, Volume 10, Issue 1, pp 97–114 | Cite as

NeuroNames: An Ontology for the BrainInfo Portal to Neuroscience on the Web

  • Douglas M. BowdenEmail author
  • Evan Song
  • Julia Kosheleva
  • Mark F. Dubach
Original Article


BrainInfo ( is a growing portal to neuroscientific information on the Web. It is indexed by NeuroNames, an ontology designed to compensate for ambiguities in neuroanatomical nomenclature. The 20-year old ontology continues to evolve toward the ideal of recognizing all names of neuroanatomical entities and accommodating all structural concepts about which neuroscientists communicate, including multiple concepts of entities for which neuroanatomists have yet to determine the best or ‘true’ conceptualization. To make the definitions of structural concepts unambiguous and terminologically consistent we created a ‘default vocabulary’ of unique structure names selected from existing terminology. We selected standard names by criteria designed to maximize practicality for use in verbal communication as well as computerized knowledge management. The ontology of NeuroNames accommodates synonyms and homonyms of the standard terms in many languages. It defines complex structures as models composed of primary structures, which are defined in unambiguous operational terms. NeuroNames currently relates more than 16,000 names in eight languages to some 2,500 neuroanatomical concepts. The ontology is maintained in a relational database with three core tables: Names, Concepts and Models. BrainInfo uses NeuroNames to index information by structure, to interpret users’ queries and to clarify terminology on remote web pages. NeuroNames is a resource vocabulary of the NLM’s Unified Medical Language System (UMLS, 2011) and the basis for the brain regions component of NIFSTD (NeuroLex, 2011). The current version has been downloaded to hundreds of laboratories for indexing data and linking to BrainInfo, which attracts some 400 visitors/day, downloading 2,000 pages/day.


NeuroNames BrainInfo Ontology Web portal Neuroanatomical nomenclature Web search 



The authors wish to thank Maryann Martone for current information on the translation of NeuroNames into OWL and Erik McArthur for assistance in the production of figures for this report. The work was supported by the International Neuroinformatics Coordinating Facility (INCF) and by grants LM-008247, MH-069259 and RR-000166 from the U.S. National Institutes of Health, to the University of Washington.


