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Cynthia Parr Phenotype RCN NESCent 25 February 2013. @ cydparr @ eol. EOL aggregates and curates across topics, across the tree of life. Scientific Databases, including BHL, GBIF, ALA, INBio , COL, Scratchpads, LifeDesks Scientific Journals. Curate . Aggregate. Comment - PowerPoint PPT Presentation
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@cydparr @eol
Cynthia ParrPhenotype RCN NESCent 25 February 2013
EOL aggregates and curates across topics, across the tree of life
Scientific Databases, includingBHL, GBIF, ALA, INBio, COL, Scratchpads, LifeDesks Scientific Journals Curate
CommentRate, Collect
eol.orgAggregate
Quality control API
Third party apps
EOL summarizes knowledge
Erosaria caputserpentisSerpent's Head Cowrie
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 - 0.228 Silicate (umol/l): 0.983 - 4.026
From Moorea Biocode
From GBIFFrom OBIS
Statistics2 years ago• 2.8 million pages – one (or
more) per taxon
• 2 million data objects
• 500 thousand pages with objects
• 100+ partner databases
• 700 curators/1000s contributors/~46,000 members
Today• 3.3 million pages – one (or
more) per taxon
• 5 million CC-licensed data objects
• Over 1 million pages with objects
• 200+ partner databases
• 1200 curators/1000s contributors/~64,000 members
We have an infrastructure . . .• Aggregation mechanisms• Names resolution• Curation mechanisms• Public and machine interfaces• User-created collections
What are the next use cases to tackle?How could ontologies & annotations help?
See structured info on EOL pages
Discover and identify“find taxa with these characteristics”
Browse the whole page semantically, link to related resources (LOD: linked open data)
Google Summer of Code with Phenoscape (Alex Ginsca)Using DBPedia Spotlight to extract associations among taxa and add to Linked Open Data cloud (Devries and Thessen)Linking names, literature, phylogeny (Page)Resolving archeological data on animal domestication in the near east (Alexandria Archive Institute)
Promote NLP text mining and crowdsourcing
– Altitude Specificity of Flower Coloration (Wright)– Species Interaction Datasets—Integration,
Visualization, and Analysis (Poelen and Mungall)– Crowd-sourced data to examine morphological
impacts of extinction risk in ray-finned fishes (Chang)
– Macroecological patterns in butterfly-hostplant associations (Ferrer-Parris)
– Discovering habitat terms in EOL contents (Pafilis)
Easy access to analyzable data “Are blue organisms more common in high altitudes?” “How can I predict vulnerability to climate change based on life history characteristics?” “What organisms should I collect to fill in gaps in genome quality data?”
• Look for data, download for all taxa• Create a collection of taxa, download all data• Use Reol: an R interface to EOL (Banbury, Omeara)http://barbbanbury.info/barbbanbury/Reol.html• Find more specialized data repositories
Dynamic online knowledge
• Support summaries with networks of evidence– E.g. Bergmann’s rule: animals living in higher
latitudes have larger body size
• As evidence grows or changes, change the knowledge summary
• Flag evidence that is in conflict with the summary
Erosaria caputserpentisSerpent's Head Cowrie
Salinity envelope (n=40)
From OBIS
Summarize data across providersFlag outlier data
The big picture
In progress: Marine computable dataDraft phylogenetic tree from Open Tree of Life project
TraitBank: access to computable descriptive information across the tree of life
Our fundersJohn D. and Catherine T. MacArthur FoundationAlfred P. Sloane FoundationSmithsonian InstitutionMarine Biological LaboratoryHarvard UniversityDavid Rubenstein and other funders and donors
All our content providers and global partners
Volunteer curators and individual contributors via Flickr, Wikimedia, and members of EOL
Thanks to