Publications

Abad-Navarro, F., & Martínez-Costa, C. (2023). A knowledge graph-based data harmonization framework for secondary data reuse. Computer Methods and Programs in Biomedicine, 107918.(full text)

Abad-Navarro, F., Martínez-Costa, C., Fernández-Breis, J.T. HURON: A quantitative framework for assessing human readability in ontologies. In IEEE Access. ( full text)

Miñarro-Giménez, J. A., Fernández-Llatas, C., Martínez-Salvador, B., Martínez-Costa, C., Marcos, M., & Fernández-Breis, J. T. (2023, June). Ontology Model for Supporting Process Mining on Healthcare-Related Data. In International Conference on Artificial Intelligence in Medicine (pp. 352-356). Cham: Springer Nature Switzerland ( full text)

Stefan Schulz,*, James T Case, Peter Hendler, Daniel Karlsson, Michael Lawley, Ronald Cornet, Robert Hausam, Harold Solbrig, Karim Nashar, Catalina Martínez-Costa, and Yongsheng Gao. SNOMED CT and Basic Formal Ontology – Convergence or Contradiction between Standards? The case of “Clinical Finding”. Applied Ontology, (Preprint), 1-31 ( full text)

Asiyah Yu Lin *, Sivaram Arabandi, Thomas Beale, James Campbell, William D. Duncan, Amanda Hicks, William R. Hogan, Mark Jensen, Ross Koppel, Catalina Martínez-Costa, Øystein Nytrø, Jihad Obeid, Jose Parente De Oliveira, Alan Ruttenberg, Selja Seppälä, Barry Smith, Dagobert Soergel, Jie Zheng, Stefan Schulz.Improving the Quality and Utility of Electronic Health Record Data Through Ontologies. Drug standards, ( full text)

Castell-Díaz, J., Miñarro-Giménez, J. A., & Martínez-Costa, C. (2023). Supporting SNOMED CT postcoordination with knowledge graph embeddings. Journal of Biomedical Informatics, 104297. ( full text)

Javier Castell-Díaz, Catalina Martínez-Costa. Towards the automatic building of SNOMED CT post coordinated expressions. (2022) SNOMED CT Expo 2022. Lisbon, Portugal. ( Presentation video)

Tilda Herrgårdh, Elizabeth Hunter, Kajsa Tunedal, Håkan Örman, Julia Amann, Francisco Abad Navarro, Catalina Martinez-Costa, John D. Kelleher, Gunnar Cedersund Digital twins and hybrid modelling for simulation of physiological variables and stroke risk doi: https://doi.org/10.1101/2022.03.25.485803 (bioarxiv preprint) (full text)

Saadullah Amin, Noon Pokaratsiri Goldstein, Morgan Wixted, Alejandro Garcia-Rudolph, Catalina Martínez-Costa, and Guenter Neumann. 2022. Few-Shot Cross-lingual Transfer for Coarse-grained De-identification of Code-Mixed Clinical Texts. In Proceedings of the 21st Workshop on Biomedical Language Processing, pages 200–211, Dublin, Ireland. Association for Computational Linguistics. (full text)

Francisco Abad-Navarro; Catalina Martínez-Costa and J. T. Fernández-Breis, “Semankey: A Semantics-Driven Approach for Querying RDF Repositories Using Keywords,” in IEEE Access, vol. 9, pp. 91282-91302, 2021 (full text)

Martinez-Costa, Catalina, and Francisco Abad-Navarro. “Towards a Semantic Data Harmonization Federated Infrastructure.” Public Health and Informatics. IOS Press, 2021. 38-42. (full text)

Daumke, P; Heitmann, KU; Heckmann, S; Martínez-Costa, C; Schulz, S Clinical Text Mining on FHIR. Stud Health Technol Inform. 2019; 264:83-87 Doi: 10.3233/SHTI190188 (full text)

Martínez-Costa C, Miñarro-Giménez JA, Hausam RR, Schulz S. Addressing the Negation Gap in SNOMED CT by Reified Negated Concepts. In JOWO 2019. (http://ceur-ws.org/Vol-2518/paper-ODLS5.pdf| full text)

Argüello-Casteleiro, M., Martínez-Costa, C., Desdiz, J., Maroto, N., Prieto, M. J. F., & Stevens, R. (2019, January). From SNOMED CT expressions to an FHIR RDF representation: Exploring the benefits of an ontology-based approach. In CEUR Workshop (pp. 1-13). (full text)

