{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T09:29:32Z","timestamp":1764667772169,"version":"3.46.0"},"reference-count":80,"publisher":"MDPI AG","issue":"4","license":[{"start":{"date-parts":[[2025,12,1]],"date-time":"2025-12-01T00:00:00Z","timestamp":1764547200000},"content-version":"vor","delay-in-days":0,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/501100000038","name":"Natural Sciences and Engineering Research Council of Canada","doi-asserted-by":"publisher","award":["RGPIN-2023-04735"],"award-info":[{"award-number":["RGPIN-2023-04735"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"NSERC Discovery Launch Supplement","doi-asserted-by":"publisher","award":["DGECR-2021-00447"],"award-info":[{"award-number":["DGECR-2021-00447"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100000038","name":"NSERC Discovery Grants","doi-asserted-by":"publisher","award":["RGPIN-2021-04120"],"award-info":[{"award-number":["RGPIN-2021-04120"]}],"id":[{"id":"10.13039\/501100000038","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":["Informatics"],"abstract":"<jats:p>Ontologies play a central role in structuring knowledge across domains, supporting tasks such as reasoning, data integration, and semantic search. However, their large size and complexity\u2014particularly in fields such as biomedicine, computational biology, law, and engineering\u2014make them difficult for non-experts to navigate. Formal query languages such as SPARQL offer expressive access but require users to understand the ontology\u2019s structure and syntax. In contrast, visual exploration tools and basic keyword-based search interfaces are easier to use but often lack flexibility and expressiveness. We introduce FuzzyVis, a proof-of-concept system that enables intuitive and expressive exploration of complex ontologies. FuzzyVis integrates two key components: a fuzzy logic-based querying model built on fuzzy ontology embeddings, and an interactive visual interface for building and interpreting queries. Users can construct new composite concepts by selecting and combining existing ontology concepts using logical operators such as conjunction, disjunction, and negation. These composite concepts are matched against the ontology using fuzzy membership-based embeddings, which capture degrees of membership and support approximate, concept-level similarity search. The visual interface supports browsing, query composition, and partial search without requiring formal syntax. By combining fuzzy semantics with embedding-based reasoning, FuzzyVis enables flexible interpretation, efficient computation, and exploratory learning. A usage scenario demonstrates how FuzzyVis supports subtle information needs and helps users uncover relevant concepts in large, complex ontologies.<\/jats:p>","DOI":"10.3390\/informatics12040133","type":"journal-article","created":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T08:49:22Z","timestamp":1764665362000},"page":"133","update-policy":"https:\/\/doi.org\/10.3390\/mdpi_crossmark_policy","source":"Crossref","is-referenced-by-count":0,"title":["Fuzzy Ontology Embeddings and Visual Query Building for Ontology Exploration"],"prefix":"10.3390","volume":"12","author":[{"ORCID":"https:\/\/orcid.org\/0009-0001-2455-8610","authenticated-orcid":false,"given":"Vladimir","family":"Zhurov","sequence":"first","affiliation":[{"name":"Faculty of Science, Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0009-0005-0534-064X","authenticated-orcid":false,"given":"John","family":"Kausch","sequence":"additional","affiliation":[{"name":"Faculty of Information and Media Studies, University of Western Ontario, London, ON N6A 