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Dumontier::Bio-ontologies 2013:Ovopubs 1

Alison Callahan and Michel DumontierCarleton University

Ovopubs: Modular data publication with minimal provenance


Data publication

• Emerging interest in publishing data on the web• microdata formats (rdfa, schema.org) and formal

knowledge representation languages (RDF/OWL) • Efforts to capturing credit/provenance of assertions– PROV-O, OAG– nanopublications (data/statements - Groth, Kuth)– microattributions (gene variation - Patrinos et al)– micropublications (discourse - Clark et al)


assertions

Nanopublication• A nanopublication claims to be the “smallest,

unambiguous unit of thought”. • A nanopublication is an RDF graph that links to

two/three graphs:– A graph containing one or more assertions– A graph containing the provenance for the assertion(s)– A graph providing information about the nanopublication

assertion provenance publication

Problems : indirection between assertion and its provenance; what if no provenance is provided? nanopub graph cannot fully contain other graphs; reasoning and easy of queries across nested graphs.


an Ovopub is an object that contains and links to data and the ovopub’s provenance

data

provenance


an assertion ovopub contains one or more connected statements

This ovopub is good for capturing knowledge in the form of statements


An ovopub also links itself to its content

rdfs:member <uri>

This explicit reification enables transitive closures over graph structures


An ovopub contains and links to its own provenance

• dc:creator <uri>• dc:created xsd:datetime• dc:license <uri>• rdf:type sio:assertion-ovopub sio:collection-ovopub

creator

timestamp

license

ovopub type


a collection ovopub contains one or more unconnected items

Item types: - object - assertion ovopub - collection ovopub

This ovopub is good for - encapsulation and

redistribution of selected content

- restriction of query execution / results


iRefIndex: Ovopub Case Study for Datasets, Records, Assertions


Future work• Actively develop the nanopublication as a community

standard for provenance-based data publication– Assess the value of directly linking assertion & provenance graphs– Generate (revised) nanopublications in Bio2RDF

• Promote nanopublication-based design patterns for:– direct/indirect data/discourse assertions– Aggregation semantics

• Use of nanopublications for scientific research– Evidence gathering (HyQue)

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Michel [email protected]

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