Miñarro-Giménez, JA; Martínez-Costa, C; Karlsson, D; Schulz, S; Gøeg, KR Qualitative analysis of manual annotations of clinical text with SNOMED CT. PLoS One. 2018; 13(12):e0209547-e0209547 Doi: 10.1371/journal.pone.0209547 [OPEN ACCESS] (full text)

Fernández-Breis, JT; Menárguez-Tortosa, M; Martínez-Costa,C; Miñarro Giménez, JA; Legaz-García, MC; Quesada-Martínez,M; Duque, A; Esteban-Gil, A; Castellanos Nieves, D Tecnologías para el Modelado, Procesamiento y Gestión de Conocimiento Proceedings of the XVIII Conferencia de la Asociación Española para la Inteligencia Artificial (CAEPIA 2018). 2018; 1246-1251.-XVIII Conferencia de la Asociación Española para la Inteligencia Artificial (CAEPIA 2018); OCT 23-27, 2018; Granada, SPAIN. (ISBN: 978-84-09-05643-9 ) [Oral Communication] (full text)

Kreuzthaler, M; Martínez-Costa, C; Kaiser, P; Schulz, S Semantic Technologies for Re-Use of Clinical Routine Data. Stud Health Technol Inform. 2017; 236(18):24-31 (full text)

Martinez-Costa, C; Schulz, S HL7 FHIR: Ontological Reinterpretation of Medication Resources. Stud Health Technol Inform. 2017; 235(23):451-455 (full text)

Martínez-Costa, C; Schulz, S Validating EHR clinical models using ontology patterns. J Biomed Inform. 2017; 76(20):124-137 Doi: 10.1016/j.jbi.2017.11.001 [OPEN ACCESS] (full text)

Miñarro-Giménez, JA; Martínez-Costa, C; López-García, P; Schulz, S Building SNOMED CT Post-Coordinated Expressions from Annotation Groups. Stud Health Technol Inform. 2017; 235(12):446-450 (full text)

Schulz, S; Boeker, M; Martinez-Costa, C The BioTop Family of Upper Level Ontological Resources for Biomedicine. Stud Health Technol Inform. 2017; 235:441-445 (full text)

Arguello Casteleiro, M; Martinez Costa, C; Des-Diz, J; Fernandez Prieto MJ; Wroe, C; Maseda Fernandez, D; Demetrio; G; Nenadic, G; Keane, J; Schulz, S; Stevens, R Experiments to create ontology-based disease models for diabetic retinopathy from different biomedical resources. Proceedings of the 10th International Conference on Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS 2017). 2017; -Semantic Web Applications and Tools for Health Care and Life Sciences; DEZ 4-7, 2017; Rome, ITALY. [Oral Communication] (full text)

KASÁČ, Zdenko; Martínez-Costa, Catalina; Kreuzthaler, Markus; Schulz, Stefan. Basics of a Drug Ontology for Annotations of Clinical Narratives Proceedings of the Joint Ontology Workshops 2017. 2017; 2050: -Proceedings of the Joint Ontology Workshops 2017; SEPT 21-23, 2017; Bozen-Bolzano, Italy. [Oral Communication]

Schulz, Stefan; Martínez-Costa, Catalina; Miñarro-Giménez, Jose Antonio. Lexical ambiguity in SNOMED CT Proceedings of the Joint Ontology Workshops 2017. 2017; 2050: -JOWO 2017 The Joint Ontology Workshops; SEPT 21-23, 2017; Bozen-Bolzano, Italy. [Oral Communication]

Legaz-Garcia, MD; Martinez-Costa, C; Menarguez-Tortosa, M; Fernandez-Breis, JT; A semantic web based framework for the interoperability and exploitation of clinical models and EHR data. KNOWL-BASED SYST. 2016; 105: 175-189. Doi: 10.1016/j.knosys.2016.05.016 (full text)

Miñarro-Giménez, JA; Martínez-Costa, C; Schulz, S Qualitative assessment of annotations using SNOMED CT Proceedings of the 7th Workshop on Ontologies and Data in Life Sciences, organized by the GI Workgroup Ontologies in Biomedicine and Life Sciences (OBML). 2016; 1692: K.1-2–Ontologies and Data in Life Sciences; SEP 29-30, 2016; Saale, GERMANY. [Oral Communication] (full text)

Martínez-Costa, C; Cornet, R; Karlsson, D; Schulz, S; Kalra, D Semantic enrichment of clinical models towards semantic interoperability. The heart failure summary use case. J Am Med Inform Assoc. 2015; 22(3): 565-576. Doi: 10.1093/jamia/ocu013 [OPEN ACCESS] (full text)