5B9, Canada"}]},{"given":"Kamran","family":"Sedig","sequence":"additional","affiliation":[{"name":"Faculty of Science, Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada"},{"name":"Faculty of Information and Media Studies, University of Western Ontario, London, ON N6A 5B9, Canada"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-3386-7079","authenticated-orcid":false,"given":"Mostafa","family":"Milani","sequence":"additional","affiliation":[{"name":"Faculty of Science, Department of Computer Science, University of Western Ontario, London, ON N6A 5B7, Canada"}]}],"member":"1968","published-online":{"date-parts":[[2025,12,1]]},"reference":[{"key":"ref_1","doi-asserted-by":"crossref","first-page":"e12596","DOI":"10.2196\/12596","article-title":"Identifying Clinical Terms in Medical Text Using Ontology-Guided Machine Learning","volume":"7","author":"Arbabi","year":"2019","journal-title":"JMIR Med. Inform."},{"key":"ref_2","doi-asserted-by":"crossref","unstructured":"Eiter, T., Ianni, G., Polleres, A., Schindlauer, R., and Tompits, H. (2006). Reasoning with Rules and Ontologies. Reasoning Web International Summer School, Springer.","DOI":"10.1007\/11837787_4"},{"key":"ref_3","doi-asserted-by":"crossref","unstructured":"Hayes, P.J. (1989). The Second Naive Physics Manifesto. Readings in Qualitative Reasoning About Physical Systems, Morgan Kaufmann.","DOI":"10.1016\/B978-1-4832-1447-4.50010-9"},{"key":"ref_4","doi-asserted-by":"crossref","first-page":"1698","DOI":"10.1016\/j.ipm.2019.05.009","article-title":"Query Expansion Techniques for Information Retrieval: A Survey","volume":"56","author":"Azad","year":"2019","journal-title":"Inf. Process. Manag."},{"key":"ref_5","doi-asserted-by":"crossref","first-page":"77903","DOI":"10.1109\/ACCESS.2020.2988685","article-title":"Semantic Integration of Heterogeneous Databases of Same Domain Using Ontology","volume":"8","author":"Ali","year":"2020","journal-title":"IEEE Access"},{"key":"ref_6","doi-asserted-by":"crossref","unstructured":"De Giacomo, G., Lembo, D., Lenzerini, M., Poggi, A., and Rosati, R. (2018). Using Ontologies for Semantic Data Integration. A Comprehensive Guide Through the Italian Database Research Over the Last 25 Years, Springer.","DOI":"10.1007\/978-3-319-61893-7_11"},{"key":"ref_7","first-page":"43","article-title":"The MASTRO System for Ontology-Based Data Access","volume":"2","author":"Calvanese","year":"2011","journal-title":"Semant. Web"},{"key":"ref_8","doi-asserted-by":"crossref","first-page":"25","DOI":"10.1038\/75556","article-title":"Gene Ontology: Tool for the Unification of Biology","volume":"25","author":"Ashburner","year":"2000","journal-title":"Nat. Genet."},{"key":"ref_9","doi-asserted-by":"crossref","unstructured":"Eilbeck, K., Lewis, S.E., Mungall, C.J., Yandell, M., Stein, L., Durbin, R., and Ashburner, M. (2005). The Sequence Ontology: A Tool for the Unification of Genome Annotations. Genome Biol., 6.","DOI":"10.1186\/gb-2005-6-5-r44"},{"key":"ref_10","doi-asserted-by":"crossref","first-page":"D1333","DOI":"10.1093\/nar\/gkad1005","article-title":"The Human Phenotype Ontology in 2024: Phenotypes Around the World","volume":"52","author":"Gargano","year":"2024","journal-title":"Nucleic Acids Res."},{"key":"ref_11","doi-asserted-by":"crossref","first-page":"D955","DOI":"10.1093\/nar\/gky1032","article-title":"Human Disease Ontology 2018 Update: Classification, Content and Workflow Expansion","volume":"47","author":"Schriml","year":"2019","journal-title":"Nucleic Acids Res."},{"key":"ref_12","first-page":"265","article-title":"Medical Subject Headings (MeSH)","volume":"88","author":"Lipscomb","year":"2000","journal-title":"Bull. Med. Libr. Assoc."