References

Ontorat Citations:

Xiang Z, Zheng J, Lin Y, He Y. Ontorat: Automatic generation of new ontology terms, annotations, and axioms based on ontology design patterns. Journal of Biomedical Semantics. 2015, 6:4  doi:10.1186/2041-1480-6-4. (Note: Please cite this reference if you cite Ontorat. Thanks.)

More Xiang Z, Lin Y, He Y. Ontorat web server for automatic ontology term generation and annotations. International Conference on Biomedical Ontologies (ICBO 2012), University of Graz, Austria, July 2012. [One page abstract][Poster][Flash Talk]

Ontology Design Patterns (ODP) references:

Burns GA1, Turner JA. Modeling functional Magnetic Resonance Imaging (fMRI) experimental variables in the Ontology of Experimental Variables and Values (OoEVV). Neuroimage. 2013 Nov 15;82:662-70. PMID: 23684873.

Mortensen JM1, Horridge M, Musen MA, Noy NF. Applications of ontology design patterns in biomedical ontologies. AMIA Annu Symp Proc. 2012;2012:643-52. PMID: 23304337.

Seddig-Raufie D1, Jansen L, Schober D, Boeker M, Grewe N, Schulz S. Proposed actions are no actions: re-modeling an ontology design pattern with a realist top-level ontology. J Biomed Semantics. 2012 Sep 21;3 Suppl 2:S2. PMID: 23046561.

Hoehndorf R1, Ngonga Ngomo AC, Pyysalo S, Ohta T, Oellrich A, Rebholz-Schuhmann D. Ontology design patterns to disambiguate relations between genes and gene products in GENIA. J Biomed Semantics. 2011 Oct 6;2 Suppl 5:S1. PMID: 22166341.

Boeker M1, Tudose I, Hastings J, Schober D, Schulz S. Unintended consequences of existential quantifications in biomedical ontologies. BMC Bioinformatics. 2011 Nov 24;12:456. PMID: 22115278.

Schulz S1, Spackman K, James A, Cocos C, Boeker M. Scalable representations of diseases in biomedical ontologies. J Biomed Semantics. 2011 May 17;2 Suppl 2:S6. PMID: 21624161.

WOP2010: The 2010 Workshop on Ontology Patterns. Check out papers: WOP 2010 Online Proceedings.

WOP2009: The 2009 Workshop on Ontology Patterns. Check out papers: WOP 2009 Online Proceedings.

Aranguren ME1, Antezana E, Kuiper M, Stevens R. Ontology Design Patterns for bio-ontologies: a case study on the Cell Cycle Ontology. BMC Bioinformatics. 2008 Apr 29;9 Suppl 5:S1. PMID: 18460183.

Aldo Gangemi. Ontology Design Patterns for Semantic Web Content, in proceedings of ISWC'05: the 4th International Semantic Web Conference, Galway, Ireland, November 6-10, 2005, Y. Gil and E. Motta and V.R. Benjamins and M.A. Musen (editors), Lecture Notes in Computer Science, Springer Verlag, 3729: 262-276, 2005.

Gangemi A1, Catenacci C, Battaglia M. Inflammation ontology design pattern: an exercise in building a core biomedical ontology with descriptions and situations. Stud Health Technol Inform. 2004;102:64-80. PMID: 15853264.

 

Quick Term Templates (QTT) references:

P. Rocca-Serra, A. Ruttenberg, M. J. O'Connor, T. Whetzel, D. Schober, J. Greenbaum, M. Courtot, S. A. Sansone, R. Scheurmann, B. Peters ( & OBI consortium). Overcoming the Ontology Enrichment Bottleneck with Quick Term Templates. Journal of Applied Ontology, 6, 13-22. Published in 2011.