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Practical interoperability
across 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 Audience
Conservation science
Virtuoso triple store
...
Term URIs from existing ontologies
•
•
•
•
•
•
•

e.g. those registered in bioportal.bioontologies.org
Statistics from Sem...
Known URIs tool

Only light reasoning so far– just to infer inverse
relationships like “eats” and “is eaten by”
GLoBI http://globalbioticinteractions.wordpress.com/
Jorrit Poelen, Chris Mungall, James Simon GoMexSi
14 datasets with 25...
GLoBI ontology work
https://github.com/jhpoelen/eol-globidata/tree/master/eol-globi-ontology
Interaction processes from Ge...
Adding data
To do
• Term evaluation and recommendations
• Map similar terms
• Map terms to upper ontology like Species
Profile Model
•...
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Practical interoperability across semantic stores of data for ecological, taxonomic, phylogenetic, and metagenomics research

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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.

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Practical interoperability across semantic stores of data for ecological, taxonomic, phylogenetic, and metagenomics research

  1. 1. Practical interoperability across semantic stores of data for blah blah blah eol.org @eol @cydparr
  2. 2. The road to TraitBank In second year of 2 year project: Marine Expert Audience Conservation science Virtuoso triple store <EOL taxon id> <hasAvgBodyMass in g> <value> <EOL taxon id> <preysOn> <scientific name> Beta testing NOW for public launch early 2014 21 datasets with 2.8 million data records for 520,000 taxa Harvest, display, curate, search, download MOST DATA NOT BORN SEMANTIC From text mining From literature tables From data papers From databases
  3. 3. Term URIs from existing ontologies • • • • • • • e.g. those registered in bioportal.bioontologies.org 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
  4. 4. Known URIs tool Only light reasoning so far– just to infer inverse relationships like “eats” and “is eaten by”
  5. 5. GLoBI http://globalbioticinteractions.wordpress.com/ Jorrit Poelen, Chris Mungall, James Simon GoMexSi 14 datasets with 25k taxa, 422k interactions, for 3k locations alpha version of ingestion, normalization, aggregation alpha version of web API alpha version of data exports
  6. 6. GLoBI ontology work https://github.com/jhpoelen/eol-globidata/tree/master/eol-globi-ontology Interaction processes from Gene Ontology Relations from OBO Relations Ontology Life cycle stages and body parts from UBERON Observation and specimen terms from various Behaviors from NeuroBehaviorOntology and Habitat keywords from Environment Ontology New terms: /eats, /interactsWith, /preysUpon, /hasHost, /hosts, /parasitizes
  7. 7. Adding data
  8. 8. 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 NOW Send your EOL login to: @cydparr parrc@si.edu

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