},{"key":"ref_13","doi-asserted-by":"crossref","unstructured":"Hoekstra, R., Breuker, J., Di Bello, M., and Boer, A. (2009). LKIF Core: Principled Ontology Development for the Legal Domain. Law, Ontologies and the Semantic Web, IOS Press.","DOI":"10.3233\/978-1-58603-942-4-21"},{"key":"ref_14","first-page":"267","article-title":"LOTED2: An Ontology of European Public Procurement Notices","volume":"7","author":"Distinto","year":"2016","journal-title":"Semant. Web"},{"key":"ref_15","doi-asserted-by":"crossref","unstructured":"Demelo, J., and Sedig, K. (2021). Forming Cognitive Maps of Ontologies Using Interactive Visualizations. Multimodal Technol. Interact., 5.","DOI":"10.3390\/mti5010002"},{"key":"ref_16","unstructured":"Seaborne, A., and Harris, S. (2013). SPARQL 1.1 Query Language, W3C."},{"key":"ref_17","doi-asserted-by":"crossref","first-page":"19","DOI":"10.1016\/j.websem.2004.07.002","article-title":"OWL-QL\u2014A Language for Deductive Query Answering on the Semantic Web","volume":"2","author":"Fikes","year":"2004","journal-title":"J. Web Semant."},{"key":"ref_18","unstructured":"Broekstra, J., and Kampman, A. (2006). An Rdf Query and Transformation Language. Semantic Web and Peer-To-Peer: Decentralized Management and Exchange of Knowledge and Information, Springer."},{"key":"ref_19","unstructured":"Sirin, E., and Parsia, B. (2007, January 6\u20137). SPARQL-DL: SPARQL Query for OWL-DL. Proceedings of the OWLED 2007 Workshop on OWL: Experiences and Directions, Innsbruck, Austria."},{"key":"ref_20","doi-asserted-by":"crossref","first-page":"4193","DOI":"10.1109\/TKDE.2025.3559023","article-title":"Ontology Embedding: A Survey of Methods, Applications and Resources","volume":"37","author":"Chen","year":"2025","journal-title":"IEEE Trans. Knowl. Data Eng."},{"key":"ref_21","unstructured":"Bordes, A., Usunier, N., Garcia-Duran, A., Weston, J., and Yakhnenko, O. (2013, January 5\u201310). Translating Embeddings for Modeling Multi-Relational Data. Proceedings of the 27th International Conference on Neural Information Processing Systems (NIPS 2013), Lake Tahoe, NV, USA. Available online: https:\/\/dl.acm.org\/doi\/10.5555\/2999792.2999923."},{"key":"ref_22","doi-asserted-by":"crossref","unstructured":"Wang, Z., Zhang, J., Feng, J., and Chen, Z. (2014, January 27\u201331). Knowledge Graph Embedding by Translating on Hyperplanes. Proceedings of the AAAI Conference on Artificial Intelligence, Qu\u00e9bec City, QC, Canada.","DOI":"10.1609\/aaai.v28i1.8870"},{"key":"ref_23","doi-asserted-by":"crossref","unstructured":"Lin, Y., Liu, Z., Sun, M., Liu, Y., and Zhu, X. (2015, January 25\u201330). Learning Entity and Relation Embeddings for Knowledge Graph Completion. Proceedings of the AAAI Conference on Artificial Intelligence, Austin, TX, USA.","DOI":"10.1609\/aaai.v29i1.9491"},{"key":"ref_24","doi-asserted-by":"crossref","unstructured":"Ristoski, P., and Paulheim, H. (2016, January 17\u201321). Rdf2vec: Rdf Graph Embeddings for Data Mining. Proceedings of the Semantic Web\u2014ISWC 2016, Kobe, Japan.","DOI":"10.1007\/978-3-319-46523-4_30"},{"key":"ref_25","doi-asserted-by":"crossref","first-page":"1813","DOI":"10.1007\/s10994-021-05997-6","article-title":"Owl2vec*: Embedding of Owl Ontologies","volume":"110","author":"Chen","year":"2021","journal-title":"Mach. Learn."},{"key":"ref_26","doi-asserted-by":"crossref","first-page":"124","DOI":"10.1145\/3748239.3748249","article-title":"Neural-Symbolic Reasoning over Knowledge Graphs: A Survey from a Query Perspective","volume":"27","author":"Liu","year":"2025","journal-title":"ACM SIGKDD Explor. Newsl."