ACGT Master Ontology

ACGT Master Ontology

The ACGT Master Ontology, which has been developed within the FP6-IST project "Advancing Clinico-Genomic Trials", has the aim to represent the domain of cancer research and management in a computationally tractable manner. The ACGT MO is built being maintained, using the Protégé-OWL free open-source ontology editor, Version 4. It is written in OWL-DL and presented as an .owl file. The ACGT MO is re-using Basic Formal Ontology (BFO) as upper level and the OBO Relation Ontology.


You can download the newest working version of ACGT MO here.


  • Biomedical Informatics Group, Artificial Intelligence Laboratory, School of Computer Science, Universidad Politécnica de Madrid, Madrid, Spain
  • eHealth Competence Centers, Universitätsklinikum Regensburg, Germany
  • Fraunhofer Institute for Biomedical Engineering, St. Ingbert, Germany
  • Institut Suisse de Bioinformatique, Switzerland
  • Institut Jules Bordet, Brussels, Belgium
  • Molecular Oncology Laboratories at the Weatherall Institute of Molecular Medicine, University of Oxford, United Kingdom
  • Paediatric Haematology and Oncology, Saarland University Hospital, Homburg, Germany
  • Siemens AG, Corporate Technology, Munich, Germany


Comment, Submission and Contact

The developers of the ACGT MO and the ACGT Consortium encourage comments and submissions to optimize and extend ACGT MO. If you have comments or questions or comments concerning the ACGT MO or if you want to submit proposals fur further classes, please contact one of the curators:

  • Dr. Mathias Brochhausen: mathias.brochhausen[AT]
  • Cristian Cocos PhD: cristi[AT]


The ACGT Consortium aims to set up a maintenance system. Details on the development can be found under "Documentation".




  • Brochhausen M, Spear AD, Cocos C, Weiler G, Martìn L, Anguita A, Stenzhorn H, Daskalaki E, Schera F, Schwarz U, Sfakianakis S; Kiefer S, Dörr M, Graf N, Tsiknakis M (2010) The ACGT Master Ontology and Its Applications - Towards an Ontology-Driven Cancer Research and Management System. Journal of Biomedical Informatics. E-published ahead of print. DOI 10.1016/j.jbi.2010.04.008
  • Brochhausen M, Weiler G, Martin L, Cocos C, Stenzhorn H, Graf N, Dörr M, Tsiknakis M, Smith B, "Applications of the ACGT Master Ontology on Cancer," In: R. Meersman, Z. Tari, P. Herrero (eds.): OTM 2008 Workshops, LNCS 5333, 2008, 1046-1055.
  • Brochhausen M, Weiler G, Cocos C, Stenzhorn H, Graf N, Doerr M, Tsiknakis M, “The ACGT Master Ontology on Cancer - a New Terminology Source for Oncological Practice,” In: Puuronen S, Pechenizkiy M, Tsymbal A, Lee DJ (eds.): Proceedings of the 21st IEEE International Symposium on Computer-Based Medical Systems, 2008, IEEE Computer Society, Los Alamitos, 324-329.
  • Smith B, Brochhausen M, "Establishing and Harmonizing Ontologies in an Interdisciplinary Health Care and Clinical Research Environment". Health, Technology and Informatics, 134, 2008, 219-234. [Preprint]
  • Tsiknakis M, Brochhausen M, Nabrzyski J, Pucaski J, Potamias G, Desmedt C, Kafetzopoulos D, “A semantic grid infrastructure enabling integrated access and analysis of multilevel biomedical data in support of post-genomic clinical trials on Cancer”, IEEE Transactions on Information Technology in Biomedicine, Special issue on Bio-Grids, 2008, Vol. 12, No. 2, pp. 205-217.
  • Weiler G, Brochhausen M, Graf N, Hoppe A, Schera F, Kiefer S, "Ontology Based Data Management Systems for post-genomic clinical Trials within an European Grid Infrastructure for Cancer Research", In: Proc of the 29th Annual International Conference of the IEEE EMBS, Lyon, France, August 23-26, 2007, pp. 6434-6437.