Miñarro-Giménez, JA; Kreuzthaler, M; Bernhardt-Melischnig, J; Martínez-Costa, C; Schulz, S Acquiring Plausible Predications from MEDLINE by Clustering MeSH Annotations. Stud Health Technol Inform. 2015; 216(12):716-720 (full text)

Schulz, S; Martínez-Costa, C Harmonizing SNOMED CT with BioTopLite: An Exercise in Principled Ontology Alignment. Stud Health Technol Inform. 2015; 216(1): 832-836. (full text)

Martínez-Costa, C; Kay, S; Outghtibridge, N; Schulz, S ContSys under Ontological Scrutiny Studies in Health Technology and Informatics, ed. Cornet, R at al. Digital Healthcare Empowering Europeans. Proc. of MIE 2015. 2015; 999-999.-MIE 2015; May 27 – 29 , 2015; Madrid, SPAIN. [Poster] (full text)

Legaz-García, Mdel C; Martínez-Costa, C; Miñarro-Giménez, JA; Fernández-Breis, JT; Schulz, S; Menárguez-Tortosa, M Ontology patterns-based transformation of clinical information. Stud Health Technol Inform. 2014; 205(12):1018-1022 (full text)

Martínez-Costa, C; Kalra, D; Schulz, S Improving EHR semantic interoperability: future vision and challenges. Stud Health Technol Inform. 2014; 205(44):589-593 (full text)

Martínez-Costa, C; Schulz, S Ontology content patterns as bridge for the semantic representation of clinical information. Appl Clin Inform. 2014; 5(3):660-669 Doi: 10.4338/ACI-2014-04-RA-0031 [OPEN ACCESS] (full text)

Miñarro-Giménez, JA; Costa, CM; Schulz, S Using concept co-occurrences for a biomedical facts acquisition. Stud Health Technol Inform. 2014; 205: 1200-1200.

Martínez-Costa, C; Karlsson, D Ontology Patterns for Clinical Information Modelling Proceedings of the 5th Workshop on Ontology and Semantic Web Patterns (WOP 2014). 2014; 61-72.-5th Workshop on Ontology and Semantic Web Patterns (WOP); OCT 19, 2014; Riva del Garda, ITALY. [Oral Communication] (full text)

Martínez-Costa, C; Schulz, S An example of approximating DL reasoning by ontology-aware RDF querying Proceedings of the 11th International Workshop on OWL: Experiences and Directions (OWLED 2014). 2014; -OWL: Experiences and Directions Workshop (OWLED); OCT 17-18, 2014; Riva del Garda, ITALY. [Poster] (full text)

Martínez-Costa, C; Schulz, S Semantic Interoperability in SemanticHealthNet The semantic interoperability challenge to exploit EHRs for enabling better care, clinical research and public health studies. 2014; -Workshop on Interoperability Challenges for enabling secondary use of Electronic Health Records; SEPT 2, 2014; Istanbul, TURKEY. [Oral Communication]

Martínez-Costa, C; Schulz, S;Kalra, D SemanticHealthNet. A Semantic Infrastructure Towards Semantic Interoperability SNOMED CT Implementation Showcase. 2014; -SNOMED CT Implementation Showcase 2014; OCT 30, 2014; Amsterdam, Netherlands. [Oral Communication]

Schulz, S; Martínez-Costa, C; Karlsson, D; Cornet, R; Brochhausen, M; Rector, A An Ontological Analysis of Reference in Health Record Statements Proceedings of the 8th International Conference on Formal Ontology in Information Systems . 2014; 267: -8th International Conference on Formal Ontology in Information Systems (FOIS); SEPT 22-25, 2014; Rio de Janeiro, BRAZIL. [Oral Communication] (full text)

Schulz, S; Martinez-Costa, C; Kreuztahler, M; Minarro-Giménez, JA; Andersen, U; Jensen, AB; Maegaard, B Semantic Relation Discovery by using Co-occurrence Information Proceedings of the fourth Workshop on Building and Evaluating Resources for Health and Biomedical Text Processing. 2014; -Fourth Workshop on Building and Evaluating Resources for Health and Biomedical Text Processing; MAY 31, 2014; Reykjavik, ICELAND. [Poster] (full text)

Martínez-Costa, C; Bosca, D; Legaz-García, MC; Tao, C; Fernández Breis, JT; Schulz, S; Chute, CG Isosemantic rendering of clinical information using formal ontologies and RDF. Stud Health Technol Inform. 2013; 192(4):1085-1085 (full text)

Martínez-Costa, C; Schulz, S Ontology-based reinterpretation of the SNOMED CT context model. Proceedings of the 4th International Conference on Biomedical Ontology. CEUR Workshop Proceedings . 2013; 1040: 90-95.-International Conference on Biomedical Ontology ; JUL 8-9, 2013; Montreal, Kanada. [Oral Communication] (full text)