},{"key":"ref_27","doi-asserted-by":"crossref","unstructured":"Kulmanov, M., Liu-Wei, W., Yan, Y., and Hoehndorf, R. (2019, January 10\u201316). EL Embeddings: Geometric Construction of Models for the Description Logic EL++. Proceedings of the Twenty-Eighth International Joint Conference on Artificial Intelligence, Macao, China. International Joint Conferences on Artificial Intelligence Organization.","DOI":"10.24963\/ijcai.2019\/845"},{"key":"ref_28","unstructured":"Jackermeier, M., Chen, J., and Horrocks, I. (2024, January 13\u201317). Dual Box Embeddings for the Description Logic EL++. Proceedings of the ACM on Web Conference 2024, Singapore."},{"key":"ref_29","unstructured":"Ganea, O., B\u00e9cigneul, G., and Hofmann, T. (2018, January 10\u201315). Hyperbolic Entailment Cones for Learning Hierarchical Embeddings. Proceedings of the 35th International Conference on Machine Learning, Stockholm, Sweden."},{"key":"ref_30","unstructured":"Sun, Z., Deng, Z.-H., Nie, J.-Y., and Tang, J. (2019, January 6\u20139). RotatE: Knowledge Graph Embedding by Relational Rotation in Complex Space. Proceedings of the International Conference on Learning Representations, New Orleans, LA, USA."},{"key":"ref_31","doi-asserted-by":"crossref","unstructured":"Zhapa-Camacho, F., and Hoehndorf, R. (2024, January 9\u201312). Lattice-Preserving ALC Ontology Embeddings. Proceedings of the International Conference on Neural-Symbolic Learning and Reasoning, Barcelona, Spain.","DOI":"10.1007\/978-3-031-71167-1_19"},{"key":"ref_32","doi-asserted-by":"crossref","unstructured":"Akremi, H., Ayadi, M.G., and Zghal, S. (2022, January 10\u201312). A Fuzzy OWL Ontologies Embedding for Complex Ontology Alignments. Proceedings of the International Conference on Discovery Science, Montpellier, France.","DOI":"10.1007\/978-3-031-18840-4_28"},{"key":"ref_33","doi-asserted-by":"crossref","first-page":"835","DOI":"10.1109\/TFUZZ.2022.3190633","article-title":"Fuzzy RDF Knowledge Graph Embeddings Through Vector Space Model","volume":"31","author":"Zhang","year":"2022","journal-title":"IEEE Trans. Fuzzy Syst."},{"key":"ref_34","unstructured":"Hinnerichs, T., Tang, Z., Peng, X., Zhang, X., and Hoehndorf, R. (2024). FALCON: Scalable Reasoning over Inconsistent ALC Ontologies. arXiv, preprint."},{"key":"ref_35","unstructured":"Gabel, T., Sure, Y., and Voelker, J. (2004). D3. 1.1. A: KAON\u2013Ontology Management Infrastructure. SEKT Informal Deliv., Available online: https:\/\/www.tgabel.de\/fileadmin\/user_upload\/documents\/Gabel_etal_KAONInf-04.pdf."},{"key":"ref_36","doi-asserted-by":"crossref","unstructured":"Horridge, M., Gon\u00e7alves, R.S., Nyulas, C.I., Tudorache, T., and Musen, M.A. (2019, January 13\u201317). Webprot\u00e9g\u00e9: A Cloud-Based Ontology Editor. Proceedings of the Companion Proceedings of the 2019 World Wide Web Conference, San Francisco, CA, USA.","DOI":"10.1145\/3308560.3317707"},{"key":"ref_37","doi-asserted-by":"crossref","first-page":"2198","DOI":"10.1093\/bioinformatics\/btm112","article-title":"OBO-Edit\u2014An Ontology Editor for Biologists","volume":"23","author":"Harris","year":"2007","journal-title":"Bioinformatics"},{"key":"ref_38","doi-asserted-by":"crossref","unstructured":"Lohmann, S., Negru, S., and Bold, D. (2014, January 25\u201329). The Prot\u00e9g\u00e9VOWL Plugin: Ontology Visualization for Everyone. Proceedings of the European Semantic Web Conference, Anissaras, Crete, Greece.","DOI":"10.1007\/978-3-319-11955-7_55"},{"key":"ref_39","doi-asserted-by":"crossref","first-page":"355","DOI":"10.12785\/amis\/080145","article-title":"Scalable Visualization of Semantic Nets Using Power-Law Graphs","volume":"8","author":"Hussain","year":"2014","journal-title":"Appl. Math. Inf. Sci."