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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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A query for all human proteins annotated to a part of apoptosis. The query is executed against the UniProt SPARQL endpoint at http://sparql.uniprot.org. To rewrite the URI scheme used by UniProt for GO classes to the URI scheme returned by Aber-OWL, Aber-OWL: SPARQL must be used with the prefix rewriting option set to true.
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Fig1: A query for all human proteins annotated to a part of apoptosis. The query is executed against the UniProt SPARQL endpoint at http://sparql.uniprot.org. To rewrite the URI scheme used by UniProt for GO classes to the URI scheme returned by Aber-OWL, Aber-OWL: SPARQL must be used with the prefix rewriting option set to true.

Mentions: We can demonstrate the possibilities of using the Aber-OWL: SPARQL query expansion service by retrieving all human proteins in UniProt [31] annotated to part_of some ’apoptotic process’. To achieve this goal, we use the SPARQL 1.1 VALUES statement to bind the results to a variable ?ontid, and then we can use this variable in the SPARQL query to retrieve all human proteins with a Gene Ontology annotation in ?ontid. The query is shown in Figure 1.Figure 1


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

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

A query for all human proteins annotated to a part of apoptosis. The query is executed against the UniProt SPARQL endpoint at http://sparql.uniprot.org. To rewrite the URI scheme used by UniProt for GO classes to the URI scheme returned by Aber-OWL, Aber-OWL: SPARQL must be used with the prefix rewriting option set to true.
© Copyright Policy - open-access
Related In: Results  -  Collection

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

Fig1: A query for all human proteins annotated to a part of apoptosis. The query is executed against the UniProt SPARQL endpoint at http://sparql.uniprot.org. To rewrite the URI scheme used by UniProt for GO classes to the URI scheme returned by Aber-OWL, Aber-OWL: SPARQL must be used with the prefix rewriting option set to true.
Mentions: We can demonstrate the possibilities of using the Aber-OWL: SPARQL query expansion service by retrieving all human proteins in UniProt [31] annotated to part_of some ’apoptotic process’. To achieve this goal, we use the SPARQL 1.1 VALUES statement to bind the results to a variable ?ontid, and then we can use this variable in the SPARQL query to retrieve all human proteins with a Gene Ontology annotation in ?ontid. The query is shown in Figure 1.Figure 1

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