2019

  • O’Connor, M. J., Warzel, D. B., Martínez-Romero, M., Hardi, J., Willrett, D., Egyedi, A. L., Eftekhari, A., Graybeal, J., Musen, M. A. (2019). Unleashing the value of Common Data Elements through the CEDAR Workbench. Proceedings of the AMIA Annual Symposium, 2019, 681–690. [paper]
  • Martínez-Romero, M., O’Connor, M. J., Egyedi, A. L., Willrett, D., Hardi, J., Graybeal, J., Musen, M. A. (2019). Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. Database: The Journal of Biological Databases and Curation, 2019. [paper]

2018

  • Bukhari, S. A. C., Martínez-Romero, M., O’ Connor, M. J., Egyedi, A. L., Willrett, D., Graybeal, J., Musen, M. A., Cheung, K.-H., Kleinstein, S. H. (2018). CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. BMC Bioinformatics, 19(1), 268. [paper]
  • Rodríguez-González, A., Costumero, R., Martínez-Romero, M., Wilkinson, M. D., Menasalvas-Ruiz, E. (2018). Extracting diagnostic knowledge from MedLine Plus: a comparison between MetaMap and cTAKES Approaches. Current Bioinformatics, 13(6), 2018. [paper]
  • Bukhari, S. A. C., O’Connor, M. J., Martínez-Romero, M., Egyedi, A. L., Willrett, D., Graybeal, J., Musen, M. A., Rubelt, F., Cheung, K.-H., Kleinstein, S. H. (2018). The CAIRR Pipeline for Submitting Standards-Compliant B and T Cell Receptor Repertoire Sequencing Studies to the National Center for Biotechnology Information Repositories. Frontiers in Immunology, 9, 1877. [paper]
  • Egyedi, A. L., O’Connor, M. J., Martínez-Romero, M., Willrett, D., Hardi, J., Graybeal, J., Musen, M. A. (2018). Using Semantic Technologies to Enhance Metadata Submissions to Public Repositories in Biomedicine. Proceedings of the 11th International Conference Semantic Web Applications and Tools for Life Sciences (SWAT4HCLS 2018) Antwerp, Belgium, December 3-6, 2018. [paper]
  • Gonçalves, R. S., Nyulas, C. I., Martínez-Romero, M., O’Connor, M. J., Graybeal, J., Musen, M. A. (2018). Using Ontologies to Drive the Creation of High-Quality Metadata in CEDAR. Demo presented at the International Semantic Web Conference 2018 (ISWC 2018). [paper]

2017

  • Gonçalves, R. S., O’Connor, M. J., Martínez-Romero, M., Graybeal, J., Musen, M. A. (2017). Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. 1st International Workshop SemSci 2017 (Enabling Open Semantic Science), co-located with ISWC 2017. October, 2017. Vienna, Austria (accepted). [arXiv]
  • Martínez-Romero, M., O’Connor, M. J., Shankar, R., Panahiazar, M., Willrett, D., Egyedi, A. L., Gevaert, O., Graybeal, J., Musen, M. A. (2017). Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. Proceedings of the AMIA 2017 Annual Symposium (AMIA 2017), Washington DC, USA, November 4-8, 2017 (accepted). [abstract]
  • Gonçalves, R. S., O’Connor, M. J., Martínez-Romero, M., Egyedi, A. L., Willrett, D., Graybeal, J., Musen, M. A. (2017). The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. Proceedings of the 16th International Semantic Web Conference (ISWC 2017), Vienna, Austria, October 21-25, 2017 (accepted).
  • Martínez-Romero, M., O’Connor, M. J., Dorf, M., Vendetti, J., Willrett, D., Egyedi, A. L., Graybeal, J., Musen, M. A. (2017). Supporting ontology-based standardization of biomedical metadata in the CEDAR Workbench. Proceedings of the 8th International Conference on Biomedical Ontology 2017 (ICBO 2017), Newcastle upon Tyne, UK, September 13-15, 2017 (accepted). [abstract]
  • Martínez-Romero, M., Jonquet, C., O’Connor, M. J., Graybeal, J., Pazos, A., Musen, M. A. (2017). NCBO Ontology Recommender 2.0: An Enhanced Approach For Biomedical Ontology Recommendation. Journal of Biomedical Semantics, 8(21), 1-22 [paper]
  • Debra Willrett, Martin J. O’Connor, Marcos Martínez-Romero, Attila L. Egyedi, Ravi D. Shankar, Purvesh Khatri, Olivier Gevaert, John Graybeal, Syed Ahmad Chan Bukhari, Kei-Hoi Cheung, Steven H. Kleinstein, John Campbell, Jeffrey A. Wiser, Kim A. Durante, Alejandra Gonzalez-Beltran, Philippe Rocca-Serra, Susanna-Assunta Sansone, Mark A. Musen (2017). Finding and Reusing Biomedical Datasets using CEDAR Metadata Repository and Tools. Poster presented at the Big Data in Biomedicine Conference. May 24-25, 2017. Stanford University, Stanford, California, USA. [poster]
  • Marcos Martínez-Romero, Martin J. O'Connor, Ravi D. Shankar, Maryam Panahiazar, Debra Willrett, Attila L. Egyedi, John Graybeal, Mark A. Musen (2017). CEDAR's predictive data entry: easier and faster creation of high-quality metadata. Poster presented at the Biocuration 2017 Conference. Winner of one of the Best Poster Awards. March 26-29, 2017. Stanford University, Stanford, California, USA. [abstract, poster]
  • Ravi D. Shankar, Marcos Martínez-Romero, Martin J. O’ Connor, John Graybeal, Purvesh Khatri, Mark A. Musen (2017). SAP – a CEDAR-based pipeline for semantic annotation of biomedical metadata. Poster presented at the Biocuration 2017 Conference. March 26-29, 2017. Stanford University, Stanford, California, USA. [poster]