},{"key":"ref_40","unstructured":"Alani, H. (2003, January 26). TGVizTab: An Ontology Visualisation Extension for Prot\u00e9g\u00e9. Proceedings of the Knowledge Capture (k-cap\u201903), Workshop on Visualization Information in Knowledge Engineering, Sanibel Island, FL, USA."},{"key":"ref_41","unstructured":"Wachsmann, L. (2025, November 20). OWLPropViz 2008. Available online: https:\/\/protegewiki.stanford.edu\/wiki\/OWLPropViz."},{"key":"ref_42","doi-asserted-by":"crossref","unstructured":"Lohmann, S., Link, V., Marbach, E., and Negru, S. (2015, January 12\u201314). WebVOWL: Web-Based Visualization of Ontologies. Proceedings of the Knowledge Engineering and Knowledge Management, Lisbon, Portugal.","DOI":"10.1007\/978-3-319-17966-7_21"},{"key":"ref_43","unstructured":"Lintern, R., and Storey, M.-A. (2005, January 18\u201321). Jambalaya Express: Ontology Visualization-on-Demand. Proceedings of the International Prot\u00e9g\u00e9 Conference, Madrid, Spain."},{"key":"ref_44","doi-asserted-by":"crossref","first-page":"895","DOI":"10.1093\/bioinformatics\/bts029","article-title":"CODEX: Exploration of Semantic Changes Between Ontology Versions","volume":"28","author":"Hartung","year":"2012","journal-title":"Bioinformatics"},{"key":"ref_45","unstructured":"Bach, B., Pietriga, E., Liccardi, I., and Legostaev, G. (April, January 28). OntoTrix: A Hybrid Visualization for Populated Ontologies. Proceedings of the 20th International Conference Companion on World Wide Web, Hyderabad, India."},{"key":"ref_46","doi-asserted-by":"crossref","first-page":"251","DOI":"10.1111\/cgf.13184","article-title":"Graffinity: Visualizing Connectivity in Large Graphs","volume":"36","author":"Kerzner","year":"2017","journal-title":"Comput. Graph. Forum"},{"key":"ref_47","doi-asserted-by":"crossref","first-page":"e10","DOI":"10.1017\/S0269888918000073","article-title":"Ontology Visualization Methods and Tools: A Survey of the State of the Art","volume":"33","author":"Lohmann","year":"2018","journal-title":"Knowl. Eng. Rev."},{"key":"ref_48","doi-asserted-by":"crossref","unstructured":"Baader, F., and Nutt, W. (2003). Basic Description Logics. The Description Logic Handbook, Cambridge University Press.","DOI":"10.1007\/978-3-540-24750-0_1"},{"key":"ref_49","unstructured":"McGuinness, D.L., and van Harmelen, F. (2004). OWL Web Ontology Language Overview, W3C."},{"key":"ref_50","unstructured":"Klyne, G., Carroll, J.J., and McBride, B. (2014). Resource Description Framework (RDF): Concepts and Abstract Syntax, W3C."},{"key":"ref_51","unstructured":"Wessel, M., and M\u00f6ller, R. (2005). A High Performance Semantic Web Query Answering Engine. Descr. Log., 147, Available online: https:\/\/ceur-ws.org\/Vol-147\/30-Wessel.pdf."},{"key":"ref_52","unstructured":"Calvanese, D., De Giacomo, G., Lembo, D., Lenzerini, M., and Rosati, R. (2007, January 6\u201312). EQL-Lite: Effective First-Order Query Processing in Description Logics. Proceedings of the International Joint Conference on Artificial Intelligence, Hyderabad, India."},{"key":"ref_53","doi-asserted-by":"crossref","first-page":"1073","DOI":"10.1016\/j.ijar.2011.05.003","article-title":"Fuzzy Ontology Representation Using OWL 2","volume":"52","author":"Bobillo","year":"2011","journal-title":"Int. J. Approx. Reason."},{"key":"ref_54","doi-asserted-by":"crossref","first-page":"842","DOI":"10.1109\/TKDE.2006.87","article-title":"Automatic Fuzzy Ontology Generation for Semantic Web","volume":"18","author":"Tho","year":"2006","journal-title":"IEEE Trans. Knowl. Data Eng."},{"key":"ref_55","doi-asserted-by":"crossref","first-page":"103","DOI":"10.1007\/s001530050006","article-title":"Residuated Fuzzy Logics with an Involutive Negation","volume":"39","author":"Esteva","year":"2000","journal-title":"Arch. Math. Log."