Aug 12

E.O. Wilson’s Life on Earth iBooks Textbook and iTunes U Course

E. O. Wilson’s Life on Earth is an innovative new iBooks Textbook for high school biology students created by the E. O. Wilson Biodiversity Foundation. Available for free on the iBooks Store, Life on Earth is accompanied by an iTunes U course called Biology: Life on Earth. The iTunes U course brings together content from the Smithsonian National Museum of Natural History, National Geographic, the Encyclopedia of Life (EOL) and other institutions with content emphasizing important themes like citizen science, evolution, climate change, and the protection of biodiversity.

Encyclopedia of Life (EOL) content and resource are available in the first section of the course: Unity and Diversity of Life on Earth. Activities include an audio interview with E.O. Wilson, creating virtual collections of species and accessing the biodiversity resources available through EOL’s iTunes U collections.

Download the Life on Earth iBook and iTunes U Course

Read more about EOL and iTunes U

quote from Charles Darwin

quote from Charles Darwin

Feb 20

Marine Biodiversity Data- let’s get organized!

The past several hundred years of marine research have left us with a real embarrassment of riches. A vast amount of information has been discovered and recorded about the world’s oceans. When we started recording it, we probably never imagined how much knowledge we would eventually have at our disposal, and how difficult it could be to wade through it all. Research groups supported by the European Marine Observation and Data Network (EMODnet) have been combing through the literature and other knowledge stores in their fields and extracting datasets of species attributes of sea birds, copepods, macro algae and other groups, and are preparing this information for dissemination online. These data will be shared via the EMODnet data portal as well as familiar venues like the World Register of Marine Species (WoRMS) and EOL Traitbank.

25 scientists from EMODnet, WoRMS, EOL, and several pioneering research groups which have been unearthing the first of these datasets met last week at the headquarters of Ifremer in France to discuss how best to continue this data hunt, which attributes to prioritize, and how best to format and disseminate them so they’ll be available and useful to researchers, policymakers, students, and ecosystem modelers.

There’s some marine trait data available on EOL already, so if you want to know which diatoms are the biggest, which worms are predatory, or which whales have the longest pregnancies, we can help you. Soon, though, a much wider array of information will be available. What kinds of marine wildlife attributes do you want to be able to look up?

Feb 13

EOL/BHL Research Sprint at NESCent - Update 3
Reports are still rolling out from last week’s Research Sprint.
The NoPlaceLikeHome team used ENVIRONMENTS to annotate North and South America Bird (Aves) information such as ecology, habitat, migration descriptions etc.  They used the SEQenv R package to visualize the results as above. Species are on the X axis and the Environment Ontology (EnvO) habitat term associations on the Y axis, with the redness (or size in the inset Wordle) based on simple term counts. This kind of visualization was originally designed for characterising the sequences of microbial samples with the environments in which they are found. It also appears to be valuable for assessing rare/frequent habitats, species habitat breadth, and researchers are beginning to answer questions about how do environments differ among species of the same genus.
The NoPlaceLikeHome team included Evangelos Pafilis (Hellenic Center for Marine Research), Rob Stevenson (U Mass Boston), and Carl Nordman (NatureServe),
For more information, see this full list of Research Sprint projects and participants.

EOL/BHL Research Sprint at NESCent - Update 3

Reports are still rolling out from last week’s Research Sprint.

The NoPlaceLikeHome team used ENVIRONMENTS to annotate North and South America Bird (Aves) information such as ecology, habitat, migration descriptions etc.  They used the SEQenv R package to visualize the results as above. Species are on the X axis and the Environment Ontology (EnvO) habitat term associations on the Y axis, with the redness (or size in the inset Wordle) based on simple term counts. This kind of visualization was originally designed for characterising the sequences of microbial samples with the environments in which they are found. It also appears to be valuable for assessing rare/frequent habitats, species habitat breadth, and researchers are beginning to answer questions about how do environments differ among species of the same genus.

The NoPlaceLikeHome team included Evangelos Pafilis (Hellenic Center for Marine Research), Rob Stevenson (U Mass Boston), and Carl Nordman (NatureServe),

For more information, see this full list of Research Sprint projects and participants.

Feb 07

Breaking results from the NESCent-EOL-BHL Research Sprint
Some parts of the bird family Corvidae (crows, jays, magpies and their allies) have more available data than others.  Colors represent a score from 1 to 5 based on how many of the following exist:
A rich EOL page
EOL TraitBank trait information
Georeferenced occurence records from Global Biodiversity Information Facility (GBIF)
Non-georeferenced GBIF records
GenBank sequence records
Phylogenetic tree from Jetz et al. 2012.
Analyses like this can guide investment into new data collection where it is most needed or allow researchers to quickly select parts of the tree of life where they can answer their research questions.  The team plans to scale this analysis to vertebrates and build a pipeline to make it easy to visualize the progress of scientific knowledge.
The research sprint team team included Jessica Oswald, Karen Cranston, Gordon Burleigh, and Cyndy Parr.  
For more information, see this full list of Research Sprint projects and participants.

