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Capturing domain knowledge from multiple sources: the rare bone disorders use case.

Groza T, Tudorache T, Robinson PN, Zankl A - J Biomed Semantics (2015)

Bottom Line: We introduce an approach that enables the loose integration of knowledge emerging from diverse sources under a single coherent interoperable resource.To accurately track the original knowledge statements, we record the provenance at very granular levels.Using RBDO, researchers are able to answer queries, such as: "What phenotypes describe a particular disorder and are common to all sources?" or to understand similarities between disorders based on divergent groupings (classifications) provided by the underlying sources.

View Article: PubMed Central - PubMed

Affiliation: School of ITEE, The University of Queensland, St Lucia, Australia.

ABSTRACT

Background: Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. The community-driven ontology curation process, however, ignores the possibility of multiple communities building, in parallel, conceptualisations of the same domain, and thus providing slightly different perspectives on the same knowledge. The individual nature of this effort leads to the need of a mechanism to enable us to create an overarching and comprehensive overview of the different perspectives on the domain knowledge.

Results: We introduce an approach that enables the loose integration of knowledge emerging from diverse sources under a single coherent interoperable resource. To accurately track the original knowledge statements, we record the provenance at very granular levels. We exemplify the approach in the rare bone disorders domain by proposing the Rare Bone Disorders Ontology (RBDO). Using RBDO, researchers are able to answer queries, such as: "What phenotypes describe a particular disorder and are common to all sources?" or to understand similarities between disorders based on divergent groupings (classifications) provided by the underlying sources.

Availability: RBDO is available at http://purl.org/skeletome/rbdo. In order to support lightweight query and integration, the knowledge captured by RBDO has also been made available as a SPARQL Endpoint at http://bio-lark.org/se_skeldys.html.

No MeSH data available.


Related in: MedlinePlus

The upper-level structure of RBDO enriched with provenance information. As a note, the PROV: Entity concept is duplicated in the figure for readability purposes.
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Fig3: The upper-level structure of RBDO enriched with provenance information. As a note, the PROV: Entity concept is duplicated in the figure for readability purposes.

Mentions: Figure 3 depicts our ontology enriched with provenance. Using this model, one can add provenance to both entities defined in the ontology, as well as relationships created between these entities. More concretely, provenance is captured for:


Capturing domain knowledge from multiple sources: the rare bone disorders use case.

Groza T, Tudorache T, Robinson PN, Zankl A - J Biomed Semantics (2015)

The upper-level structure of RBDO enriched with provenance information. As a note, the PROV: Entity concept is duplicated in the figure for readability purposes.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4414390&req=5

Fig3: The upper-level structure of RBDO enriched with provenance information. As a note, the PROV: Entity concept is duplicated in the figure for readability purposes.
Mentions: Figure 3 depicts our ontology enriched with provenance. Using this model, one can add provenance to both entities defined in the ontology, as well as relationships created between these entities. More concretely, provenance is captured for:

Bottom Line: We introduce an approach that enables the loose integration of knowledge emerging from diverse sources under a single coherent interoperable resource.To accurately track the original knowledge statements, we record the provenance at very granular levels.Using RBDO, researchers are able to answer queries, such as: "What phenotypes describe a particular disorder and are common to all sources?" or to understand similarities between disorders based on divergent groupings (classifications) provided by the underlying sources.

View Article: PubMed Central - PubMed

Affiliation: School of ITEE, The University of Queensland, St Lucia, Australia.

ABSTRACT

Background: Lately, ontologies have become a fundamental building block in the process of formalising and storing complex biomedical information. The community-driven ontology curation process, however, ignores the possibility of multiple communities building, in parallel, conceptualisations of the same domain, and thus providing slightly different perspectives on the same knowledge. The individual nature of this effort leads to the need of a mechanism to enable us to create an overarching and comprehensive overview of the different perspectives on the domain knowledge.

Results: We introduce an approach that enables the loose integration of knowledge emerging from diverse sources under a single coherent interoperable resource. To accurately track the original knowledge statements, we record the provenance at very granular levels. We exemplify the approach in the rare bone disorders domain by proposing the Rare Bone Disorders Ontology (RBDO). Using RBDO, researchers are able to answer queries, such as: "What phenotypes describe a particular disorder and are common to all sources?" or to understand similarities between disorders based on divergent groupings (classifications) provided by the underlying sources.

Availability: RBDO is available at http://purl.org/skeletome/rbdo. In order to support lightweight query and integration, the knowledge captured by RBDO has also been made available as a SPARQL Endpoint at http://bio-lark.org/se_skeldys.html.

No MeSH data available.


Related in: MedlinePlus