},{"key":"ref_56","doi-asserted-by":"crossref","first-page":"632","DOI":"10.1016\/j.ijar.2010.01.001","article-title":"Fuzzy Description Logics and t-Norm Based Fuzzy Logics","volume":"51","author":"Armengol","year":"2010","journal-title":"Int. J. Approx. Reason."},{"key":"ref_57","unstructured":"Stoilos, G., Straccia, U., Stamou, G., and Pan, J.Z. (September, January 29). General Concept Inclusions in Fuzzy Description Logics. Proceedings of the 2006 Conference on ECAI 2006: 17th European Conference on Artificial Intelligence, Riva del Garda, Italy."},{"key":"ref_58","doi-asserted-by":"crossref","first-page":"23","DOI":"10.1016\/j.artint.2014.09.001","article-title":"The Limits of Decidability in Fuzzy Description Logics with General Concept Inclusions","volume":"218","author":"Borgwardt","year":"2015","journal-title":"Artif. Intell."},{"key":"ref_59","doi-asserted-by":"crossref","unstructured":"Borgwardt, S., and Pe\u00f1aloza, R. (2017, January 4\u20136). Fuzzy Description Logics\u2013a Survey. Proceedings of the Scalable Uncertainty Management, Granada, Spain.","DOI":"10.1007\/978-3-319-67582-4_3"},{"key":"ref_60","doi-asserted-by":"crossref","first-page":"273","DOI":"10.1613\/jair.2279","article-title":"Reasoning with Very Expressive Fuzzy Description Logics","volume":"30","author":"Stoilos","year":"2007","journal-title":"J. Artif. Intell. Res."},{"key":"ref_61","doi-asserted-by":"crossref","first-page":"1","DOI":"10.1016\/j.fss.2005.03.005","article-title":"Making Fuzzy Description Logic More General","volume":"154","year":"2005","journal-title":"Fuzzy Sets Syst."},{"key":"ref_62","unstructured":"Borgwardt, S., and Pe\u00f1aloza, R. (2012, January 10\u201314). Undecidability of Fuzzy Description Logics. Proceedings of the 13th International Conference on Principles of Knowledge Representation and Reasoning (KR\u201912), Rome, Italy."},{"key":"ref_63","unstructured":"Borgwardt, S., Distel, F., and Pe\u00f1aloza, R. (2014, January 20\u201324). Decidable G\u00f6del Description Logics Without the Finitely-Valued Model Property. Proceedings of the Fourteenth International Conference on Principles of Knowledge Representation and Reasoning, Vienna, Austria."},{"key":"ref_64","unstructured":"Schr\u00f6der, L., and Pattinson, D. (2011, January 19\u201322). Description Logics and Fuzzy Probability. Proceedings of the 22nd International Joint Conference on Artificial Intelligence, IJCAI 2011, Barcelona, Spain."},{"key":"ref_65","doi-asserted-by":"crossref","first-page":"1045","DOI":"10.1016\/j.ic.2008.03.006","article-title":"Automata Can Show PSPACE Results for Description Logics","volume":"206","author":"Baader","year":"2008","journal-title":"Inf. Comput."},{"key":"ref_66","doi-asserted-by":"crossref","unstructured":"Bobillo, F., and Straccia, U. (2007, January 23\u201326). A Fuzzy Description Logic with Product t-Norm. Proceedings of the 2007 IEEE International Fuzzy Systems Conference, London, UK.","DOI":"10.1109\/FUZZY.2007.4295443"},{"key":"ref_67","doi-asserted-by":"crossref","first-page":"503","DOI":"10.1613\/jair.1.11661","article-title":"Ontology Reasoning with Deep Neural Networks","volume":"68","author":"Hohenecker","year":"2020","journal-title":"J. Artif. Intell. Res."},{"key":"ref_68","doi-asserted-by":"crossref","first-page":"12","DOI":"10.1016\/j.knosys.2015.11.017","article-title":"The Fuzzy Ontology Reasoner FuzzyDL","volume":"95","author":"Bobillo","year":"2016","journal-title":"Knowl.-Based Syst."