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

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, Norway
http://www.slideshare.net/MikelEganaAranguren/opplgalaxy-enhancing-ontology-exploitation-in-
galaxy-with-oppl
9/12/2011

2. Index
What is OPPL-Galaxy?
Use cases
Implementation
Availability
Conclusions
OPPL-Galaxy

3. What is OPPL-Galaxy?
OPPL-Galaxy

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 ?whole
Ontology WHERE ?part != Nothing New ontology
BEGIN
ADD ?part SubClassOf part_of only ?whole
END;
OPPL-Galaxy

5. What is OPPL-Galaxy
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

6. What is OPPL-Galaxy
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

7. What is OPPL-Galaxy
Ontology refactoring (Axiomatic enrichment, ODPs, … )
OPPL Detection of structures (Antipatterns, … )
Advanced querying (Reasoning+regexps, …)
Ontology trimming
OPPL-Galaxy

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 workflows
OPPL-Galaxy

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 workflows
OPPL-Galaxy

10. What is OPPL-Galaxy
Ontology User OPPL script
Ontology User
OPPL-Galaxy

11. Use cases
http://miuras.inf.um.es/OPPL-Galaxy
OPPL-Galaxy

12. Workflows
Gene Ontology
Gene Annotation file (GOA)
Ontology (GO)
OPPL
script 1
OPPL
script 2
Onto-toolkit
OPPL-Galaxy

13. Workflows
GO
GO
OPPL-Galaxy
OPPL 2
OPPL 1 ?hepatocyte_process:CLASS,
?hepatocyte_process_label:CONSTANT = MATCH(".?hepatocyte.+"),
?localisation_sibling:CLASS
?has_part_hepatocyte_process:CLASS,
SELECT
?part_of_or_regulates:OBJECTPROPERTY
ASSERTED ?localisation_sibling SubClassOf GO_0008150
SELECT
WHERE ?localisation_sibling != GO_0051179
ASSERTED ?hepatocyte_process.IRI label ?hepatocyte_process_label,
BEGIN
?hepatocyte_process subClassOf ?part_of_or_regulates some
ADD ?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. Ontology debugging
BioPAX
?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. Ontology debugging
BioPAX
?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. 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. Refactoring: application of ODPs
Person 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.html
OPPL-Galaxy

18. Implementation
OPPL-Galaxy

19. Implementation
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

20. Implementation
OPPL API
OWL API
Reasoner
OPPL wrapper
Galaxy
OPPL-Galaxy

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;
Galaxy
OPPL-Galaxy

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;
Galaxy
OPPL-Galaxy

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;
Galaxy
OPPL-Galaxy

24. Availability
OPPL-Galaxy

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 GPL
OPPL-Galaxy

26. Conclusions
OPPL-Galaxy

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 biologists
OPPL-Galaxy

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