2016

  • Marcos Martínez-Romero, Martin J. O'Connor, Ravi D. Shankar, Maryam Panahiazar, Debra Willrett, Attila L. Egyedi, John Graybeal, Mark A. Musen (2016). Faster and Better Metadata Authoring using CEDAR's Value Recommendations. Poster and demo presented at the BD2K All-Hands Meeting. November 29 - December 1, 2016. North Beteshda, Maryland, USA. [abstract, poster]
  • John Graybeal, Marcos Martínez-Romero, Michael Dorf, Jennifer Vendetti, Martin O'Connor, Mark A. Musen (2016). Increasing NCBO BioPortal and CEDAR Synergy for BD2K. Poster presented at the BD2K All-Hands Meeting. November 29 - December 1, 2016. North Beteshda, Maryland, USA. [abstract, poster]
  • Ravi D. Shankar, Marcos Martínez-Romero, Martin J. O'Connor, John Graybeal, Purvesh Khatri, Mark A. Musen (2016). SAP – A CEDAR-based Pipeline for Semantic Annotation of Biomedical Metadata. Poster presented at the BD2K All-Hands Meeting. November 29 - December 1, 2016. North Beteshda, Maryland, USA. [abstract, poster]
  • Mark A. Musen, Syed Ahmad Chan Bukhari, John Campbell, Kei-Hoi Cheung, Michel Dumontier, Kim A. Durante, Attila L. Egyedi, Olivier Gevaert, Alejandra Gonzalez-Beltran, John Graybeal, Purvesh Khatri, Steven H. Kleinstein, Martin J. O’Connor, Maryam Panahiazar, Philippe Rocca-Serra, Marcos Martínez-Romero, Susanna-Assunta Sansone, Ravi D. Shankar, Debra Willrett (2016). CEDAR: Easing Authoring of Metadata to Make Biomedical Data Sets More Findable and Reusable. Poster presented at the BD2K All-Hands Meeting. November 29 - December 1, 2016. North Beteshda, Maryland, USA. [abstract, poster]
  • Martin J O’Connor, Marcos Martínez-Romero, Attila L Egyedi, Debra Willrett, John Graybeal, Mark A Musen. A Standards-Based Model for Metadata Exchange. Talk given at the BD2K All-Hands Meeting. November 29 - December 1, 2016. North Beteshda, Maryland, USA. [abstract]
  • Martin J O’Connor, Marcos Martínez-Romero, Attila L Egyedi, Debra Willrett, John Graybeal, Mark A Musen. An Open Repository Model for Acquiring Knowledge About Scientific Experiments. Proceedings of the 20th International Conference on Knowledge Engineering and Knowledge Management (EKAW 2016), Bologna, Italy, November 19-23, 2016. Lecture Notes in Computer Science, Vol. 10024 2016. [paper]
  • Mark A. Musen, Martin O’Connor, Marcos Martínez-Romero, Attila Levente Egyedi, Debra Willrett, John Graybeal (2016). CEDAR: Better Data Sharing Through the Authoring of Better Metadata. System Demonstration at the AMIA 2016 Annual Symposium. November 12 - 16, 2016. Chicago, IL. [abstract]
  • Rodríguez-González, A., Martínez-Romero, M., Costumero, R., Wilkinson, M. D., Menasalvas-Ruiz, E. Extracting diagnostic knowledge from MedLine Plus: a comparison between MetaMap and cTAKES approaches. Current Bioinformatics, PACBB 2015 Special Issue, 2016. Accepted.

