Abstract
There is an increasing use of ontologies in the biomedical domain, so ensuring their high quality is required. Reuse of content is a best practice in ontology engineering, whose non-optimal implementation may lead to lead to loss of information and, therefore, of readability of the ontology for both humans and machines. We present twelve metrics for analyzing lack of human readability in ontologies. We applied these metrics to the OBO Foundry repository, which contains an orthogonal collection of biological and biomedical ontologies, and has content reuse as a design principle. For this study, we have also generated an orthogonal view of the repository, which can be seen as a single ontology representing the merged repository. The comparison between both perspectives permitted to identify that the readability for some types of entities and annotations decrease due to how reuse is implemented.
This is a preview of subscription content, log in via an institution to check access.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Legaz-García, M.C., Miñarro-Giménez, J.A., Menárguez-Tortosa, M., Fernández-Breis, J.T.: Generation of open biomedical datasets through ontology-driven transformation and integration processes. J. Biomed. Semant. 7(1), 1–17 (2016). https://doi.org/10.1186/s13326-016-0075-z
Reimer, A.P., Milinovich, A.: Using UMLS for electronic health data standardization and database design. J. Am. Med. Inform. Assoc. 27(10), 1520–1528 (2020)
He, Y., et al.: CIDO, a community-based ontology for coronavirus disease knowledge and data integration, sharing, and analysis. Sci. Data 7(1), 181 (2020)
Gaudet-Blavignac, C., Foufi, V., Bjelogrlic, M., Lovis, C.: Use of the systematized nomenclature of medicine clinical terms (SNOMED CT) for processing free text in health care: systematic scoping review. J. Med. Internet Res. 23(1), e24594 (2021)
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)
Smith, B., et al.: The OBO foundry: coordinated evolution of ontologies to support biomedical data integration. Nat. Biotechnol. 25(11), 1251–1255 (2007)
Lobentanzer, S., et al.: Democratizing knowledge representation with BioCypher. Nat. Biotechnol. 41, 1–4 (2023)
Zheng, F., Abeysinghe, R., Cui, L.: Identification of missing concepts in biomedical terminologies using sequence-based formal concept analysis. BMC Med. Inform. Decis. Mak. 21, 1–14 (2021)
Rector, A., Iannone, L.: Lexically suggest, logically define: quality assurance of the use of qualifiers and expected results of post-coordination in SNOMED CT. J. Biomed. Inform. 45(2), 199–209 (2012)
van Damme, P., Quesada-Martínez, M., Cornet, R., Fernández-Breis, J.T.: From lexical regularities to axiomatic patterns for the quality assurance of biomedical terminologies and ontologies. J. Biomed. Inform. 84, 59–74 (2018)
Quesada-Martínez, M., Mikroyannidi, E., Fernández-Breis, J.T., Stevens, R.: Approaching the axiomatic enrichment of the Gene Ontology from a lexical perspective. Artif. Intell. Med. 65(1), 35–48 (2015)
Halper, M., et al.: Guidelines for the reuse of ontology content. Appl. Ontol. 18(1), 5–29 (2023)
Kamdar, M.R., Tudorache, T., Musen, M.A.: A systematic analysis of term reuse and term overlap across biomedical ontologies. Semant. Web 8(6), 853–871 (2017)
Quesada-Martínez, M., Fernández-Breis, J.T.: Studying the reuse of content in biomedical ontologies: an axiom-based approach. In: ten Teije, A., Popow, C., Holmes, J.H., Sacchi, L. (eds.) AIME 2017. LNCS (LNAI), vol. 10259, pp. 3–13. Springer, Cham (2017). https://doi.org/10.1007/978-3-319-59758-4_1
Chen, J., et al.: OWL2Vec*: embedding of OWL ontologies. Mach. Learn. 110(7), 1813–1845 (2021). https://doi.org/10.1007/s10994-021-05997-6
Abad-Navarro, F., Martínez-Costa, C., Fernández-Breis, J.T.: HURON: a quantitative framework for assessing human readability in ontologies. IEEE Access 11, 101833–101851 (2023)
Abad-Navarro, F., Quesada-Martínez, M., Duque-Ramos, A., Fernández-Breis, J.T.: Analysis of readability and structural accuracy in SNOMED CT. BMC Med. Inform. Decis. Mak. 20(10), 1–21 (2020)
Horridge, M., Bechhofer, S.: The OWL API: a java API for OWL ontologies. Semant. Web 2(1), 11–21 (2011)
Courtot, M., et al.: MIREOT: the minimum information to reference an external ontology term. Appl. Ontol. 6(1), 23–33 (2011)
Ong, E., et al.: Ontobee: a linked ontology data server to support ontology term dereferencing, linkage, query and integration. Nucleic Acids Res. 45(D1), D347–D352 (2017)
Wilkinson, M.D., et al.: The FAIR guiding principles for scientific data management and stewardship. Sci. Data 3(1), 1–9 (2016)
Acknowledgements
This research has been funded by MCIN/AEI/10.13039/501100011033 [grant number PID2020-113723RB-C22].
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2024 The Author(s), under exclusive license to Springer Nature Switzerland AG
About this paper
Cite this paper
Redondo-Aniorte, F.J., Abad-Navarro, F., Fernández-Breis, J.T. (2024). Analysis of the Impact of Orthogonality in the Readability of the OBO Foundry Ontologies. In: Rocha, Á., Adeli, H., Dzemyda, G., Moreira, F., Poniszewska-Marańda, A. (eds) Good Practices and New Perspectives in Information Systems and Technologies. WorldCIST 2024. Lecture Notes in Networks and Systems, vol 987. Springer, Cham. https://doi.org/10.1007/978-3-031-60221-4_16
Download citation
DOI: https://doi.org/10.1007/978-3-031-60221-4_16
Published:
Publisher Name: Springer, Cham
Print ISBN: 978-3-031-60220-7
Online ISBN: 978-3-031-60221-4
eBook Packages: Intelligent Technologies and RoboticsIntelligent Technologies and Robotics (R0)