OPPL-Galaxy: 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

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OPPL-Galaxy: Enhancing ontology exploitation in Galaxy with OPPL

  1. 1. OPPL-Galaxy: Enhancing  ontology exploitation in  Galaxy with OPPL Mikel Egaña Aranguren (megana@fi.upm.es) Ontology Engineering Group School of Computer Science UPM, Spain Jesualdo Tomás Fernández-Breis (jfernand@um.es) School of Computer Science UM, Spain Erick Antezana (erick.antezana@bio.ntnu.no) Department of Biology NTNU, Norwayhttp://www.slideshare.net/MikelEganaAranguren/opplgalaxy-enhancing-ontology-exploitation-in- galaxy-with-oppl 9/12/2011
  2. 2. Index What is OPPL-Galaxy? Use cases Implementation Availability ConclusionsOPPL-Galaxy
  3. 3. What is OPPL-Galaxy?OPPL-Galaxy
  4. 4. What is OPPL-Galaxy Ontology Pre Processor Language (OPPL) Scripting Language for automating ontology manipulation  ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?wholeOntology WHERE ?part != Nothing New ontology BEGIN ADD ?part SubClassOf part_of only ?whole END; OPPL-Galaxy
  5. 5. What is OPPL-Galaxy GalaxyJeremy 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
  6. 6. What is OPPL-Galaxy GalaxyJeremy 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
  7. 7. What is OPPL-Galaxy Ontology refactoring (Axiomatic enrichment, ODPs, … ) OPPL Detection of structures (Antipatterns, … ) Advanced querying (Reasoning+regexps, …) Ontology trimmingOPPL-Galaxy
  8. 8. What is OPPL-Galaxy Ontology refactoring (Axiomatic enrichment, ODPs, … ) OPPL Detection of structures (Antipatterns, … ) Advanced querying (Reasoning+regexps, …) Ontology trimming Analysis history Analysis shareability Galaxy Combinations of tools Complex workflowsOPPL-Galaxy
  9. 9. What is OPPL-Galaxy Ontology refactoring (Axiomatic enrichment, ODPs, … ) OPPL Detection of structures (Antipatterns, … ) Advanced querying (Reasoning+regexps, …) Ontology trimming Analysis history Analysis shareability Galaxy Combinations of tools Complex workflowsOPPL-Galaxy
  10. 10. What is OPPL-Galaxy Ontology User OPPL script Ontology UserOPPL-Galaxy
  11. 11. Use cases   http://miuras.inf.um.es/OPPL-GalaxyOPPL-Galaxy
  12. 12. Workflows Gene Ontology Gene Annotation file (GOA)Ontology (GO)OPPL script 1OPPL script 2 Onto-toolkit OPPL-Galaxy
  13. 13. Workflows GO GO OPPL-Galaxy OPPL 2OPPL 1 ?hepatocyte_process:CLASS, ?hepatocyte_process_label:CONSTANT = MATCH(".?hepatocyte.+"),?localisation_sibling:CLASS ?has_part_hepatocyte_process:CLASS,SELECT ?part_of_or_regulates:OBJECTPROPERTYASSERTED ?localisation_sibling SubClassOf GO_0008150 SELECTWHERE ?localisation_sibling != GO_0051179 ASSERTED ?hepatocyte_process.IRI label ?hepatocyte_process_label,BEGIN ?hepatocyte_process subClassOf ?part_of_or_regulates someADD ?localisation_sibling DisjointWith GO_0051179 (?has_part_hepatocyte_process and not GO_0051179)END; WHERE ?hepatocyte_process != GO_0008150 BEGIN ADD ?hepatocyte_process subClassOf !actsOn some ?has_part_hepatocyte_process END; OPPL-Galaxy P12235 GO P19971 Onto-toolkit GOA UniProtKB P12235 SLC25A4 GO:0000002 UniProtKB P19971 TYMP GO:0000002 UniProtKB P36776 LONP1 GO:0000002 UniProtKB P39210 MPV17 GO:0000002 OPPL-Galaxy