  1. Anthoney, T. R. (1994). Neuroanatomy and the neurologic exam: a thesaurus of synonyms, similar sounding non-synonyms and terms of variable meaning. Boca Raton: CRC.Google Scholar
  2. Arbib, M. A., & Amari, S.-I. (1988) (Eds.), Dynamic interactions in neural networks: models and data, vol. 1. Research notes in neural computing. Springer, New YorkGoogle Scholar
  3. Berners-Lee, T., Hendler, J., & Lassila, O. (2001). The semantic web. Scientific American, 284(5), 34–44.CrossRefGoogle Scholar
  4. Bowden, D. M. (2000). Atlases for informatics and quantitative neuroanatomy. In R. F. Martin & D. M. Bowden (Eds.), Primate brain maps. Amsterdam: Elsevier Science.Google Scholar
  5. Bowden, D. M., & Dubach, M. F. (2004). Neuroanatomical nomenclature and ontology, Chapter 2. In S. Koslow & S. Subramaniam (Eds.), Databasing the brain: Data to knowledge. New York: Wiley.Google Scholar
  6. Bowden, D. M., & Martin, R. F. (1995). NeuroNames brain hierarchy. Neuroimage, 2, 63–83.PubMedCrossRefGoogle Scholar
  7. BrainInfo (2010a) NeuroMaps Mapper: Macaque, University of Washington, Seattle, USA, (accessed 19 October 2010).
  8. BrainInfo (2010b) Location in English Hierarchy of Brain Structures, University of Washington, Seattle, USA, (accessed 30 September, 2010).
  9. BrainInfo (2010c) NeuroNames Ontology of Mammalian Neuroanatomy: NN2010, University of Washington, Seattle, USA, (accessed 5 September, 2010)
  10. BrainInfo (2010d) Arcuate nucleus of the hypothalamus, University of Washington, Seattle, USA, (accessed 31 March, 2011)
  11. Bug, W. J., Ascoli, G. A., Grethe, J. S., Gupta, A., Fennema-Notestine, C., Laird, A. R., et al. (2008). The NIFSTD and BIRNLex vocabularies: building comprehensive ontologies for neuroscience. Neuroinform, 6, 175–194.CrossRefGoogle Scholar
  12. Carpenter, M. B., & Sutin, J. (1983). Human Neuroanatomy. Baltimore: Williams & Wilkins.Google Scholar
  13. CRBS (2010) Center for Research in Biological Systems, University of California at San Diego, (accessed 8 September, 2010).
  14. Crosby, E. C., Humphrey, T., & Lauer, E. W. (1962). Correlative anatomy of the nervous system. New York: Macmillan.Google Scholar
  15. Dong, H. W. (2004). Allen Reference Atlas, Allen Institute for Brain Science, Seattle, (accessed 31 March, 2011).
  16. Google (2011). Google, Mountainview, CA, (accessed 20 April, 2011).
  17. Hof, P. R., Young, W. G., Bloom, F. E., Belichenko, P. V., & Celio, M. R. (2000). Comparative cytoarchitectonic Atlas of the C57BL/6 and 129/Sv mouse brains. Amsterdam: Elsevier.Google Scholar
  18. IANC. (1983). Nomina anatomica, international anatomical nomenclature committee. Baltimore: Williams & Wilkins.Google Scholar
  19. INCF (2011). International neuroinformatics coordinating facility, Karolinska Institute and Royal Institute of Technology, Stockholm, Sweden. (accessed 11 June 2011).
  20. Kahle, W., & Frotscher, M. (2001). Taschenatlas der Anatomie, vol. 3, nervensystem und sinnesorgane. Stuttgart: Georg Thieme Verlag.Google Scholar
  21. NeuroLex (2011). NeuroLex: The Neuroscience Lexicon, University of California at San Diego, CA, (accessed 9 June, 2011).
  22. NIF (2011). Neuroscience Information Framework, version 3.5. University of California at San Diego, (accessed 30 May 2011).
  23. NLM (2010). Medical Subject Headings, National Library of Medicine, (accessed 6 October 2010).
  24. Ono, M., Kubik, S., & Abernathey, C. D. (1990). Atlas of the cerebral sulci. Stuttgart: Thieme.Google Scholar
  25. Paxinos, G. (Ed.). (1990). The human nervous system. San Diego: Academic.Google Scholar
  26. Paxinos, G., & Franklin, K. B. J. (2001). The mouse brain in stereotaxic coordinates (2nd ed.). San Diego: Academic.Google Scholar
  27. PubMed (2009) PubMed, National Library of Medicine, Bethesda, MD. (accessed 20 April, 2011)
  28. Puelles, L., Martinez-de-la-Torre, M., Paxinos, G., Watson, C., & Martinez, S. (2007). The chick brain in stereotaxic coordinates. An atlas featuring neuromeres and mammalian homologies. San Diego: Elsevier Academic.Google Scholar
  29. Riley, H. A. (1943). An atlas of the basal ganglia, brain stem and spinal cord. Baltimore: Williams & Wilkins.Google Scholar
  30. Schiebler, T. H., Schmidt, W., & Zilles, K. (1999). Anatomie, 8. Auflage. Berlin: Springer.Google Scholar
  31. Stephan, H. (1975). Allocortex. In W. Bargmann (Ed.), Handbuch der mikroskopischen Anatomie des Menschen, Vol. 4, Nervensystem, Part 9. Berlin: Springer.Google Scholar
  32. Swanson, L. W. (2000). What is the brain? Trends in Neuroscience, 23, 519–527.CrossRefGoogle Scholar
  33. Swanson, L. W. (2004). Brain maps: Structure of the rat brain (3rd ed.). Oxford: Elsevier Academic.Google Scholar
  34. UMLS (2011). Unified Medical Language System, National Library of Medicine, Bethesda, Maryland, (accessed 31 March, 2011).
  35. Wikipedia (2010a). Ontology (information science), (accessed 31 March, 2011).
  36. Wikipedia (2010b). List of regions in the human brain. (accessed 6 October, 2010).
  37. Wikipedia (2011). Wikipedia,, San Francisco, CA, (accessed 20 April, 2011).

Copyright information

© Springer Science+Business Media, LLC 2011

Authors and Affiliations

  • Douglas M. Bowden
    • 1
    Email author
  • Evan Song
    • 1
  • Julia Kosheleva
    • 1
  • Mark F. Dubach
    • 1
  1. 1.National Primate Research Center and Department of Psychiatry and Behavioral SciencesUniversity of WashingtonSeattleUSA

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