2015

  • O'Connor, Martin J., Graybeal, John B., Martínez-Romero, M., Musen, Mark A. (2015). Linking Ontologies and ISO/IEC 11179 in the CEDAR Metadata Repository. Abstract presented at the Metadata Open Forum on ISO/IEC 11179. National Institutes of Health, Natcher Conference Center, Bethesda, Maryland.
  • Mark A. Musen, John Campbell, Kei-Hoi Cheung, Michel Dumontier, Kim A. Durante, Attila L. Egyedi, Olivier Gevaert, Alejandra Gonzalez-Beltran, John Graybeal, Purvesh Khatri, Steven H. Kleinstein, Martin J. O’Connor, Maryam Panahiazar, Philippe Rocca-Serra, Marcos Martínez-Romero, Susanna-Assunta Sansone, Ravi D. Shankar, Samson W. Tu, Jeffrey A. Wiser (2015). The Center for Expanded Data Annotation and Retrieval. Poster presented at the BD2K All-Hands Grantee Meeting, November 2015, NIH Main Campus, Bethesda, MD.
  • Musen, M. A., Bean, C. A., Cheung, K. H., Dumontier, M., Durante, K. A., Gevaert, O., Gonzalez-Beltran, A., Khatri, P., Kleinstein, S. H., O’Connor, M. J., Pouliot, Y., Rocca-Serra, P., Sansone, S. A., Wiser, J. A., the CEDAR Team (2015). Participation as part of the CEDAR Team. The Center for Expanded Data Annotation and Retrieval. Journal of the American Medical Informatics Association (JAMIA), (650), 1–6. [paper]
  • Rodríguez-González, A., Martínez-Romero, M., Costumero, R., Wilkinson, M., Menasalvas-Ruiz E. (2015). Diagnostic Knowledge Extraction from MedlinePlus: An Application for Infectious Diseases. Proceedings of the 9th International Conference on Practical Applications of Computational Biology & Bioinformatics (PACBB 2015). Advances in Intelligent Systems and Computing, Volume 375, 2015, pp 79-87. This paper received the Scientific Quality Award at the PACBB 2015 Conference. [paper]
  • Munteanu, C. R, Aguiar-Pulido, V., Freire, A., Martínez-Romero, M., Porto-Pazos, A., Pereira, J., Dorado, J. Graph-based Processing of Macromolecular Information, Current Bioinformatics, 2015, 10(5), 606-631. [paper]
  • Mato, A., Pazos, A., Pereira, J., Munteanu, C. R., Pedreira, N., Martínez-Romero, M., Vázquez-Naya, J. M., Amigo, J. (2015). Herramientas Bioinformáticas para la Investigación en Cáncer Colorrectal. In book: "Abordaje Multidisciplinar de Cáncer Colorrectal" (ISBN: 978-84-8408-795-3, section 5, pp. 515-532). [book]

2014

  • Rodríguez, A., Martínez-Romero, M., Egaña, M., Wilkinson, M. Nanopublishing Clinical Diagnoses: Tracking Diagnostic Knowledge Base Content and Utilization, 2014. Proceedings of the 2014 IEEE 27th International Symposium on Computer-Based Medical Systems, 335-340.
  • Martínez-Romero, M., Vázquez-Naya, J. M., Pereira, J., and Pazos, A. BiOSS: A system for biomedical ontology selection. Computer Methods and Programs in Biomedicine, 2014, 114, 125-140. [paper]