  14. 14. Ontology debuggingBioPAX ?target:CLASS, ?prop:OBJECTPROPERTY, ?filler:CLASS SELECT ASSERTED ?target SubClassOf ?prop only ?filler WHERE FAIL ?target SubClassOf ?prop some ?filler BEGIN ADD ?target SubClassOf !OnlyBadPracticeResult END; 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.OPPL-Galaxy
  15. 15. Ontology debuggingBioPAX ?target:CLASS, ?prop:OBJECTPROPERTY, ?filler:CLASS SELECT ASSERTED ?target SubClassOf ?prop only ?filler WHERE FAIL ?target SubClassOf ?prop some ?filler BEGIN ADD ?target SubClassOf !OnlyBadPracticeResult END; !!! 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.OPPL-Galaxy
  16. 16. Refactoring: OBO2OWL puning . . . . . . . . OBO OWL OWL (Punned) OWL (Punned, triples) ?x:CLASS, ?x:CLASS, ?y:INDIVIDUAL = create(?x.RENDERING) ?y:INDIVIDUAL, SELECT ?x SubClassOf Thing ?z:CLASS, WHERE ?x != Nothing, ?x != Thing ?w:INDIVIDUAL, BEGIN ?p:OBJECTPROPERTY ADD ?y Type ?x SELECT ASSERTED ?x SubClassOf ?p some ?z, END; ASSERTED ?y Type ?x, ASSERTED ?w Type ?z WHERE ?x != Nothing, ?x != Thing BEGIN ADD ?y ?p ?w END;OPPL-Galaxy
  17. 17. Refactoring: application of ODPsPerson subClassOf hasheight some high ?x:CLASS, ?y:OBJECTPROPERTY = MATCH("has((w+))"), ?z:CLASS, ?feature:CLASS = create(?y.GROUPS(1)) SELECT ASSERTED ?x subClassOf ?y some ?z BEGIN REMOVE ?x subClassOf ?y some ?z, ADD ?x subClassOf !hasFeature some (?feature and !hasValue some ?z) END;Person subClassOf hasFeature some (height and hasValue some high) 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.htmlOPPL-Galaxy
  18. 18. ImplementationOPPL-Galaxy
  19. 19. ImplementationURI mapping file (If imports)Input ontology: OWL, OBO, ...OPPL flat fileOutput ontology: OWL (RDF/XML) or OBOAdd inferred subsumptions as assertionsMerge ontologies (If imports)Reasoner: Pellet, FaCT++, HermiT OPPL-Galaxy
  20. 20. Implementation OPPL API OWL API Reasoner OPPL wrapper GalaxyOPPL-Galaxy
  21. 21. Implementation OPPL API OWL API Reasoner Ontology OPPL  options ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing BEGIN OPPL wrapper ADD ?part SubClassOf part_of only ?whole END; GalaxyOPPL-Galaxy
  22. 22. Implementation OPPL API OWL API Reasoner Ontology OPPL  options ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing BEGIN OPPL wrapper ADD ?part SubClassOf part_of only ?whole END; GalaxyOPPL-Galaxy
  23. 23. Implementation Galaxy tools OPPL API OWL API Modified  ontology Download Reasoner ontology Ontology OPPL  options ?whole:CLASS, ?part:CLASS SELECT ?part SubClassOf part_of some ?whole WHERE ?part != Nothing BEGIN OPPL wrapper ADD ?part SubClassOf part_of only ?whole END; GalaxyOPPL-Galaxy
  24. 24. AvailabilityOPPL-Galaxy
  25. 25. 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 GPLOPPL-Galaxy
  26. 26. ConclusionsOPPL-Galaxy
  27. 27. Conclusions OPPL: automate ontology manipulation OPPL-Galaxy: exploit automated ontology manipulation:  In combination with other genomics tools In complex workflows History, shared execution, reproduce execution, …   Ontology refactoring, complex querying, ontology pruning, … Inference Ultimately, automate ontology manipulation in a “natural”  environment for biologistsOPPL-Galaxy
  28. 28. 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

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