EVS Edit: A Customized Protégé Ontology Editor for NIH Enterprise Vocabulary Services—Architecture, Plugins, Automation Workflows, and Biomedical Ontology Curation
DOI:
https://doi.org/10.22399/ijcesen.5431Keywords:
Biomedical Ontology, EVS Edit, NCI Thesaurus, Ontology Curation, Protégé, PROMPT WorkflowAbstract
NCI Thesaurus is one of the largest production biomedical ontologies in the NIH National Cancer Institute (NCI) Enterprise Vocabulary Services (EVS) with over 176,000 concepts, 115,000 definitions, and 400,000 relationships. The NCI's ontology curation environment is the NCI EVS Edit, a customized version of the Stanford Protégé ontology editor with additional plug-ins, the NCI Edit Tab plugin suite. Developed initially in Protégé 3.4 and ported fully to Protégé 5.x with the open-source nci-protege5 project, EVS Edit supports EVS-specific business rules, concurrent multi-editor workflows, automated terminology curation, quality control, versioning, and publication. This article describes the technical architecture, Protégé plugin suite, automation pipelines, and NIH-specific integration of the EVS Edit application. Batch loading‚ the PROMPT review cycle‚ the monthly NCIt pipeline publication process‚ and ingesting to the LexEVS triple store‚ EVSRESTAPI‚ and the EVS Explore browser have been shown to improve NCIt curation processes as well as processes for partner terminologies (e.g.‚ Clinical Data Interchange Standards Consortium Controlled Terminology) for quality‚ reproducibility‚ and editor efficiency. Error rates are reported below one percent post-publication, support for fifteen or more concurrent editors, batch-load speeds increased by around ten times, and release cadences were reduced from sixty days to thirty. The article also discusses future directions of work such as AI-assisted curation and Web Ontology Language 2 Description Logic reasoning.
References
[1] Musen, M. A. (2015). The Protégé project: A look back and a look forward. AI Matters, 1(4), 4-12. https://doi.org/10.1145/2757001.2757003 DOI: https://doi.org/10.1145/2757001.2757003
[2] Noy, N. F., & Musen, M. A. (2003). The PROMPT suite: Interactive tools for ontology merging and mapping. International Journal of Human-Computer Studies, 59(6), 983-1024. https://doi.org/10.1016/j.ijhcs.2003.08.002 DOI: https://doi.org/10.1016/j.ijhcs.2003.08.002
[3] Tudorache, T., Nyulas, C., Noy, N. F., & Musen, M. A. (2013). WebProtégé: A collaborative ontology editor and knowledge acquisition tool for the Web. Semantic Web, 4(1), 89-99. https://doi.org/10.3233/SW-2012-0057 DOI: https://doi.org/10.3233/SW-2012-0057
[4] de Coronado, S., Wright, L. W., Fragoso, G., Haber, M. W., Hahn-Dantona, E. A., Hartel, F. W., Quan, S. L., Safran, T., Thomas, N., & Whiteman, L. (2009). The NCI Thesaurus quality assurance life cycle. Journal of Biomedical Informatics, 42(3), 530-539. https://doi.org/10.1016/j.jbi.2009.01.003 DOI: https://doi.org/10.1016/j.jbi.2009.01.003
[5] Fragoso, G., de Coronado, S., Haber, M., Hartel, F., & Wright, L. (2004). Overview and utilization of the NCI Thesaurus. Comparative and Functional Genomics, 5(8), 648-654. https://doi.org/10.1002/cfg.445 DOI: https://doi.org/10.1002/cfg.445
[6] Hartel, F. W., de Coronado, S., Dionne, R., Fragoso, G., & Golbeck, J. (2005). Modeling a description logic vocabulary for cancer research. Journal of Biomedical Informatics, 38(2), 114-129. https://doi.org/10.1016/j.jbi.2004.09.001 DOI: https://doi.org/10.1016/j.jbi.2004.09.001
[7] Horridge, M., Parsia, B., & Sattler, U. (2010). Justifications for entailments in expressive description logics. Journal of Automated Reasoning, 45(2), 121-143. https://lat.inf.tu-dresden.de/research/papers/2018/RuScTi-RR-18.pdf
[8] Sirin, E., Parsia, B., Grau, B. C., Kalyanpur, A., & Katz, Y. (2007). Pellet: A practical OWL-DL reasoner. Journal of Web Semantics, 5(2), 51-53. https://doi.org/10.1016/j.websem.2007.03.004 DOI: https://doi.org/10.1016/j.websem.2007.03.004