},{"key":"ref_69","first-page":"307","article-title":"Optimizing Tableau Reasoning in ALC Extended with Uncertainty","volume":"Volume 250","author":"Haarslev","year":"2007","journal-title":"Proceedings of the 20th International Workshop on Description Logics (DL 2007)"},{"key":"ref_70","doi-asserted-by":"crossref","first-page":"258","DOI":"10.1016\/j.eswa.2011.07.016","article-title":"DeLorean: A Reasoner for Fuzzy OWL 2","volume":"39","author":"Bobillo","year":"2012","journal-title":"Expert Syst. Appl."},{"key":"ref_71","unstructured":"Bobillo, F., Delgado, M., and G\u00f3mez-Romero, J. (2006, January 5). A Crisp Representation for Fuzzy SHOIN with Fuzzy Nominals and General Concept Inclusions. Proceedings of the Second International Conference on Uncertainty Reasoning for the Semantic Web-Volume 218, Athens, GA, USA."},{"key":"ref_72","doi-asserted-by":"crossref","first-page":"535","DOI":"10.1109\/TBDATA.2019.2921572","article-title":"Billion-Scale Similarity Search with GPUs","volume":"7","author":"Johnson","year":"2019","journal-title":"IEEE Trans. Big Data"},{"key":"ref_73","unstructured":"(2025, November 26). Chroma contributors Chroma (ChromaDB): An Open-Source Embedding\/Vector Database 2025. Available online: https:\/\/github.com\/chroma-core\/chroma."},{"key":"ref_74","doi-asserted-by":"crossref","unstructured":"Cowell, L.G., and Smith, B. (2009). Infectious Disease Ontology. Infectious Disease Informatics, Springer.","DOI":"10.1007\/978-1-4419-1327-2_19"},{"key":"ref_75","doi-asserted-by":"crossref","first-page":"871","DOI":"10.1109\/TKDE.2003.1209005","article-title":"An Approach for Measuring Semantic Similarity Between Words Using Multiple Information Sources","volume":"15","author":"Li","year":"2003","journal-title":"IEEE Trans. Knowl. Data Eng."},{"key":"ref_76","doi-asserted-by":"crossref","unstructured":"Nagar, A., and Al-Mubaid, H. (2008, January 17\u201319). A New Path Length Measure Based on Go for Gene Similarity with Evaluation Using Sgd Pathways. Proceedings of the 2008 21st IEEE International Symposium on Computer-Based Medical Systems, Jyv\u00e4skyl\u00e4, Finland.","DOI":"10.1109\/CBMS.2008.27"},{"key":"ref_77","doi-asserted-by":"crossref","first-page":"116","DOI":"10.1109\/TCBB.2013.149","article-title":"A New Path Based Hybrid Measure for Gene Ontology Similarity","volume":"11","author":"Bandyopadhyay","year":"2013","journal-title":"IEEE\/ACM Trans. Comput. Biol. Bioinform."},{"key":"ref_78","unstructured":"Vinci, L. (2025, November 13). FALCON (GitHub Repository). Available online: https:\/\/github.com\/lilv98\/FALCON."},{"key":"ref_79","doi-asserted-by":"crossref","first-page":"388","DOI":"10.1002\/cfg.496","article-title":"Plant Ontology (PO): A Controlled Vocabulary of Plant Structures and Growth Stages","volume":"6","author":"Jaiswal","year":"2005","journal-title":"Comp. Funct. Genom."},{"key":"ref_80","doi-asserted-by":"crossref","first-page":"11","DOI":"10.1016\/j.artmed.2017.07.002","article-title":"Owlready: Ontology-Oriented Programming in Python with Automatic Classification and High Level Constructs for Biomedical Ontologies","volume":"80","author":"Lamy","year":"2017","journal-title":"Artif. Intell. Med."}],"container-title":["Informatics"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/www.mdpi.com\/2227-9709\/12\/4\/133\/pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2025,12,2]],"date-time":"2025-12-02T09:27:09Z","timestamp":1764667629000},"score":1,"resource":{"primary":{"URL":"https:\/\/www.mdpi.com\/2227-9709\/12\/4\/133"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2025,12,1]]},"references-count":80,"journal-issue":{"issue":"4","published-online":{"date-parts":[[2025,12]]}},"alternative-id":["informatics12040133"],"URL":"https:\/\/doi.org\/10.3390\/informatics12040133","relation":{},"ISSN":["2227-9709"],"issn-type":[{"value":"2227-9709","type":"electronic"}],"subject":[],"published":{"date-parts":[[2025,12,1]]}}}