1. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 1 OWL: PAX of Mind or the AX? Experiences of Using OWL in the Development of BioPAX Joanne Luciano 1 & Robert Stevens 2 1 Harvard Medical School, 2 Manchester University OWL-ED DC, April 1-2, 2008 Gaithersburg, MD, USA

2. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 2 BioPAX The Vision Integrate biological processes data of different types The Reality - An abstraction of the different types of processes that enable them to co-exist - A controlled vocabulary for them What went wrong? - No real interest of using OWL features or reasoners - No real examples of why using them would be of any value

3. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 3 The domain: Biological pathways Metabolic Pathways Molecular Interaction Networks Signaling Pathways Main categories:

4. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 4 A few technical factors the complexity of the language and its syntax the open world assumption was foreign to people the logical framework was unfamiliar the steep learning curve the lack of tutorials and examples the lack of tools of any quality the general lack of experience (new language) the BioPAX community did not have a coherent set of requirements

5. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 5 A few social factors there was disagreement (two camps, OWL and XML Schema) OWL was not seen as necessary by all members OWL of the community and it required considerably more work there were existing known methods mentality: do enough to do the job at hand done human nature: to resist the new or unknown

6. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 6 Why bother? Much basic scientific research produces pathway data –environmental research, energy research, genetic and clinical research, and virtually all of life science research today –At some point, the question is asked “What pathways are involved?" Therefore, it is important to provide a mechanism for access and reuse to these data –enable it to have broad impact for science The major problem for researchers who use pathway databases has been that the representations of pathway data within these resources are not consistent or interchangeable

7. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 7 At the conceptual level In signaling pathways, it is the activation or inhibition of a process (apoptosis) in metabolic pathways, a series of chemical reactions transform a chemical molecule (glucose → pyruvate)

8. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 8 At the syntax level HumanCyc’s term: D-glucose-6-phosphate KEGG’s term: D-Glucose-6P It is clear we are referring to the same molecule, i.e. the same real world class of instances, The vocabulary label used to name these instances differs and while this difference is insignificant for a human reader, it is significant for computational processing.

9. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 9 Reasons for choosing OWL-DL OWL’s Expressivity Future uses: Enable reasoning

10. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 10 Reasons for choosing OWL-DL Future uses: Enable reasoning (whatever that means) –Future (not us, not now) –Reasoning by Choosing OWL-DL it would it would “be enabled” –(didn’t really think much about this)

11. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 11 Mistakes in using OWL (nothing new here) Bad Conceptualizations –confusion about what was being represented biological processes or database records of biological processes –Utility class, a concept used in Java, not in biology, was a Poor Understanding of OWL –Assumed axioms were disjoint –Domain and range –Open world assumptions and implications –Semantics in comments rather than in the ontology –What was said in the ontology, was not what was meant OWL as an EXPORT File Format For more details see Luciano and Stevens (2007)

12. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 12 Social Factors BioPathways Consortium enabled Chris Sander by obtaining a commitment for funding by Dept of Energy Chris in turn funded 2 people to get the initiative organized (The DEF Group), An initial group of stakeholders decided to organize a “core group” for decisions and hold meetings “by-invitation-only”

13. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 13 Social Factors Ignorance –of the task –of how to achieve it Internal biases… –Which tool first there were none then there were (promises) then there were none –XML-Schema vs-OWL

14. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 14 Social Factors Understanding of OWL increased –Knowledge (papers, tutorials) became increasingly available –Tools for OWL become available Discovery of mistakes made However, remember “future” –Pressure to release Breakdown – in-fighting, undermining, ugliness (more mistakes!)

15. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 15 What Went Right Helped the Semantic Web community spread the word about OWL by having a user to point to Community outreach helped BioPAX adoption BioPAX brought the wider community together Created the higher level abstraction that included generalize concepts common to the different “pathway” conceptualizations –Upper level ontology for pathways

16. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 16 Looking ahead Current Starting Point multiple OWL syntaxes multiple tools support materials methodologies for development

17. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 17 Looking ahead NEED tools to support developers: –analyze the semantic complexity needed to support use cases –facilitate development in a staged process with increasing complexity at each stage –support basic requirements first, controlled vocabularies, taxonomies, (XML data exchange) then interoperability (SBML/BioPAX) –then support richer semantics enabling integration, inference, and possibly integrated or in-line rules

18. 4/1/2008 OWL-ED 2008, Gaithersburg, MD 18 Conclusions and Lessons Learnt OUCH, that hurt, don’t do that again Assess –complexity of the use cases –needs of the community –capability of the language (and its limitations) –tools available Process –support subsequent levels of complexity on sound foundation (O??-Foundry) Evaluate –correct (specification) –complete/comprehensive (concepts and detail) –utility/effectiveness (use cases)