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Aber-OWL: a framework for ontology-based data access in biology.

Hoehndorf R, Slater L, Schofield PN, Gkoutos GV - BMC Bioinformatics (2015)

Bottom Line: We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies.Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature.When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.

View Article: PubMed Central - PubMed

Affiliation: Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia. robert.hoehndorf@kaust.edu.sa.

ABSTRACT

Background: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning.

Results: We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL is freely available at http://aber-owl.net .

Conclusions: Aber-OWL provides a framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies. When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.

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Related in: MedlinePlus

A SPARQL query for markers significantly associated withventricular septal defect. The query is executed against the GWAS Central SPARQL endpoint at http://fuseki.gwascentral.org/query.html.
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Fig2: A SPARQL query for markers significantly associated withventricular septal defect. The query is executed against the GWAS Central SPARQL endpoint at http://fuseki.gwascentral.org/query.html.

Mentions: We can also utilize the Aber-OWL infrastructure for more powerful queries that use inference over the ontology structure and utilize the results in a SPARQL query. For example, we can use Aber-OWL: SPARQL to query GWAS Central [32] for markers that have been identified in GWAS studies as significant for ventricular septal defects (Figure 2).Figure 2


Aber-OWL: a framework for ontology-based data access in biology.

Hoehndorf R, Slater L, Schofield PN, Gkoutos GV - BMC Bioinformatics (2015)

A SPARQL query for markers significantly associated withventricular septal defect. The query is executed against the GWAS Central SPARQL endpoint at http://fuseki.gwascentral.org/query.html.
© Copyright Policy - open-access
Related In: Results  -  Collection

License 1 - License 2
Show All Figures
getmorefigures.php?uid=PMC4384359&req=5

Fig2: A SPARQL query for markers significantly associated withventricular septal defect. The query is executed against the GWAS Central SPARQL endpoint at http://fuseki.gwascentral.org/query.html.
Mentions: We can also utilize the Aber-OWL infrastructure for more powerful queries that use inference over the ontology structure and utilize the results in a SPARQL query. For example, we can use Aber-OWL: SPARQL to query GWAS Central [32] for markers that have been identified in GWAS studies as significant for ventricular septal defects (Figure 2).Figure 2

Bottom Line: We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies.Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature.When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.

View Article: PubMed Central - PubMed

Affiliation: Computational Bioscience Research Center, King Abdullah University of Science and Technology, 4700 KAUST, Thuwal, 23955-6900, Saudi Arabia. robert.hoehndorf@kaust.edu.sa.

ABSTRACT

Background: Many ontologies have been developed in biology and these ontologies increasingly contain large volumes of formalized knowledge commonly expressed in the Web Ontology Language (OWL). Computational access to the knowledge contained within these ontologies relies on the use of automated reasoning.

Results: We have developed the Aber-OWL infrastructure that provides reasoning services for bio-ontologies. Aber-OWL consists of an ontology repository, a set of web services and web interfaces that enable ontology-based semantic access to biological data and literature. Aber-OWL is freely available at http://aber-owl.net .

Conclusions: Aber-OWL provides a framework for automatically accessing information that is annotated with ontologies or contains terms used to label classes in ontologies. When using Aber-OWL, access to ontologies and data annotated with them is not merely based on class names or identifiers but rather on the knowledge the ontologies contain and the inferences that can be drawn from it.

Show MeSH
Related in: MedlinePlus