Getting the best from two worlds: Converting between OBO and OWL formats

CEUR Workshop Proceedings

Volumn 849, Issue , 2012, Pages

  Dritsou, Vicky ^a   Mitraka, Elvira ^a,b   Topalis, Pantelis ^a   Louis, Christos ^a,b  

^a INSTITUTE OF MOLECULAR BIOLOGY AND BIOTECHNOLOGY   (Greece)

^b UNIVERSITY OF CRETE   (Greece)

Author keywords

[No Author keywords available]

Indexed keywords

BIO-ONTOLOGIES; BIOMEDICAL DOMAIN; FORMAL SEMANTICS; MODEL ORGANISMS; ONTOLOGY LANGUAGE;

BIRDS;

EID: 84892562413     PISSN: 16130073     EISSN: None     Source Type: Conference Proceeding    
DOI: None     Document Type: Conference Paper

References (27)

1. Information Artifact Ontology, http://code.google.com/p/information- artifact-ontology/
2. OBOEdit OWL Plugin, http://smi-protege.stanford.edu/nigam/OboEditPlugin. zip
3. Oboformat: Parser and OWLAPI mapping for OBO Format, http://code.google. com/p/oboformat/
4. oboInOwl Mapping, http://www.bioontology.org/wiki/index.php/OboInOwl:Main Page
5. OWLTools Java API, http://code.google.com/p/owltools/
6. Sequence Ontology, http://www.sequenceontology.org/
7. The OBO Ontology Release Tool, http://code.google.com/p/owltools/wiki/ Oort
8. The Protégé Ontology Editor and Knowledge Acquisition System, http://protege.stanford.edu
9. Antezana, E., Egaña, M., Baets, B.D., Kuiper, M., Mironov, V.: ONTO-PERL: An API for supporting the development and analysis of bio-ontologies. Bioinformatics 24(6) (2008)
10. Ashburner, M., Ball, C.A., Blake, J.A., Botstein, D., Butler, H., Cherry, J.M., Davis, A.P., Dolinski, K., Dwight, S.S., Eppig, J.T., Harris, M.A., Hill, D.P., Issel-Tarver, L., Kasarskis, A., Lewis, S., Matese, J.C., Richardson, J.E., Ringwald, M., Rubin, G.M., Sherlock, G.: Gene Ontology: Tool for the unification of biology. Nature Genetics 25, 25-29 (2000)
11. Beisswanger, E., Lee, V., jae Kim, J., Rebholz-Schuhmann, D., Splendiani, A., Dameron, O., Schulz, S., Hahn, U.: Gene Regulation Ontology (GRO): Design Principles and Use Cases. In: MIE. pp. 9-14 (2008)
12. Coulet, A., Smail-Tabbone, M., Benlian, P., Napoli, A., Devignes, M.D.: SNP-Ontology for semantic integration of genomic variation data (2006)
13. Day-Richter, J., Harris, M.A., Haendel, M., Lewis, S.: Obo-edit-an ontology editor for biologists. Bioinformatics 23, 2198-2200 (August 2007)
14. Golbreich, C., Horridge, M., Horrocks, I., Motik, B., Shearer, R.: OBO and OWL: Leveraging Semantic Web Technologies for the Life Sciences. In: ISWC/ASWC (2007)
15. Golbreich, C., Horrocks, I.: The OBO to OWL mapping, GO to OWL 1.1! In: OWLED (2007)
16. Gruber, T.R.: A translation approach to portable ontology specifications. Knowledge Acquisition 5, 199-220 (June 1993)
17. Haarslev, V., Möller, R.: Racer system description. In: IJCAR. pp. 701-706 (2001)
18. Hoehndorf, R., Batchelor, C., Bittner, T., Dumontier, M., Eilbeck, K., Knight, R., Mungall, C.J., Richardson, J.S., Stombaugh, J., Westhof, E., Zirbel, C.L., Leontis, N.B.: The RNA Ontology (RNAO): An ontology for integrating RNA sequence and structure data. Applied Ontology 6(1), 53-89 (2011)
19. Hoehndorf, R., Oellrich, A., Dumontier, M., Kelso, J., Rebholz-Schuhmann, D., Herre, H.: Relations as patterns: bridging the gap between OBO and OWL. BMC Bioinf. 11, 441 (2010)
20. Horridge, M., Bechhofer, S.: The OWL API: A Java API for Working with OWL 2 Ontologies. CEUR Workshop Proceedings, vol. 529. CEUR-WS.org (2008)
21. McGuinness, D.L., van Harmelen, F.: OWL Web Ontology Language, W3C Recommendation, http://www.w3.org/TR/owl-features/
22. Moreira, D.A., Musen, M.A.: OBO to OWL: a protégé OWL tab to read/save OBO ontologies. Bioinformatics 23(14), 1868-1870 (2007)
23. Mungall, C., Emmert, D.B.: A Chado case study: an ontology-based modular schema for representing genome-associated biological information. In: Bioinformatics. pp. 337-346 (2007)
24. Mungall, C., Ireland, A.: The OBO Flat File Format Guide, version 1.4, http://www.geneontology.org/GO.format.obo-14.shtml
25. Tirmizi, S.H., Aitken, S., Moreira, D.A., Mungall, C., Sequeda, J., Shah, N.H., Miranker, D.P.: Mapping between the OBO and OWL ontology languages. J Biomed Semantics 2 Suppl 1, S3 (2011)
26. Topalis, P., Mitraka, E., Bujila, I., Deligianni, E., Dialynas, E., Siden-Kiamos, I., Troye-Blomberg, M., Louis, C.: IDOMAL: an ontology for malaria. Malar Journal 9 (2010)
27. Tsarkov, D., Horrocks, I.: FaCT++ description logic reasoner: System description. In: In Proc. of the Int. Joint Conf. on Automated Reasoning (IJCAR 2006. pp. 292-297 (2006) Diseases