practical interoperability across semantic stores of data for ecological, taxonomic, phylogenetic,...
DESCRIPTION
Presented at the Biodiversity Information Standards (Taxonomic Databases Working Group) 2013 meeting in Florence, Italy on 31 October 2013. Essentially, an introduction to aspects of the back end of the new trait repository of Encyclopedia of Life.TRANSCRIPT
Practical interoperabilityacross semantic stores of data for blah blah blah
eol.org@eol@cydparr
The road to TraitBank In second year of 2 year project: Marine
Expert AudienceConservation science
Virtuoso triple store<EOL taxon id> <hasAvgBodyMass in g> <value><EOL taxon id> <preysOn> <scientific name>
Beta testing NOW for public launch early 201421 datasets with 2.8 million data records for 520,000 taxa
Harvest, display, curate, search, download
MOST DATA NOT BORN SEMANTIC
From text miningFrom literature tablesFrom data papersFrom databases
Term URIs from existing ontologies
• Statistics from Semantic Science Integrated Ontology• Units Ontology• Environments Ontology EnvO• Gene Ontology• ETHAN (Natural history, with Joel Sachs)• Vertebrate Trait Ontology• Plant Trait Ontology
• Where necessary: request terms• Last resort: create provisional terms with
http://eol.org/schema/terms/xxxx• Of course, also using unique EOL taxon identifiers, which we’ve
mapped to identifiers of other projects
e.g. those registered in bioportal.bioontologies.org
Known URIs tool
Only light reasoning so far– just to infer inverse relationships like “eats” and “is eaten by”
14 datasets with 25k taxa, 422k interactions, for 3k locationsalpha version of ingestion, normalization, aggregationalpha version of web APIalpha version of data exports
GLoBI http://globalbioticinteractions.wordpress.com/Jorrit Poelen, Chris Mungall, James Simon GoMexSi
GLoBI ontology workhttps://github.com/jhpoelen/eol-globi-data/tree/master/eol
-globi-ontology
Interaction processes from Gene OntologyRelations from OBO Relations OntologyLife cycle stages and body parts from UBERONObservation and specimen terms from variousBehaviors from NeuroBehaviorOntology and Habitat keywords from Environment Ontology
New terms:/eats, /interactsWith, /preysUpon, /hasHost, /hosts, /parasitizes
Adding data
To do
• Term evaluation and recommendations• Map similar terms• Map terms to upper ontology like Species
Profile Model• Leverage reasoning for data validation
To access to the Beta test, happening NOWSend your EOL login to:
@cydparr [email protected]