EOL and Science: Yes we can!
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EOL and Science: Yes we can!

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A six-minute talk presented in the Smithsonian National Museum of Natural History Senate of Scientists Lightnng Round 2, 13 April 2012i

A six-minute talk presented in the Smithsonian National Museum of Natural History Senate of Scientists Lightnng Round 2, 13 April 2012i

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  • My name is Cyndy Parr and I’ve been the director of the EOL species group and here at the Smithsonian for four years, I was originally a behavioral ecologist interested in birds but I’ve been involved in informatics research for the last fifteen years.As you may know, Encyclopedia of Life is a web site providing global access to knowledge about life on earth.Global – the whole worldAccess – free, and freely re-usableKnowledge – synthesized, not rawLife on Earth – biological diversity
  • We have miliions of pages with at least a name with more than 4 million data objects distributed on those pages, so that nearly a million of these pages have some sort of content. Up to now, we’ve focused on our more general audiences, which are most of the 55,000 registered members. But my talk today will show that we ARE being used by scientists, and we have great potential to be used more for science.
  • EOL takes information from about 200 sources so far, mostly scientific databases, but also including Flickr and Wikipedia, and automatically sorts it onto on taxon pages. Our curators can then trust or untrust it, or anybody can provide comments or ratings. About a thousand credentialed scientists have already volunteered to help with quality control. Actions and comments get fed back to the original providers, and the material on EOL is also available to other applications via an Application Programming Interface, which I’ll talk more about in a moment.We’re partnering with over two hundred scientific databases as well as public conribution sites like Flickr and Wikipedia.100+ partner databases700 curators/1000s contributors/46,000 members2.8 million pages500 thousand pages with Creative Commons contentOver 2 million data objects and >1 million pages with links to research literatureTraffic in past year: 1.7 million unique users, 6.2 million page views
  • I want to emphasize that EOL deals in summarized knowledge, not raw specimen data. For example, for the serpents head cowrie, we have images like this from the Mooreabiocode project, but instead of serving the individual specimen data, we get the overall distribution of specimen data on a map from GBIF. We also get a summary of environmental data associated with specimens in the Ocean Biogeographic Information System database. Imagine if we could do a summary like this across databases.
  • This is a graphical way of presenting the summarized data from OBIS, which Jen Hammock on my staff worked on with Edward Van den berghe and our team at the Marine Biological Lab. The salinity range for the species is shown here as just a smal, specific slice of the global ocean minimum and maximums.Looking just at 15 content providers we already work with, it is possible that numeric data such as lifespan or average body weight is already available for more than 800,000 species
  • BHL, which is funded as part of the encyclopedia of Life and linked to EOL pages. we know that scientists are using BHL. Martin Kalfatovic and his team recently did an analysis and found that more than 10% of the DOI-tagged monographs were used, probably in scholarly citations, in just five months.(out of 100K possible)
  • We have a feature where users can create customized collections of pages or objects on EOL.A scientist could search for a characteristic, say, red flowers, and create a collection of those taxa. Actually, we’ve been doing this with blue coloration in the “Life is blue” collection. If you wanted to test what might be driving the evolution of coloration, you could write a program that uses EOL to get all the Genbank IDs for those species identifiers or some other EOL partner that we’ve mapped to each of those taxon pages, and then use those to go to that database and pull raw data to analyze. For example, genetic sequences, or specimen locations. In the future we hope to make step 2 and step 3 even easier, so you might just be able to click a button and download lots of raw data for your collection from certain data sources.
  • You can also use EOL for crowd-sourcing. For example, Jennifer Hammock has started a collection called “Mystery associates” and asked people to try to identify the partners shown in photos that have some sort of ecological association. When they’ve been identified, like this sea star and anemone predation interaction, then she moves the image to the “known associates” collection. This adds to the information we have from a bunch of partners on food web interactions, and then would be available for foodweb modelers. There are many other possible ways that the large crowds on EOL could be harnessed to generate new datasets from EOL content. And this is all possible to some degree now.
  • For the future, we are working on a few new angles. First, we are working to get a more phylogenetic organization available on EOL, because that will definitely help those who are doing comparative analyses and who want a true evolutionary framework. The deadline for submitting a large tree is this weekend, Monday really. The second challenge is to propose research work using computable data and EOL in some concrete way. Perhaps as I suggested with using collections to harvest computable data or perhaps using text mining. Here the deadline is next month for the idea, and then we’re providing funds to accomplish the pilot project over the next year.Finally, in September here in Washington we’re bringing in computer scientists and biologists who have an interest in broad scale data-intensive science using biodiversity data. We expect this to lead to other projects and enhancements of the EOL platform.All this could, in my personal opinion, lead up to EOL beginning to serve as The Smithsonian’s phenotype repository. Parallel with genbank, we could be the initial point of entry for ecologists or other biologists seeking large-scale structured information about the observable characteristics of organisms.

