Neurodegenerative Disease Data Ontology

  • Ana Kostovska
  • Ilin Tolovski
  • Fatima Maikore
  • the Alzheimer’s Disease Neuroimaging Initiative
  • Larisa Soldatova
  • Panče PanovEmail author
Conference paper
Part of the Lecture Notes in Computer Science book series (LNCS, volume 11828)


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.


Neurodegenerative diseases datasets Ontology 



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 ( 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 ( For up-to-date information on the study, visit 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.


  1. 1.
    Alzheimer’s Disease Neuroimaging Initiative: ADNI 1 Procedures ManualGoogle Scholar
  2. 2.
    Alzheimer’s Disease Neuroimaging Initiative: ADNI 2 Procedures ManualGoogle Scholar
  3. 3.
    Alzheimer’s Disease Neuroimaging Initiative: ADNI GO Procedures ManualGoogle Scholar
  4. 4.
    Maikore, F.S., Haddi, E., Soldatova, L.: A framework for it support of clinical laboratory standards. Int. J. Priv. Health Inf. Manage. 6(2), 13–25 (2018)Google Scholar
  5. 5.
    Gamberger, D., et al.: Clusters of male and female Alzheimer’s disease patients in the Alzheimer’s Disease Neuroimaging Initiative (ADNI) database. Brain Inform. 3(3), 169–179 (2016)CrossRefGoogle Scholar
  6. 6.
    Jensen, M., et al.: The neurological disease ontology. J. Biomed. Seman. 4(1), 42 (2013)CrossRefGoogle Scholar
  7. 7.
    Maikore, F., et al.: An ontology for clinical laboratory standard operating procedures. In: Proceedings of the Joint Ontology Workshops 2017 (2017)Google Scholar
  8. 8.
    Mileski, V., et al.: Multi-dimensional analysis of PPMI data. In: Proceedings of the 8th IPS Students’ Conference 2016, Ljubljana, Slovenia, pp. 175–178 (2016)Google Scholar
  9. 9.
    Panov, P., Soldatova, L., Džeroski, S.: Ontology of core data mining entities. Data Min. Knowl. Disc. 28(5–6), 1222–1265 (2014)CrossRefGoogle Scholar
  10. 10.
    Panov, P., Soldatova, L.N., Džeroski, S.: Generic ontology of datatypes. Inf. Sci. 329, 900–920 (2016)CrossRefGoogle Scholar
  11. 11.
    Scheuermann, R.H., Ceusters, W., Smith, B.: Toward an ontological treatment of disease and diagnosis. Summit Transl. Bioinform. 2009, 116 (2009)Google Scholar
  12. 12.
    Smith, B., et al.: The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25(11), 1251 (2007)CrossRefGoogle Scholar
  13. 13.
    The Parkinson’s Progression Markers Initiative: PPMI Case Report FormsGoogle Scholar
  14. 14.
    The Parkinson’s Progression Markers Initiative: PPMI Study ProtocolGoogle Scholar
  15. 15.
    Whetzel, P.L., et al.: Bioportal: enhanced functionality via new web services from the national center for biomedical ontology to access and use ontologies in software applications. Nucleic Acids Res. 39(Suppl. 2), W541–W545 (2011)CrossRefGoogle Scholar

Copyright information

© Springer Nature Switzerland AG 2019

Authors and Affiliations

  • Ana Kostovska
    • 1
    • 2
  • Ilin Tolovski
    • 1
    • 2
  • Fatima Maikore
    • 3
  • the Alzheimer’s Disease Neuroimaging Initiative
  • Larisa Soldatova
    • 3
  • Panče Panov
    • 1
    • 2
    Email author
  1. 1.Department of Knowledge TechnologiesJožef Stefan InstituteLjubljanaSlovenia
  2. 2.Jožef Stefan International Postgraduate SchoolLjubljanaSlovenia
  3. 3.Department of ComputingGoldsmiths University of LondonLondonUK

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