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?
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.
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:
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.
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:
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.
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 firstname.lastname@example.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.
Mr. Robert Corrigan, +1-202-633-8730; email@example.com
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
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.
This is the classic game of Memory - remember where you saw a species and try to find its match! There is also a quiz that challenges you to match species names with the pictures.
Try one of our memory games by visiting this site and looking under “Featured Games”. You don’t need to login to play, simply click on a game icon. To create your own Memory Game, you will need to create a login and password.
You’ll see some changes with the latest update to Memory. In addition to speed improvements, you can now also play against Elephas, the computer with a good memory. Good luck!
Note: EOL Memory works best in Google Chrome, Firefox and Safari internet browsers
In the recent NESCent Research Sprint Call for Proposals we invited biologists to think of questions that EOL and BHL could help answer. We’ll provide an informatician to extract and integrate the data that are needed. Some fantastic ideas have already been suggested by Rod Page in his iPhylo post.
To help you come up with do-able, interesting, big data questions, here is a snapshot as of early October 2013 of what we have on EOL. Some numbers are rounded to the nearest 1000. Also see our daily statistics for more information and feel free to ask questions in the EOL Forum.
3.6 million taxon pages (aka taxon concepts):
Of these 3.6 million pages, 1,368,301 pages have some content associated with them. The balance are pages with a name, but no content…yet.
These pages represent the aggregation and reconciliation of:
31.8 million name usages provided to EOL by its partners (name-taxon-source combinations) of which…
From 19 taxonomic hierarchy providers available via the API, as well as
250+ other taxonomic sources we’ve mapped across
6 million data objects
also 30,000 sounds and 10,000 videos
For your text-mining pleasure, EOL’s text objects are distributed across the following top 6 subjects:
Early next year we’ll introduce support for structured data. So far we have:
21 trait datasets
268,000 taxa with some trait data
170 types of traits (including types of relations between taxa)
2.8 million trait data records
Common trait types include:
Beta testing for these new features starts Monday, October 28, 2013. If you would like to be a beta tester, please email us at firstname.lastname@example.org to sign up. If you know of a great dataset of traits that is freely shareable, please let us know!
Questions about the NESCent-EOL-BHL Research Sprint? Contact Cyndy Parr or Craig McClain.