Practical interoperability across semantic stores of data for blah blah blah
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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

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Practical interoperability across semantic stores of data for blah blah blah

Practical interoperabilityacross semantic stores of data for blah blah blah

eol.org

@eol

@cydparr


The road to traitbank

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


Term uris from existing ontologies

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


Known uris tool

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

GLoBI http://globalbioticinteractions.wordpress.com/JorritPoelen, Chris Mungall, James Simon GoMexSi

14 datasetswith 25k taxa,422k interactions, for 3k locations

alpha version of ingestion, normalization, aggregation

alpha version of web API

alpha version of data exports


Globi ontology work https github com jhpoelen eol globi data tree master eol globi ontology

GLoBI ontology workhttps://github.com/jhpoelen/eol-globi-data/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


Adding data

Adding data


To do

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:

@[email protected]


  • Login