meeting had 483 participants from all over the world (42 countries!).

The set up and program were excellent, with a good diversity of speakers and perspectives.  Among my favorites were Jorge Soberon’s presentation on the need for integration across subdisciplines and fields and at varying scales. Nancy Knowlton’s presentation questioning whether we need to name biodiversity in order to study it and learn from it was probably the most controversial and thought-provoking. And Sandra Knapp’s presentation documenting the motivations and paths that the Solenum project used was informative and a great case study for how to effectively stimulate participation from a broad and diverse group of specialists.

The afternoon breakout session topics were broad and yet, interestingly, produced many common themes.  Group topics included ecology, cybertaxonomy, standards, developing countries, education, and conservation.  Common themes included a need for better standards, better metadata, simplification of contributions and involvement, and better templates. Also discussed were the importance of team building and collaboration, the key role of ecosystem services, and maintaining open access to information.

The main things that I will take away from the meeting are that there have been great advances in biodiversity informatics in the last 20 years, but there is still a long way to go. The field needs to articulate its goals better and communicate these goals with the public and policy makers in a more effective manner. Data sharing and collaboration are critically important to everyone, and major projects like EOL and GBIF need to take the lead in urging standards, creating templates and tools, and outreach.  We have a long way to go, but a great role to play.

Special thanks to the staff at the QE2 conference centre.  The facility is beautiful; bright and airy with stunning views of Westminster Abbey. Also special thanks to the organizing committee for bringing together a great group of speakers and participants.  I hope this becomes an annual thing!  A final thanks to NHM for hosting a lovely evening event (pictured above). Without them, I would not have been able to take the great photo of Jim Hanken and Sir Richard Owen below…

We are excited to announce that we’re now indexing videos as well as images from Flickr.  Videos uploaded to the EOL group in Flickr and tagged with a species name will now be featured in EOL species pages.  Visit the Honeybee (Apis mellifera) page to see some recent video additions by Arthur Chapman and Valter Jacinto . Since the group began less than 6 months ago contributors have submitted over 13,000 photos and now over 200 videos which are shown in EOL species pages. Follow the instructions on our group homepage and learn how to submit and tag your photos and videos. We encourage everyone to check out the EOL Flickr group and start submitting photos and videos today!

After a few weeks of preparation, we are now ready to release the code that runs the www.eol.org website into the open source community.  The code is written in Ruby on Rails and is released under the MIT License.  There are many moving parts to the system, including code needed for data indexing, harvesting, names finding algorithms, data model creation, as well as all the code used to generate the actual web pages.   This release includes all of the Ruby code used to generate the webpages for the www.eol.org website, including the full data model and includes all the code to set up your own miniature version of eol.org running on your Mac (or PC…).  All that is missing is all of the wonderful data, but the code comes with enough sample data, called “fixtures”, to get you going!  Some other parts of the system written in PHP (such as indexing and names finding algorithms) will be released separately.

To get started, check out the project homepages on Google Code or GitHub.

Hi Folks,

As some of you may or may not have noticed, without any fanfare, we released a substantial update to the Encyclopedia of Life website on January 5, 2009.  We are calling it version 2, and in fact, if you look at the footer of the www.eol.org pages, you will now see our internal version number right there (today at 2.0.11).

So what’s new, you ask?  Well, a whole bunch actually:

1. You can now tag images and then search for species associated with those images (e.g. “blue”, “marine”).  You can tag any image you want and once several people tag an image in the same way, it is promoted to a “public” tag viewable by all.
2. You can comment on species, images or blocks of text.  Content providers will then be able to see your comments to help improve their material.
3. You can add your own images to the EOL Flickr Group that, when tagged correctly, will automatically appear in EOL species pages.
4. We now distinguish between “trusted” and “unknown” content with clear messages and colors and will soon invite curators to help indicate the trust level of content.
5. And of course, many new species pages and more content, adding to the overall richness of the experience.

For a more complete listing of what’s been added, along with some screen-shots, head on over to the “What’s New?” page.  We’ve already begun working on the next set of features to add, with some great additions like public APIs high on the list.  The real fun will begin once the APIs are released and we begin seeing mashups between EOL and other projects - we can’t wait.

Thanks and enjoy,

Peter

We’ve opened up another way for everyone to help build the Encyclopedia of Life.

You may have noticed we still need lots of pictures. You can now now share your best photos and videos of organisms with us by adding them to a Flickr group. For more details, see the description and instructions on the Encyclopedia of Life Images group page. Even if you don’t have your own images to share, you can help add “machine tags” with the species identifications to those that don’t yet have them — these will help us display them on the right pages.

This won’t be the only way to contribute, but many of us already love Flickr, and we hope others will want to give it a try.   The images should start showing up on the site later this year. There already are more than a thousand from the first few enthusiastic group members, including these striking examples (all are CC-licensed; photo credits to Jeff Whitlock, Sarsifer, Valter Jacinto).

The EOL-sponsored Drupal Sprint is in the final hour and there has been some immense success. The crux of this 4-day event was to attach metadata to terms and to enable relationships among terms. This sort of background work means that in the context of biology, we have a mechanism to store information about whether or not a term (i.e. a scientific name) is a synonym of another, whether a species has a relationship with another species (e.g. is a parasite of, is a predator of, etc.). There were some contributed modules that started this whole process. These can be found on the Taxonomy Drupal Groups website for the sprint.

Left to Right:

Simon Rycroft, Nathaniel Catchpole, Anthony Goddard, Lisa Walley, Roger Espinosa, Matthias Hutterer, Cyndy Parr, Dan Morrison, Chacha Sikes, David Shorthouse, Benjamin Doherty, Vitthal Kudal, Alexey Shipunov, Ben Melancon (missing: Vince Smith)

A big thanks goes out to the BioSync team at the Field Museum in Chicago who orchestrated much of the organization. Without their assistance and facility, the sprint would most certainly have been difficult to pull off.

UPDATE! (July 31, 2008): The code sprint will now take place September 8-11, 2008

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.

Jonathan Clapp
Software Developer

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.

Ken-ichi Ueda told me about iNaturalist.org, a wonderful site he, Nathan Agrin, and Jessica Kline have created for their Masters at UC Berkeley’s School of Information. To quote from the web site:

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.

Jon Udell has a great podcast where he interviews Janis Dickinson, who directs the citizen science program at at Cornell’s Laboratory of Ornithology. On his blog Jon writes:

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.