How the Encyclopedia of Life is wrangling organismal attribute data
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The document discusses the Encyclopedia of Life's (EOL) efforts to aggregate and standardize organism attribute data from various sources. Some key points: - EOL harvests data from over 240 content providers and hosts over 1.1 million species pages. It receives over 3.3 million annual visitors from 235 countries. - EOL is developing a TraitBank to aggregate trait data from various datasets, totaling over 128,000 data points for over 20,000 taxa so far. It aims to make this data easily accessible and analyzable. - Challenges include standardizing data from different sources and filling gaps, but aggregated trait data could help answer questions about topics like species interactions, tissue
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How the Encyclopedia of Life is wrangling organismal attribute data
- 1. eol.org @eol @cydparr How the Encyclopedia of Life is wrangling organismal attribute data
- 2. How EOL works EOL Crowds Harvest Third party applications
- 3. EOL Today Key Milestones in 2013 1.1 million species pages 240+ content providers 3.3 million unique annual visitors from 235 countries
- 4. 0 100000 200000 300000 400000 500000 600000 700000 800000 Distribution MolecularBiology Multiple topics TypeInformation Habitat ConservationStatus Threats Morphology Conservation Management Trends Size Associations Uses TrophicStrategy Cyclicity & Life Cycle PopulationBiology Reproduction Migration Taxonomy LifeExpectancy Identification Behaviour Ecology Diseases Number of text objectsSubjectoftextobject
- 5. Text mining, crowdsourcing, standardizing see http://eol.org/info/fellows Co-occurrence, term extraction & linked data Thessen & Devries EnvO habitat terms Pafilis et al. Altitude Specificity of Flower Coloration Wright Morphological impacts of extinction risk in fish Chang Butterfly-hostplant associations Ferrer-Parris et al. Species Interactions Poelen & Mungall et al.
- 6. 14 datasets containing 25k taxa, 422k interactions, for 3k locations alpha version of ingestion, normalization, aggregation alpha version of web API alpha version of data exports Dr. Katy Börner led Information Visualization MOOC GLoBI http://globalbioticinteractions.wordpress.com/
- 7. EOL TraitBank Funded: Marine focus Virtuoso triple store, re-using URIs where possible 5 datasets 128,050 data points for 20,896 taxa Harvest and display on data tab Downloads, fancy searching Machine access
- 10. Uploads & harvests will be by spreadsheet and Darwin Core Archive Support for annotation and curation Please contact me to be part of the private beta
- 11. Easy access to analyzable trait data “Are blue organisms more common in high altitudes?” “Does the evolution of mammalian bacula appear to be related to the pattern of promiscuous mating?” “What organisms should I collect to fill in gaps in genome quality tissue collections?” • Look for trait, download for all taxa • Create a collection of taxa, download all data • Use Reol: an R interface to EOL (Banbury, O’Meara) http://reolblog.wordpress.com/ • Find more specialized data repositories
- 12. But also . . .
- 13. Thanks Funding & other contributions Sloan Foundation Smithsonian Institution David Rubenstein Marine Biological Laboratory Harvard University Our content partners Thousands of individual contributors, and hundreds of volunteer curators Image credits Jenny from Taipei Cynthia Parr Chief Scientist @eol @cydparr parrc@si.edu Alexandria Archive: Sarah Kansa, Eric Kansa, 34 othe zooarchaeologists GLoBI: Jorrit Poelen (lead/software), Chris Mungall (ontologies), James Simons (biologist) and Robert Reiz (software). Datasets shared by: Peter D. Roopnarine, Rachel Hertog, Carlos García- Robledo, James Simons, Jenny L. Wrast, C. Barnes, International Council for the Exploration of the Sea (ICES), Jose R. Ferrer Paris, Senol Akin, Malcolm Storey (BioInfo.org.uk), Ivy E. Baremore, Joel Sachs (SPIRE), Colt W. Cook, David A. Blewett
- 14. Quick math In Phenoscape 57 publications had 565,158 anatomical trait descriptions for 2,527 kinds of organisms = 223 traits/organism In ZFIN 38,189 trait descriptions for 4,727 genes for Zebra Fish 1.9 million species on the planet = LOTS OF TRAITS
- 15. Anatolia Zooarchaeology Case Study led by Alexandria Archive Institute 1. 14 different sites 2. 34+ zooarchaeologists 3. Decoding, cleanup, metadata documentation 4. 220,000+ specimens 5. 450 entities linked to 143 EOL taxon concepts 6. Anatomical entities linked to Uberon.org 7. Biometrics linked to measurement ontology 8. Collaborative analysis http://opencontext.org/
Editor's Notes
- We have a working infrastructure as well as more than 200 partners, We harvest and sort text and multimedia by topic and by species and put it on our pages. Curation + user-added content from the crowds is added to the mix.This is fed back to providers, giving them traffic, quality control on their own content, and new content for them to use And, we are already seeing spinoff products. We make it easy for developers, and everything is either public domain or CC-licensed so it can be re-used.
- We now have over a million pages with content, some of it is even in other languages like Arabic, Spanish, and Chinese. And we are getting traffic mostly from the general public, from all over the world.
- Most of our 5.4 million content objects are text blobs and here are the subjects of that text. Most often, our text objects are about distribution. But there are many other subjects involved including essays that include multiple subjects.
- Except for the first, links for that one on request
- Information Visualization MOOC (Massive Open Online Course) led by Dr. Katy Börner of Indiana University, students TwyBethard (United States), Andrew Miles (United Kingdom), Edward Kok (Netherlands) and Mattia Della Libera (Italy) used GloBI data to create an insightful visualization of spatial marine food webs in the Gulf of Mexico.
- Starting with marine dataIn the most simplistic view, we’ll be storing triplesThis data will be organized on a data tab, sorting out the data into the 35 or so “topics” that we currently have text chapters for, and we will also allow powerful downloading and searching capabilityFinally we’ll be setting up ways for other applications to grab the data and do interesting things with it. We already have a tool for making field guides,The approach here builds on our innovations for EOL and adds some proven technology called the “semantic web” to our domain. The next step takes this chain of innovation even further.
- Drawing data from the literature, from online databases, and from published datasets as in Dryad, summarizing collections databases
- Everyone wants to know theattributes of organismsPeople exploring the world find something and want to be able to search on characteristics they can seeTeachers want their students to become adept at analyzing data, and how better than to work with real numerical information about the size of organisms or their behavior or what their sensitivity is to temperature and what might happen in the face of climate changeSo while scientists were saying they needed us to provide data they could analyze, we heard the same thing from our educators, too.
- Phenoscape is a database that is looking at anatomical traits in fishes. Looking just at 57 publications they have more than 500K descriptions for 2500 kinds of organisms.ZFIN is a model organism database for zebrafish, a common model organism for developmental biologists. In just this one species they have captured nearly 40,000 traits – just for ONE very well-studied SPECIES
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