EOL and Science: Yes we can! Presentation Transcript

  • 1. Science and eol.orgYes we can! @cydparr @eol
  • 2. EOL Scope & Engagement• All species• Global• Many audiences – enthusiasts – learners – citizen scientists – scientists
  • 3. EOL aggregates and curatesScientific Databases, includingBHL, GBIF, ALA, INBio, COL,Scratchpads, LifeDesksScientific Journals Curate Aggregate Comment Rate, Collect eol.org Quality control, prioritization API Third party apps
  • 4. From Moorea Biocode Summarizing knowledge Not managing raw dataErosaria caputserpentisSerpents Head Cowrie … summaries can be data, too. Depth range based on 51 specimens in 2 taxa. Water temperature and chemistry ranges based on 40 samples. Environmental ranges Depth range (m): -5 - 67 Temperature range (°C): 23.011 - 28.496 Nitrate (umol/L): 0.048 - 0.923 Salinity (PPS): 33.821 - 35.837 Oxygen (ml/l): 4.349 - 4.825 Phosphate (umol/l): 0.088 - 0.228From GBIF Silicate (umol/l): 0.983 - 4.026 From OBIS
  • 5. Erosaria caputserpentisSerpents Head Cowrie Salinity envelope (n=40) From OBIS
  • 6. Citation of Biodiversity Heritage LibraryBHL assigned 40,000Digital Object Identifiersto monograph titlesIn 5 months endingMarch 2012, there were5,333 resolutionattempts (i.e. uses) ofthe DOIs for 4,562unique titles. From Martin Kalfatovic
  • 7. Using EOL collectionsto get computable data Step 1: Search on EOL for organisms with characteristics of interest. Add each one to an EOL collection. Step 2: Write a program using EOL API methods to retrieve the external database identifiers for the species in that collection. Step 3: Add to your program code to retrieve data using external database APIs. Step 4: Analyze, rinse, repeat. From Arthur Chapman
  • 8. Crowd-sourcing for computable dataLovell and Libby Langstroth, Calphotos Foodwebs.org
  • 9. We can do morePhylogenetic tree challenge http://eol.org/info/tree_challenge Free trip to iEvoBio, deadline 15 AprilComputable data challenge http://eol.org/info/data_challenge $50,000, deadline 22 MaySemantic reasoning workshop, in SeptemberThe Smithsonian’s Phenotype Repository or Gateway?
  • 10. Summing up• EOL offers powerful aggregating, summarizing, searching, curating, and crowd-sourcing features• EOL content is already usable for research• Enhancements to EOL for science research are underwayWhat questions do you want to answer?What data or features do you need?
  • 11. Thanks toOur funders John D. and Catherine T. MacArthur Foundation Alfred P. Sloane Foundation Smithsonian Institution Marine Biological Laboratory Harvard University David Rubenstein and other funders and donorsAll our content providers and global partnersVolunteer curators and individual contributors via Flickr, Wikimedia, and members of EOL