Breaking results from the NESCent-EOL-BHL Research Sprint

Some parts of the bird family Corvidae (crows, jays, magpies and their allies) have more available data than others.  Colors represent a score from 1 to 5 based on how many of the following exist:

  1. A rich EOL page
  2. EOL TraitBank trait information
  3. Georeferenced occurence records from Global Biodiversity Information Facility (GBIF)
  4. Non-georeferenced GBIF records
  5. GenBank sequence records

Phylogenetic tree from Jetz et al. 2012.

Analyses like this can guide investment into new data collection where it is most needed or allow researchers to quickly select parts of the tree of life where they can answer their research questions.  The team plans to scale this analysis to vertebrates and build a pipeline to make it easy to visualize the progress of scientific knowledge.

The research sprint team team included Jessica Oswald, Karen Cranston, Gordon Burleigh, and Cyndy Parr.  

For more information, see this full list of Research Sprint projects and participants.

Feb 05

EOL/BHL Research Sprint at NESCent - Update 1

A group of researchers has gathered this week in Durham, North Carolina at the National Evolutionary Synthesis Center (NESCent) to tackle some fascinating projects about the ecology, evolution, and conservation of biodiversity. What these projects have in common is that that they are all using information from the Encyclopedia of Life or the Biodiversity Heritage Library to answer their questions.

Here are some of the projects:

  1. Esther Quintero and Anne Thessen are text mining data from EOL and BHL in order to statistically assess the conservation risk of species of Mexican amphibians.
  2. Elise Larsen and Yan Wong will figure out how to automatically extract color information from EOL images of butterflies. Variation in color may determine species’ responses to habitat edges and to climate change.
  3. Gordon Burleigh, Scott Chamberlain, Craig McClain, and Meghan Balk are asking if co-occuring sister species in vertebrates show more divergence in body size (for example) than sister species that do not co-occur.
  4. Nicole Angeli and colleagues, along with Javier Otegui, are considering potential co-extinction of mutualistic species due to range shifts in order to inform conservation planning efforts for at-risk species.

Aside from consumption of copious amounts of coffee, we’re consuming and generating vast amounts of data.

Please stay tuned to the EOL blog for some hints of what we are learning, and follow our progress on Twitter this week via the #eolbhl hashtag.

EOL and BHL acknowledge the Richard Lounsbery Foundation for supporting this exciting research sprint.

Jan 27

TraitBank release notes

OK, we’ve now officially launched TraitBank after a period of quiet testing and over a year of planning, development and late-night Taco Bell visits.
New to TraitBank?   Learn the TraitBank basics then try out our nifty new TraitBank data search facility for starters.
We are eager to hear your responses to the new functionality and data.  Please note that there are already quite a few things on our list of “things we’d like to do”. We would value your feedback to help us focus on what’s most important to you.
  1. Data records and attributes in TraitBank are just the tip of the iceberg so far.  We’ll planning to add many more sources, including detailed morphological data, so stay tuned. If you want your own dataset to appear on EOL pages, please contact us.
  2. We’re very interested in basic visualizations of TraitBank data that could help people explore and draw meaning from large amounts of data. If you develop such visualizations using EOL, please do let us know.
  3. We are aware that we still have more than one attribute with the same label and the same or similar definitions. Where we can we plan to merge these. In some cases we can re-import the data but in others we’ll need to tell our system that the two attributes are similar enough that we can merge them,
  4. It isn’t possible yet to search or download ecological association data records. 
  5. As with most text mining projects, the data from one of our largest sources, ENVIRONMENT-EOL are not perfectly clean.  They will be improving over time.  Please leave comments on all wrong or awkward data records, and if you are a curator please do use the hide link to keep them from being shown to all users.
  6. We know that some attributes are subsets of others or of some higher category (such as “size”) but we haven’t enabled any interesting semantics that help out machine reasoning.
  7. While we have some information about type specimens in TraitBank, we haven’t come to a final solution on the best way to deal with types.  Your input would be welcome.
  8. Some basic statistics about TraitBank holdings are already in our site statistics, but there’s much more we could do with this.
  9. We know that it will be useful to have an advanced search that allows you to combine attributes with each other or with a geographic search.  
  10. For those of you who want machine access to the data we are considering a SPARQL endpoint and/or API access.  For the moment, we are facilitating downloads that are as complete as possible.
  11. We will be developing richer documentation over the next few months. Please let us know what you are most interested in knowing.
Please add your comments to this post, or send an email to secretariat@eol.org with your comments.  Thanks!

