Date post: | 01-Sep-2014 |
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Challenges for semantics in EOL
Cynthia ParrNational Museum of Natural HistorySmithsonian Institution
Phenotype Ontology RCNNESCent25 February 2011
http://www.eol.org• All species known to science• Summary descriptions across
biology domains• Freely accessible• Available from a single portal
in a common format• Quality• Always growing
Catalogue of Life
IUCN
GBIF
Biodiversity Heritage Library
Content providersDatabasesJournalsLifeDesksPublic contribution
Curating
CommentingTagging
EOL is a Content Curation Community
Typical species page
Objects can come from many partnersObjects are sorted by topic and by taxonEach partner gets credit
http://www.eol.org/content_partner
Curation, Comments, Tags
Not
Statistics
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
http://NodeXL.codeplex.com
Schema
Very coarsely structured33 subjects (TDWG Species Profile Model)
No numeric dataMinimal controlled vocabulariesAPI
Corvidae
We have an infrastructure . . .Aggregation mechanismsNames resolutionCuration mechanismsPublic and machine interfaces
Version 2 (August) vastly improved support for community interaction
Version 3 (???)
Rich page calculations
TaxonKey 1 Value
Key 2 Value
Key 3 Value
Key 1 Unit Label URI
Key 2 Unit Label URI
Key 3 Unit Label URI
Possible path to semantics
What could we do?
Organize info on EOL pages
Index by taxonSort into one of the 33
SPM subjectsImprove discoverability
Serve data by API or query interface
“Give me all the information you have about the elbow joint and life histories in rodents”
Make the whole page semantically browsable (LOD: linked open data)TaxonText blobsCharacter dataMetadata
Consistency checks
CuratorsCrowd-sourcingReasoning…
… inferring summaries….mining for patterns?… hypothesis testing?
ievobio.org
Image credits
Michal Koupý Lorraine PhelanDavid J Patterson Dmitry Mozzherin