Martínez-Costa, C; Menárguez-Tortosa, M; Fernández-Breis, JT Interoperability of EHR Systems Based on Semantic Representation and Transformation Models In: Sicilia, MA; Balazote, P editors(s). Interoperability in Healthcare Information Systems. p. 59-81. 2013 (full text)

Martínez-Costa, C; Schulz, S Ontology-Based Reengineering of the SNOMED CT Context Model. In: Peek, N; Marín Morales, R; Peleg, M editors(s). Artificial Intelligence in Medicine. 7885: Berlin Heidelberg: Springer; p. 216 - 220. 2013(ISBN: 978-3-642-38325-0) (full text)

Martínez-Costa, C; Karlsson, D; Schulz, S SEMANTIC INTEROPERABILITY BY ONTOLOGY BASED REPRESENTATION OF CLINICAL INFORMATION In: Ammenwerth, E; Hörbst, A; Hayn, D; Schreier, G; editors(s). Health Informatics meets eHealth - von der Wissenschaft zur Anwendung und zurück. Big Data - eHealth von der Datenanalyse bis zum Wissensmanagement. 293: 1080 Wien, Piaristengasse 19: Druckerei Riegelnik; p. 65-71. 2013(ISBN: 978-3-85403-29)

Schulz, S; Martínez-Costa, C How Ontologies Can Improve Semantic Interoperability in Health Care In: Riaño, D; Lenz, R; Miksch, S; Peleg, M; Reichert, M; Teije, A editors(s). Lecture Notes in Computer Science. 8268: Berlin Heidelberg: Springer International Publishing; p. 1-10. 2013(ISBN: 978-3-319-03915-2) (full text)

Legaz-García, Mdel C; Martínez-Costa, C; Menárguez-Tortosa, M; Fernández-Breis, JT Recommendation of Standardized Health Learning Contents using Archetypes and Semantic Web Technologies. Stud Health Technol Inform. 2012; 180(12):963-967 (full text)

Maldonado, JA; Costa, CM; Moner, D; Menárguez-Tortosa, M; Boscá, D; Miñarro Giménez, JA; Fernández-Breis, JT; Robles, M Using the ResearchEHR platform to facilitate the practical application of the EHR standards. J Biomed Inform. 2012; 45(4):746-762 Doi: 10.1016/j.jbi.2011.11.004 [OPEN ACCESS] (full text)

Menrguez-Tortosa, M; Martnez-Costa, C; Fernndez-Breis, JT A Generative Tool for Building Health Applications Driven by ISO 13606 Archetypes. J Med Syst. 2012; 36(5):3063-3075 Doi: 10.1007/s10916-011-9783-1 (full text)

Legaz-García, MC; Martínez-Costa, C; Menárguez-Tortosa, M; Fernández-Breis, JT. Exploitation of ontologies for the management of clinical archetypes in ArchMS. KR-MED Series CEUR Workshop Proceedings. 2012; 897: -3rd International Conference on Biomedical Ontology (ICBO 2012); JUL 21-25, 2012; Graz, Austria. [Oral Communication] (full text)

Martínez-Costa, C; Queiroz de Andrade, A; Karlsson, D; Kalra, D; Schulz, S Towards the Harmonization of Clinical Information and Terminologies by Formal Representation European Journal for Biomedical Informatics (EJBI). 2012; -13th International HL7 Interoperability Conference (IHIC 2012). Science for Real World Applications; SEPT 27-28, 2012; Vienna, AUSTRIA. [Oral Communication]

Martínez-Costa, C; Schulz, S Semantic Interoperability for Health Network (SemanticHealthNet) SNOMED CT Implementation Showcase 2012. 2012; -SNOMED CT Implementation Showcase 2012; OCT 25-26, 2012; Stockholm, SWEDEN. [Oral Communication]

Costa, CM; Menárguez-Tortosa, M; Fernández-Breis, JT Clinical data interoperability based on archetype transformation. J Biomed Inform. 2011; 44(5): 869-880. Doi: 10.1016/j.jbi.2011.05.006 [OPEN ACCESS] (full text)

Martínez-Costa, C; Menárguez-Tortosa, M; Fernández-Breis, JT An approach for the semantic interoperability of ISO EN 13606 and OpenEHR archetypes. J Biomed Inform. 2010; 43(5):736-746 Doi: 10.1016/j.jbi.2010.05.013 (full text)

