9/12/2011 OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL Mikel Egaña Aranguren ([email protected]) Ontology Engineering Group School of Computer Science UPM, Spain Jesualdo Tomás Fernández-Breis ([email protected]) School of Computer Science UM, Spain Erick Antezana ([email protected]) Department of Biology NTNU, Norway http://www.slideshare.net/MikelEganaAranguren/opplgalaxy-enhancing-ontology-exploitation-in- galaxy-with-oppl
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OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL
Biomedical ontologies are key to the success of Semantic Web technologies in Life Sciences; therefore, it is important to provide appropriate tools for their development and further exploitation. The Ontology Pre Processor Language (OPPL) can be used for automating the complex manipulation needed to devise biomedical ontologies with richer axiomatic content, which in turn pave the way towards advanced biological data analyses. We present OPPL-Galaxy, an OPPL wrapper for the Galaxy platform, and a series of examples demonstrating its functionality for enriching ontologies. As Galaxy provides an integrated framework to make use of various bioinformatics tools, the functionality delivered by OPPL to manipulate ontologies can be combined along with the tools and workflows devised in Galaxy. As a result, those workflows can be used to perform more thorough analyses of biological information by exploiting extant biological knowledge codified in (enriched) biomedical ontologies
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9/12/2011
OPPL-Galaxy: Enhancing ontology exploitation in
Galaxy with OPPL
Mikel Egaña Aranguren ([email protected])Ontology Engineering GroupSchool of Computer Science
UPM, Spain
Jesualdo Tomás Fernández-Breis ([email protected])School of Computer Science
Scripting Language for automating ontology manipulation
Ontology New ontology
?whole:CLASS,?part:CLASSSELECT ?part SubClassOf part_of some ?whole WHERE ?part != NothingBEGINADD ?part SubClassOf part_of only ?wholeEND;
OPPL-Galaxy
What is OPPL-Galaxy
Jeremy Goecks, Anton Nekrutenko, James Taylor, and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11(8):R86+, 2010.
OPPL-Galaxy
Galaxy
OPPL-Galaxy
What is OPPL-Galaxy
Jeremy Goecks, Anton Nekrutenko, James Taylor, and The Galaxy Team. Galaxy: a comprehensive approach for supporting accessible, reproducible, and transparent computational research in the life sciences. Genome Biology, 11(8):R86+, 2010.
Alan Rector, Nick Drummond, Matthew Horridge, Jeremy Rogers, Holger Knublauch, Robert Stevens, Hai Wang, and Chris Wroe. OWL pizzas: Practical experience of teaching OWL-DL: Common errors and common patterns. In LNCS 3257, 2004.
?target:CLASS,?prop:OBJECTPROPERTY,?filler:CLASS SELECT ASSERTED ?target SubClassOf ?prop only ?fillerWHERE FAIL ?target SubClassOf ?prop some ?filler BEGIN ADD ?target SubClassOf !OnlyBadPracticeResult END;
BioPAX
OPPL-Galaxy
Ontology debugging
OPPL-Galaxy
Alan Rector, Nick Drummond, Matthew Horridge, Jeremy Rogers, Holger Knublauch, Robert Stevens, Hai Wang, and Chris Wroe. OWL pizzas: Practical experience of teaching OWL-DL: Common errors and common patterns. In LNCS 3257, 2004.
?target:CLASS,?prop:OBJECTPROPERTY,?filler:CLASS SELECT ASSERTED ?target SubClassOf ?prop only ?fillerWHERE FAIL ?target SubClassOf ?prop some ?filler BEGIN ADD ?target SubClassOf !OnlyBadPracticeResult END;
?x:CLASS,?y:OBJECTPROPERTY = MATCH("has((\w+))"),?z:CLASS,?feature:CLASS = create(?y.GROUPS(1))SELECT ASSERTED ?x subClassOf ?y some ?zBEGINREMOVE ?x subClassOf ?y some ?z,ADD ?x subClassOf !hasFeature some (?feature and !hasValue some ?z)END;
Person subClassOf hasheight some high
Person subClassOf hasFeature some (height and hasValue some high)
OPPL-Galaxy
Implementation
OPPL-Galaxy
Implementation
OPPL-Galaxy
URI mapping file (If imports)
Input ontology: OWL, OBO, ...
OPPL flat file
Output ontology: OWL (RDF/XML) or OBO
Add inferred subsumptions as assertions
Merge ontologies (If imports)
Reasoner: Pellet, FaCT++, HermiT
OPPL-Galaxy
Implementation
Galaxy
OPPL wrapper
OPPL APIOWL APIReasoner
OPPL-Galaxy
Implementation
Galaxy
OPPL options
Ontology
?whole:CLASS,?part:CLASSSELECT ?part SubClassOf part_of some ?whole WHERE ?part != NothingBEGINADD ?part SubClassOf part_of only ?wholeEND;
OPPL wrapper
OPPL APIOWL APIReasoner
OPPL-Galaxy
Implementation
Galaxy
OPPL options
Ontology
?whole:CLASS,?part:CLASSSELECT ?part SubClassOf part_of some ?whole WHERE ?part != NothingBEGINADD ?part SubClassOf part_of only ?wholeEND;
OPPL wrapper
OPPL APIOWL APIReasoner
OPPL-Galaxy
Implementation
Galaxy
OPPL options
Ontology
?whole:CLASS,?part:CLASSSELECT ?part SubClassOf part_of some ?whole WHERE ?part != NothingBEGINADD ?part SubClassOf part_of only ?wholeEND;
Galaxy tools
Downloadontology
OPPL wrapper
OPPL APIOWL APIReasoner
Modified ontology
OPPL-Galaxy
Availability
OPPL-Galaxy
Availability
OPPL-Galaxy at Galaxy tool shed Ontology manipulation: http://toolshed.g2.bx.psu.edu/