1. Pantelis Topalis and Emmanuel Dialynas

2.  Ontology content  Data annotation with ontologies  Tools to handle and visualize ontologies OWL – OBO parsers Ontology browser  Outstanding issues  IRBase

3. Ontology content  Present ontologies in VB TADS (tick anatomy) TGMA (mosquito anatomy) MIRO (insecticide resistance) IDOMAL (malaria ontology)  Future ontologies Dengue ontology Chagas ontology  + relevant external ontologies

4. Ontology content  IDOMAL extensions Drug resistance Natural drugs/remedies Genetically modified Plasmodia  Repositioning of branches to describe better reality (e.g. taxon is a informational entity)  Convert IDOMAL into OWL format.

5. IDOMAL vs IDO  Latest version of IDO has inconsistencies (e.g. resistance is a disposition but susceptibility is a quality )  PROPOSAL: A meeting with ViPR, PATRIC and EupathDB/PlasmoDB people to discuss the issue.

6. Parsing OBO to OWL and vice versa  2 broadly known file formats for ontologies: OBO (Open biomedical ontologies – All VB ontologies) OWL (Web Ontology Language, broadly known web standard – IDO, Parasite Lifecycle Ontology)  Two “competitors”, each with its pros and cons  Existing scripts to import an ontology into Chado require OBO formatted ontologies.  Automatic conversion between the two formats is desired in order to deal with interoperability issues

8. obo2owl  Tools have been proposed for converting obo ontologies to owl automatically: i. The OWLDEF 1 method and software ii. OBO Converter 2 Protégé tab iii. OWL Tools 3  Testing showed deficiencies  None of them can deal with large ontology files. 1 Available at http://bioonto.de/obo2owl/http://bioonto.de/obo2owl/ 2 Available at http://www.bioontology.org/OBO-converterhttp://www.bioontology.org/OBO-converter 3 Available at http://code.google.com/p/owltools/http://code.google.com/p/owltools/

9. owl2obo  The same tools exist for the reverse conversion as well  All of these produce a valid obo file, as long as the owl file follows some rules, e.g. uses the IDs specified by the OBO Foundry  A tool that converts completely independent owl files to obo is not available

10. 1. Perl script that converts obo ontologies to owl ontologies Can deal with very large files as well 2. Perl script that converts owl ontologies to obo No requirement for a mapping between obo and owl in order to convert the statements Our solution

11. Data annotation with ontologies  GO terms in gene pages  MIRO/IDOMAL terms in PopBio section  Proposal: Ontology terms in CAP  IDOMAL terms ??? EupathDB link  Dengue terms ??? ViPR link

12. OUTREACH  How to incorporate more ontologically aware datasets in VB.  How to promote interoperability between VB and EupathDB/PlasmoDB and ViPR. We need extended search capabilities and ways to retrieve data from various sources. The use of common ontologies is the necessary backbone.

13. IRbase  Recent work: Adopted Units Ontology Developed software and ISAtab templates to transfer data to Chado  Future plans Search at main site Bring in new data ??? Data curators ??? “Official” IR database ???

14. Ontology Browser @ VB  Need to have our own VB browser Keep visitors in our site Bioportal is frequently inaccessible External browsers do not provide all required features, image displaying for anatomy ontologies  As ontology complexity increases so does parsing and importing  Not all ontologies currently available for public browsing  Put any effort required to have a functional browser at VB.

15. Ontology Browser @ VB  Problems due to circular references between terms on different ontologies  Detectable only at the database level where multiple ontologies have been loaded.  As more ontologies are included in VB the more likely to have this problem.

16. Ontology Browser @ VB  Need to add displays for term properties images  Streamlined process ontology and browser in one package

17. GAZ is hard to play with  Must have for PopBio/IRbase  Enormous, 450K+ terms  Latest OBOEdit cannot load latest GAZ  Chado loaders complains about cyclic references  It takes 6-8 CPU days to import  Not available for browsing on the web  Two approaches in progress: Optimize loaders, 10fold increased performance for MIRO Convert obo to owl and back