Robles, M; Fernández-Breis, JT; Maldonado, JA; Moner, D; Martínez-Costa, C; Bosca, D; Menárguez-Tortosa, M ResearchEHR: use of semantic web technologies and archetypes for the description of EHRs. Stud Health Technol Inform. 2010; 155(5):129-135 (full text)

Martínez-Costa, C; Menárguez-Tortosa, M; López Lóped P.D; Rubio González M.M; Fernández Breis, J.T ArchForms: Automatic generation of applications based on ISO 13606 archetypes Proceedings of the Second Spanish OpenHealth Symposium. 2010; -Second Spanish OpenHealth Symposium; NOV 10-11, 2010; Madrid, SPAIN. [Oral Communication]

Martínez-Costa, C; Miñarro-Giménez, J.A; Menárguez-Tortosa,M; Valencia-García, R; Fernández-Breis, J.T Flexible Semantic Querying of Clinical Archetypes Proceedings of the Knowledge-Based and Intelligent Information and Engineering Systems conference. 2010; 597-606.-KES 2010, Special Session on Application of Knowledge Models in Healthcare; SEPT 8-10, 2010; Cardiff, WALES. (ISBN: 978-3-642-15386-0 ) [Oral Communication] (full text)

Menárguez-Tortosa, M; Martínez-Costa, C; Fernández Breis, J.T Validating Archetypes using OWL Reasoning. Proceedings of the Second Spanish OpenHealth Symposium. 2010; -Second Spanish OpenHealth Symposium; NOV 10-11, 2010; Madrid, SPAIN. [Oral Communication]

Martínez-Costa, C; Menárguez-Tortosa, M; Maldonado, J.A; Fernández-Breis, J.T Semantic Web technologies for managing EHR-related clinical knowledge. In: Gang Wu editors(s). Semantic Web. InTech; p. 201-119. 2010(ISBN: 978-953-7619-54-1) (full text)

Martínez-Costa, C; Menárguez-Tortosa,M; Fernández-Breis, J.T ARCHFORMS: GENERACIÓN AUTOMÁTICA DE APLICACIONES ISO 13606 In: Sociedad Espanola de Informática de la Salud (SEIS) editors(s). Las TIC en la Sostenibilidad de los Sistemas para la Salud y el Bienestar. 2010(ISBN: 978-84-692-9230-3)

Miranda-Mena, T; Martínez-Costa, C; Moner, D; Menárguez-Tortosa, M; Maldonado, J.A; Robles-Viejo, M; Fernández-Breis, J.T Motor de integración universal para aplicaciones sanitarias avanzadas In: Sociedad Espanola de Informática de la Salud (SEIS) editors(s). Las TIC en la Sostenibilidad de los Sistemas para la Salud y el Bienestar. 2010(ISBN: ISBN 978-84-692-9230)

Martínez-Costa, C; Menárguez-Tortosa, M; Fernández-Breis, JT Towards ISO 13606 and openEHR archetype-based semantic interoperability. Stud Health Technol Inform. 2009; 150(5):260-264 ( full text)

Martínez-Costa, C; Menárguez-Tortosa, M; Fernández-Breis, JT; Maldonado, JA A model-driven approach for representing clinical archetypes for Semantic Web environments. J Biomed Inform. 2009; 42(1):150-164 Doi: 10.1016/j.jbi.2008.05.005 (full text)

Martínez-Costa, C; Menárguez-Tortosa, M; Fernández Breis, J.T Ontology-based archetype interoperability and management Proceedings of the First Symposium on Healthcare Systems Interoperability. 2009; -First OpenHealth Symposium; APR 29-30, 2009; Madrid, SPAIN. [Oral Communication]

Martínez-Costa, C; Menárguez-Tortosa, M; Valencia-García, R; Maldonado,J.A;Fernández Breis, J.T Transformación automática de arquetipos UNE-EN 13606 y openEHR para facilitar la interoperabilidad semántica. In: Sociedad Espanola de Informática de la Salud (SEIS) editors(s). Inforsalud 2009. Hacia el acceso electrónico a los Servicios de Salud y Sociosanitarios. p. 70-75. 2009(ISBN: 978-84-691-9561-1)

Fernandez-Breis, JT; Menarguez-Tortosa, M; Martinez-Costa, C; Fernandez-Breis, E; Herrero-Sempere, J; Moner, D; Sanchez, J; Valencia-Garcia, R; Robles, M A Semantic Web-based System for Managing Clinical Archetypes. Conf Proc IEEE Eng Med Biol Soc. 2008; 2008(5):1482-1485 Doi: 10.1109/IEMBS.2008.4649448 ( full text)