2013

  • Gómez-Pérez, A., Martínez-Romero, M., Rodríguez-González, A., Vázquez, G., & Vázquez-Naya, J. M. (2013). Ontologies in Medicinal Chemistry: Current Status and Future Challenges. Current Topics in Medicinal Chemistry (Special Issue on Artificial Intelligence Techniques in Medicinal Chemistry), 2013, 13(5). [paper]
  • Martínez-Romero, M., Vázquez-Naya, J. M., Pereira, J., Pereira, M., Pazos, A., & Baños, G. (2013). The iOSC3 system: using ontologies and SWRL rules for intelligent supervision and care of patients with acute cardiac disorders. Computational and Mathematical Methods in Medicine (Special Issue on Methods and Models for Diagnosis and Prognosis in Medical Systems), 2013, 1-13. [paper]
  • Martínez-Romero, M., Vázquez-Naya, J. M., Porto, A., Pazos, A. (2013). El blog como un recurso de innovación educativa en la enseñanza universitaria. In book “Actuaciones y Experiencias de Innovación Educativa en la Docencia de la Radiología y Medicina Física de la Universidad Española” (ISBN: 978-1-291-38912-8, pp. 137-151)
  • Maestro, F. J., Martínez-Romero, M., Vazquez-Naya, J. M., Pereira, J., & Pazos, A. (2013). Ethical and legal issues in the clinical practice of primary health care. Frontiers in Bioscience, E5, 435-445. [paper]
  • Martínez-Romero, M., Vázquez-Naya, J. M., Pereira, J., Pereira, M., Pazos, A., & Baños, G. (2013). Developing a System for Advanced Monitoring and Intelligent Drug Administration in Critical Care Units using Ontologies. International Journal of Knowledge-based and Intelligent Engineering Systems, 17(1), 45-53. [paper]
  • Martínez-Romero, M., Vázquez-Naya, J. M., Nóvoa, F. J., Vázquez, G., Pereira, J. (2013). A genetic algorithms-based approach for optimizing similarity aggregation in ontology matching. Presented at the International Work Conference on Artificial Neural Networks 2013 (IWANN 2013), Tenerife, Spain, 2013. Lecture Notes in Computer Science 7902, 435-444. [paper]
  • Novoa, F. J., Traba, L., Martínez-Romero, M. (2013). Sistema de Información basado en Imagen en un Servicio de Hemodinámica. In book: "Líneas estratégicas de las Tecnologías de la Información y las Comunicaciones en Salud" (ISBN-10: 84-15413-18-1, ISBN-13: 978-84-15413-18-9, pp. 43-66). [paper]

2012

  • Martínez-Romero, M., Vázquez-Naya, J. M., Pereira, J., Pazos, A., Pereira, M., & Baños, G. (2012). An Ontology-based Expert System for Decision Support in Cardiac Intensive Care Environments, presented at the 16th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems (KES 2012), San Sebastián, 2012.
  • Martínez-Romero, M., Vázquez, J. M., Pereira, J., Pereira, M., Porto, A., Baños, G. (2012). Nuevas Técnicas de Gestión del Conocimiento en Salud. Un Sistema para la Administración Inteligente de Fármacos en Unidades de Cuidados Intensivos. In book: “Tecnologías NBIC en Salud: El papel protagonista de la Nanociencia. Aplicación de especial interés al Cáncer Colorrectal” (ISBN: 978-84-15413-15-8, pp. 51-59).
  • Martínez-Romero, M., Vázquez-Naya, J. M., Pereira, J., & Pazos, A. (2012). A Multi-criteria Approach for Automatic Ontology Recommendation using Collective Knowledge. Recommender Systems for the Social Web. Intelligent Systems Reference Library, 32, 89-103. Springer-Verlag. [paper]

2011

  • Martínez-Romero, M., Vázquez-Naya, J. M., Traba, L., & Nóvoa, F. J. (2011) Contenidos multimedia para la docencia con PowerPoint. In book "Innovación docente en Radiología y Medicina Física en las Universidades Españolas" (ISBN: 978-1-4709-6422-1, pp. 235-247).
  • Groba, B., Pousada, T., Canosa, N., Mato, V., & Martínez-Romero, M. (2011) La plataforma de teleformación Moodle. In book "Innovación docente en Radiología y Medicina Física en las Universidades Españolas" (ISBN: 978-1-4709-6422-1, pp. 221-233).
  • Pereira, M. A., Vázquez-Naya, J. M., Martínez-Romero, M., Mato, V., Pintos, J., Pereira, J., & Baños, G. (2011). Sistema Experto para la Monitorización de Pacientes de la Unidad de Cuidados Críticos utilizando Ontologías. IV Jornada de Investigación Biomédica de Vigo (presentación póster). Vigo, España.
  • Nóvoa, F. J., Ezquerra, N., Traba, L., Villar, M., Pereira, J., Vázquez-Rodríguez, J. M., Vázquez, N., Martínez-Romero, M., & Mato, V. (2011). Extraction of Quantitative Anatomical Information from Coronary Angiographies. Current Bioinformatics, 6(2), 233-250. [paper]
  • Torres, A., Martínez-Romero, M., Vázquez-Naya, J. M., Pereira, M., González, A., & Pereira, J. (2011). Development of a Knowledge Based System for an Intensive Care Environment using Ontologies. Journal of Information Technology Research (Special Issue on "Medical Diagnosis Systems"). [paper]

