OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL
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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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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
Transcript of OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL
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
UM, Spain
Erick Antezana ([email protected])Department of Biology
NTNU, Norway
http://www.slideshare.net/MikelEganaAranguren/opplgalaxy-enhancing-ontology-exploitation-in-galaxy-with-oppl
OPPL-Galaxy
Index
What is OPPL-Galaxy?
Use cases
Implementation
Availability
Conclusions
OPPL-Galaxy
What is OPPL-Galaxy?
OPPL-Galaxy
What is OPPL-Galaxy
OPPL-Galaxy
Ontology Pre Processor Language (OPPL)
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.
OPPL-Galaxy
Galaxy
OPPL-Galaxy
What is OPPL-Galaxy
OPPL-Galaxy
Ontology refactoring (Axiomatic enrichment, ODPs, … )Detection of structures (Antipatterns, … )Advanced querying (Reasoning+regexps, …)Ontology trimming
OPPL
OPPL-Galaxy
What is OPPL-Galaxy
OPPL-Galaxy
Ontology refactoring (Axiomatic enrichment, ODPs, … )Detection of structures (Antipatterns, … )Advanced querying (Reasoning+regexps, …)Ontology trimming
OPPL
Analysis historyAnalysis shareabilityCombinations of toolsComplex workflows
Galaxy
OPPL-Galaxy
What is OPPL-Galaxy
OPPL-Galaxy
Ontology refactoring (Axiomatic enrichment, ODPs, … )Detection of structures (Antipatterns, … )Advanced querying (Reasoning+regexps, …)Ontology trimming
OPPL
Analysis historyAnalysis shareabilityCombinations of toolsComplex workflows
Galaxy
OPPL-Galaxy
What is OPPL-Galaxy
Ontology OPPL scriptUser
Ontology User
OPPL-Galaxy
WorkflowsGeneOntology (GO)
OPPL script 1
OPPL script 2
Onto-toolkit
Gene Ontology Annotation file (GOA)
OPPL-Galaxy
OPPL-Galaxy
Workflows
OPPL-Galaxy
?localisation_sibling:CLASSSELECT ASSERTED ?localisation_sibling SubClassOf GO_0008150WHERE ?localisation_sibling != GO_0051179BEGIN ADD ?localisation_sibling DisjointWith GO_0051179END;
?hepatocyte_process:CLASS, ?hepatocyte_process_label:CONSTANT = MATCH(".?hepatocyte.+"),?has_part_hepatocyte_process:CLASS,?part_of_or_regulates:OBJECTPROPERTYSELECT ASSERTED ?hepatocyte_process.IRI label ?hepatocyte_process_label,?hepatocyte_process subClassOf ?part_of_or_regulates some (?has_part_hepatocyte_process and not GO_0051179)WHERE ?hepatocyte_process != GO_0008150BEGIN ADD ?hepatocyte_process subClassOf !actsOn some ?has_part_hepatocyte_process END;
UniProtKB P12235 SLC25A4 GO:0000002UniProtKB P19971 TYMP GO:0000002UniProtKB P36776 LONP1 GO:0000002UniProtKB P39210 MPV17 GO:0000002
OPPL-Galaxy
OPPL-Galaxy
Onto-toolkitP12235P19971
GOGO
GO
GOA
OPPL 1OPPL 2
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;
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;
!!!
BioPAX
OPPL-Galaxy
Refactoring: OBO2OWL puning
OPPL-Galaxy
OBO OWL OWL (Punned) OWL (Punned, triples)
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?x:CLASS, ?y:INDIVIDUAL = create(?x.RENDERING) SELECT ?x SubClassOf ThingWHERE ?x != Nothing, ?x != ThingBEGIN ADD ?y Type ?x END;
?x:CLASS, ?y:INDIVIDUAL,?z:CLASS, ?w:INDIVIDUAL,?p:OBJECTPROPERTY SELECT ASSERTED ?x SubClassOf ?p some ?z, ASSERTED ?y Type ?x, ASSERTED ?w Type ?zWHERE ?x != Nothing, ?x != ThingBEGIN ADD ?y ?p ?w END;
OPPL-Galaxy
Refactoring: application of ODPs
Ondrej Sváb-Zamazal, Vojtech Svátek, Luigi Iannone: Pattern-Based Ontology Transformation Service Exploiting OPPL and OWL-API. EKAW 2010
http://www.gong.manchester.ac.uk/odp/html/Entity_Feature_Value.html
OPPL-Galaxy
?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/
OPPL-Galaxy source http://toolshed.g2.bx.psu.edu/repos/mikel-egana-aranguren/oppl
Public Galaxy instance with OPPL-Galaxy
http://sele.inf.um.es:8080/
OPPL scripts: http://oppl2.sourceforge.net/taggedexamples/
OPPL-Galaxy works in UNIX (Mac OS X, GNU/Linux)
OPPL-Galaxy is GPL
OPPL-Galaxy
OPPL-Galaxy
Conclusions
OPPL-Galaxy
Conclusions
OPPL: automate ontology manipulation
OPPL-Galaxy: exploit automated ontology manipulation: In combination with other genomics toolsIn complex workflowsHistory, shared execution, reproduce execution, …
Ontology refactoring, complex querying, ontology pruning, …
Inference
Ultimately, automate ontology manipulation in a “natural” environment for biologists
OPPL-Galaxy
OPPL-Galaxy
Acknowledgements
Mikel Egaña Aranguren is funded by the Marie Curie Cofund programme (FP7)
Jesualdo Tomás Fernández Breis is funded by the Spanish Ministry of Science and Innovation (Grant TIN2010-21388-C02-02)
OPPL-Galaxy