[9] Glimm, B., Horrocks, I., Motik, B., Stoilos, G., & Wang, Z. (2014). HermiT: An OWL 2 reasoner. Journal of Automated Reasoning, 53(3), 245-269. https://doi.org/10.1007/s10817-014-9305-1 DOI: https://doi.org/10.1007/s10817-014-9305-1
[10] Tudorache, T. (2020). Ontology engineering: Current state, challenges, and future directions. Semantic Web, 11(1), 125-138. https://doi.org/10.3233/SW-190382 DOI: https://doi.org/10.3233/SW-190382
[11] Cuenca Grau, B., Horrocks, I., Motik, B., Parsia, B., Patel-Schneider, P., & Sattler, U. (2008). OWL 2: The next step for OWL. Journal of Web Semantics, 6(4), 309-322. https://doi.org/10.1016/j.websem.2008.05.001 DOI: https://doi.org/10.1016/j.websem.2008.05.001
[12] Stevens, R., & Lord, P. (2009). Application of ontologies in bioinformatics. In Handbook on Ontologies (pp. 735-756). Springer. https://doi.org/10.1007/978-3-540-92673-3_33 DOI: https://doi.org/10.1007/978-3-540-92673-3_33
[13] Schober, D., Tudose, I., Svatek, V., & Boeker, M. (2012). OntoCheck: Verifying ontology naming conventions and metadata completeness in Protégé 4. Journal of Biomedical Semantics, 3(Suppl 2), S4. https://doi.org/10.1186/2041-1480-3-S2-S4 DOI: https://doi.org/10.1186/2041-1480-3-S2-S4
[14] Smith, B., Ashburner, M., Rosse, C., Bard, J., Bug, W., Ceusters, W., Goldberg, L. J., Eilbeck, K., Ireland, A., Mungall, C. J., Leontis, N., Rocca-Serra, P., Ruttenberg, A., Sansone, S. A., Scheuermann, R. H., Shah, N., Whetzel, P. L., & Lewis, S. (2007). The OBO Foundry: Coordinated evolution of ontologies to support biomedical data integration. Nature Biotechnology, 25(11), 1251-1255. https://doi.org/10.1038/nbt1346 DOI: https://doi.org/10.1038/nbt1346
[15] Solbrig, H. R., Hong, N., Murphy, S. N., & Jiang, G. (2017). Modeling and validating HL7 FHIR profiles using semantic web Shape Expressions. Journal of Biomedical Informatics, 67, 90-100. https://doi.org/10.1016/j.jbi.2017.02.009 DOI: https://doi.org/10.1016/j.jbi.2017.02.009
[16] Hanna, J., Joseph, E., Brochhausen, M., & Hogan, W. R. (2013). Building a drug ontology based on RxNorm and other sources. Journal of Biomedical Semantics, 4, 44. https://doi.org/10.1186/2041-1480-4-44 DOI: https://doi.org/10.1186/2041-1480-4-44
[17] Mortensen, J. M., Musen, M. A., & Noy, N. F. (2013). Crowdsourcing the verification of relationships in biomedical ontologies. AMIA Annual Symposium Proceedings, 2013, 1020-1029. https://www.researchgate.net/publication/260254186_Crowdsourcing_the_Verification_of_Relationships_in_Biomedical_Ontologies
[18] Pathak, J., Solbrig, H. R., Buntrock, J. D., Johnson, T. M., & Chute, C. G. (2009). LexGrid: A framework for representing, storing, and querying biomedical terminologies from simple to sublime. Journal of the American Medical Informatics Association, 16(3), 305-315. https://www.sciencedirect.com/science/article/abs/pii/S1067502709000371 DOI: https://doi.org/10.1197/jamia.M3006
[19] Muhlbradt, E. E. (2023). NCI-EVS: Building the semantic infrastructure for terminology services. Journal of the Society for Clinical Data Management, 3(2), 1-12. https://www.jscdm.org/article/id/134/
[20] Bona, J. P., Brochhausen, M., & Hogan, W. R. (2019). Enhancing the drug ontology with semantically-rich representations of National Drug Codes and RxNorm unique concept identifiers. BMC Bioinformatics, 20(Suppl 21), 708. https://doi.org/10.1186/s12859-019-3192-8 DOI: https://doi.org/10.1186/s12859-019-3192-8
[21] Nadkarni, P. M., Ohno-Machado, L., & Chapman, W. W. (2011). Natural language processing: An introduction. Journal of the American Medical Informatics Association, 18(5), 544-551. https://doi.org/10.1136/amiajnl-2011-000464 DOI: https://doi.org/10.1136/amiajnl-2011-000464
[22] Whetzel, P. L., Noy, N. F., Shah, N. H., Alexander, P. R., Nyulas, C., Tudorache, T., & Musen, M. A. (2011). BioPortal: Enhanced functionality via new Web services. Nucleic Acids Research, 39(Suppl 2), W541-W545. https://doi.org/10.1093/nar/gkr469 DOI: https://doi.org/10.1093/nar/gkr469
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