Announcing TraitBank

FOR IMMEDIATE RELEASE

Encyclopedia of Life releases TraitBank

Landmark open repository of species facts and measurements now available to support research, education and conservation goals

Washington, D.C., January 27, 2014 – The Encyclopedia of Life (EOL) today announces the first release of TraitBank™, a comprehensive, searchable and open digital repository for organism traits, measurements, interactions and other facts for all species and groups of species.  It fills an urgent need among global research, education and conservation communities for a reliable, curated, comprehensive source of trusted data across the tree of life, as well as the need for a public platform for sharing scientific data in a consistent, accessible manner.

With TraitBank, EOL can help scientists develop and test hypotheses explaining patterns in nature, or estimate food webs by identifying organisms known to interact with each other.  It can also be used to address “easy to ask but difficult to answer” questions such as “Which whales weigh more than 10,000 kg?” and “Which plants have blue flowers?”

Developed with support from the Alfred P. Sloan Foundation, TraitBank (http://eol.org/traitbank) is integrated into the fabric of the EOL website (http://eol.org), where it leverages EOL’s existing infrastructure for taxonomic names, content organization, curation roles and search.  Data records are aggregated from a wide variety of sources, including databases, literature tables, spreadsheets and individual contributors.  At launch, TraitBank features over 3 million records related to more than 250 attributes for over 250,000 taxa (species and groups of species) obtained from 27 data sources.  It is expected to grow substantially as existing and new trait data records are loaded into TraitBank over time.

“TraitBank is unique in serving up reliable real-world data for the entire tree of life,” said Dr. Drew Purves, head of the Computational Ecology and Environmental Science Group at Microsoft Research Cambridge. “To those of us trying to build Global Ecosystem Models, it’s like someone just handed us a list of parts.”

“TraitBank will help accelerate the research process by providing a free, open and accessible way for investigators to share and discover species traits, measurements and interactions,” said Bob Corrigan, Director of Operations for the Encyclopedia of Life.  “The motivation behind TraitBank was to make it easy for users to get a comprehensive picture of these data for any given species or group of species, and then give them access to the underlying publications and data sets quickly.  We’re delighted to share TraitBank with the world, and we’re looking forward to working with scientists and educators to make it as useful to them as possible.”

The EOL team has the capacity to help researchers make the best use of existing TraitBank capabilities and provide expertise for data mobilization, extraction and analysis efforts.  EOL is also interested in reviewing opportunities to extend TraitBank’s capabilities to support project-specific requirements, and it invites biodiversity researchers to take advantage of the significant investments and expertise behind TraitBank as part of their grants and other sponsored projects.  To learn more, please contact the EOL Secretariat at secretariat@eol.org.

About the Encyclopedia of Life: The Encyclopedia of Life (EOL) operates as an ongoing collaboration among its international partners with the mission to raise awareness and understanding of living nature.  Participants include the Atlas of Living Australia (Australia), the Biodiversity Heritage Library, the Chinese Academy of Sciences (China), CONABIO (Mexico), the Global Biodiversity Information Facility (GBIF), Harvard University, the New Library of Alexandria (Egypt), the Marine Biological Laboratory, the Norwegian Biodiversity Information Centre (Norway) and the Smithsonian Institution. With additional support from a global network of content partners, curators and users, EOL works to provide free, open, multilingual, digital access to trusted information on all known species at http://eol.org.

###

Contact:

Mr. Robert Corrigan, +1-202-633-8730; bcorrigan@eol.org

Nov 20

EOL Podcast Highlights - Women in Science

                  Image Credit: Randi D. Rotjan, Ph.D., Associate Research Scientist, New England Aquarium

The following podcasts from the Encyclopedia of Life’s One Species at a Time Podcast series feature female scientists in the field!

Listen to each podcast and make sure to check out the “Meet the Scientist” interview links.

EOL Podcast Highlights - Women in Science

The One Species at a Time podcast series is supported by the Harvard Museum of Comparative Zoology

Image Credit: Randi D. Rotjan, Ph.D., Associate Research Scientist, New England Aquarium

Nov 18

New One Species at a Time Podcast: Dolphins

Image Credit:Howard Goldstein, NOAA Fisheries. World Register of Marine Species. CC BY-NC-SA

You have probably seen cans of tuna in your local supermarket marked “dolphin safe.” That label means the tuna was fished in a way that spares most dolphins from being killed in the tuna fleet’s giant nets. In this podcast, biologist and guest reporter Matt Leslie brings us a story about tuna, the intertwined fate of fisheries and dolphins, and the work of scientists.

Listen to the podcast

The One Species at a Time podcast series is supported by the Harvard Museum of Comparative Zoology.