Abstract
In this paper, we report on the ontology for the representation of brain diseases data - NDDO. The proposed ontology facilitates semantic annotation of datasets containing neurodegenerative diagnostic data (i.e. clinical, imaging, biomarker, etc.) and disease progression data collected on patients by the hospitals. Rich semantic annotation of datasets is essential for efficient support of data mining, for example for the identification of suitable algorithms for data analytics, text mining, and reasoning over distributed data and knowledge sources. To address the data analytics perspective, we reused and extended our previous work on ontology of data types (OntoDT) and ontology of core data mining entities (OntoDM-core) to represent specific domain datatypes that occur in the domain datasets. We demonstrate the utility of NDDO on two use cases: semantic annotation of datasets, and incorporating information about clinical procedures used to produce neurodegenerative data.
the Alzheimer’s Disease Neuroimaging Initiative—Data used in preparation of this article were obtained from the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database (adni.loni.usc.edu). As such, the investigators within the ADNI contributed to the design and implementation of ADNI and/or provided data but did not participate in analysis or writing of this report. A complete listing of ADNI investigators can be found at: http://adni.loni.usc.edu/wp-content/uploads/how_to_apply/ADNI_Acknowledgement_List.pdf.
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Notes
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See the HBP Call for Expression of Interest on comprehensive ontologies for brain diseases at https://www.humanbrainproject.eu/en/collaborate/open-calls/.
- 3.
ADNI webpage: http://adni.loni.usc.edu/.
- 4.
PPMI webpage: http://www.ppmi-info.org/.
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URL: Protégé web page: http://protege.stanford.edu.
- 6.
NDDO Git URL: http://source.ijs.si/ppanov/nddo/tree/master/Development.
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NDDO at BioPortal: https://bioportal.bioontology.org/ontologies/NDDO.
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Acknowledgements
The authors would like to acknowledge the support of the Slovenian Research Agency through the project J2-9230 and the Public Scholarship, Development, Disability and Maintenance Fund of the Republic of Slovenia through its scholarship program.
Data collection and sharing for this project was funded by the Alzheimer’s Disease Neuroimaging Initiative (ADNI) (National Institutes of Health Grant U01 AG024904) and DOD ADNI (Department of Defense award number W81XWH-12-2-0012). ADNI is funded by the National Institute on Aging, the National Institute of Biomedical Imaging and Bioengineering, and through generous contributions from the following: AbbVie, Alzheimer’s Association; Alzheimer’s Drug Discovery Foundation; Araclon Biotech; BioClinica, Inc.; Biogen; Bristol-Myers Squibb Company; CereSpir, Inc.; Cogstate; Eisai Inc.; Elan Pharmaceuticals, Inc.; Eli Lilly and Company; EuroImmun; F. Hoffmann-La Roche Ltd and its affiliated company Genentech, Inc.; Fujirebio; GE Healthcare; IXICO Ltd.; Janssen Alzheimer Immunotherapy Research & Development, LLC.; Johnson & Johnson Pharmaceutical Research & Development LLC.; Lumosity; Lundbeck; Merck & Co., Inc.; Meso Scale Diagnostics, LLC.; NeuroRx Research; Neurotrack Technologies; Novartis Pharmaceuticals Corporation; Pfizer Inc.; Piramal Imaging; Servier; Takeda Pharmaceutical Company; and Transition Therapeutics. The Canadian Institutes of Health Research is providing funds to support ADNI clinical sites in Canada. Private sector contributions are facilitated by the Foundation for the National Institutes of Health (www.fnih.org). The grantee organization is the Northern California Institute for Research and Education, and the study is coordinated by the Alzheimer’s Therapeutic Research Institute at the University of Southern California. ADNI data are disseminated by the Laboratory for Neuro Imaging at the University of Southern California.
Data used in the preparation of this article were obtained from the Parkinson’s Progression Markers Initiative (PPMI) database (www.ppmi-info.org/data). For up-to-date information on the study, visit www.ppmi-info.org. PPMI–a public-private partnership–is funded by the Michael J. Fox Foundation for Parkinson’s Research and funding partners, including AbbVie, Allergan, Avid, Biogen, BioLegend, Bristol-Myers Squibb, GE Healthcare, Genentech, GlaxoSmithKline, Lilly, Lundbeck, Merck, Meso Scale Discovery, Pfizer Inc., Piramal Imaging, F. Hoffmann-La Roche AG, Sanofi Genzyme, Servier, Takeda, Teva, UCB, and Global Capital.
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Kostovska, A., Tolovski, I., Maikore, F., the Alzheimer’s Disease Neuroimaging Initiative., Soldatova, L., Panov, P. (2019). Neurodegenerative Disease Data Ontology. In: Kralj Novak, P., Šmuc, T., Džeroski, S. (eds) Discovery Science. DS 2019. Lecture Notes in Computer Science(), vol 11828. Springer, Cham. https://doi.org/10.1007/978-3-030-33778-0_19
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