2010

  • Martínez-Romero, M., Vázquez-Naya, J. M., Munteanu, C. R., Pereira, J., & Pazos, A. (2010). An Approach for the Automatic Recommendation of Ontologies Using Collaborative Knowledge. 14th International Conference on Knowledge-Based and Intelligent Information & Engineering Systems (KES 2010). Cardiff, Wales, UK. Lecture Notes in Artificial Intelligence, 6277, 74-81. [paper]
  • Vázquez-Naya, J. M., Martínez-Romero, M., Porto-Pazos, A. B., Nóvoa, F., Valladares-Ayerbes, M., Pereira, J., et al. (2010). Ontologies of Drug Discovery and Design for Neurology, Cardiology and Oncology. Current Pharmaceutical Design, 16, 2724-2736. [paper]
  • Martínez-Romero, M., Vázquez-Naya, J., Rabuñal, R., Pita-Fernandez, S., Macenlle, R., Castro-Alvariño, J., et al. (2010). Artificial Intelligence Techniques for Colorectal Cancer Drug Metabolism: Ontologies and Complex Networks. Current Drug Metabolism, 11(4), 347-368. [paper]
  • Vázquez, J. M., Martínez-Romero, M., Pereira, J., & Munteanu, C. R. (2010). Improving Ontology Alignment through Genetic Algorithms. Soft Computing Methods for Practical Environmental Solutions: Techniques and Studies (pp. 240-258). New York. [paper]
  • Vázquez, J. M., Martín, F., Martínez-Romero, M., & Nóvoa, F. J. (2010). Aplicaciones médicas de las nanotecnologías en relación con las otras tecnologías NBIC. Nuevas Fronteras Tecnológicas. Redes NANOROADMAP e IBERO-NBIC (Vol. 1(10), pp. 190-209). Madrid: Ciencia y Tecnología para el Desarrollo (CYTED).

2009

  • Orozco, K., Barreiro, A., Mato, V., Nóvoa, F. J., Vázquez, J. M., Martínez-Romero, M., et al. (2009). Experiencia en el desarrollo de un sistema de acceso al HIS y al PACS en el IMQ San Rafael de A Coruña. Paper presented at the INFORSALUD 2009, Madrid, Spain.
  • Martínez-Romero, M., Vázquez, J. M., Pereira, J., & Ezquerra, N. (2009). Ontology Alignment Techniques. Encyclopedia of Artificial Intelligence (Vol. 3, pp. 1290-1295). [paper]
  • Vázquez, J. M., Martínez-Romero, M., Pereira, J., & Pazos, A. (2009). Ontology Alignment Overview. Encyclopedia of Artificial Intelligence (Vol. 3, pp. 1283-1289). [paper]

2008

  • Martínez-Romero, M., Vázquez, J. M., López, M. G., Arnal, F. M., González-Conde, B., Pereira, J., et al. (2008). Semantic Data Integration in a System for Cancer Studies. Acta Informatica Medica, 16(2), 64-67. [paper]
  • Martínez-Romero, M., Vázquez, J. M., López, M. G., Arnal, F. M., González-Conde, B., Pereira, J., et al. (2008). Semantic Integration of Data in an Information System for Multicenter Epidemiological Studies on Cancer. Poster presented at the 21st International Congress of the European Federation for Medical Informatics (MIE2008). Gothenburg, Sweden. [abstract]
  • Martínez-Romero, M., Vázquez, J. M., Pereira, J., & Pazos, A. (2008). Annotation of Colorectal Cancer Data Using the UMLS Metathesaurus. 12th International Conference on Knowledge Based and Intelligent Information & Engineering Systems (KES 2008). Lecture Notes in Artificial Intelligence, 5178(2), 58-65. [paper]
  • Vázquez, J. M., Martínez-Romero, M., López, M. G., González-Conde, B., Arnal, F. M., Pereira, J., et al. (2008). An Ontology-Based Information System for Multicenter Epidemiologic Studies on Cancer. Paper presented at the 1st IEEE International Conference on Health Informatics (HEALTHINF 2008), Funchal, Madeira, Portugal. [paper]
  • Ezquerra, N., Nóvoa, F. J., Pazos, A., & Martínez-Romero, M. (2008). Interacción hombre-máquina y usabilidad: Diseño centrado en el usuario. Tecnologías de la Información y las Comunicaciones en la autonomía personal, dependencia y accesibilidad (pp. 179-185). Santiago de Compostela, España: Fundación Alfredo Brañas.

2007

  • Vázquez, J. M., Martínez-Romero, M., López, M. G., Gonzalez-Conde, B., Arnal, F. M., Pereira, J., et al. (2007). Development of an Information System for Multicenter Epidemiologic Studies on Cancer. Paper presented at the 6th International Special Topic Conference on Information Technology Applications in Biomedicine (ITAB2007), Tokyo, Japan. [paper]