Read the CEDAR publications

2026

Hardi, J., O’Connor, M.J., Martínez-Romero, M., Rosario, J.G., Fisher, S.A., Musen, M.A. Automated Standardization of Legacy Biomedical Metadata Using an Ontology-Constrained LLM Agent. American Medical Informatics Association Annual Symposium (AMIA), 2026.

O’Connor, M.J., Martínez-Romero, M., Egyedi, A.L., Akdogan, M.U., Dorf, M., Musen, M.A. Author Once, Publish Everywhere: Portable Metadata Authoring with the CEDAR Embeddable Editor. Data Science Journal, 25:2, pp 1-18, 2026.

2025

Musen, M.A., O’Connor, M.J., Hardi, J., Martínez-Romero, M. Knowledge Engineering for Open Science: Building and Deploying Knowledge Bases for Metadata Standards. AI Magazine, 47(1), 2025.

O’Connor, M.J., Hardi, J., Martínez-Romero, M., Somasundaram, S., Honick, B., Fisher, S.A., Pillai, A., Musen, M.A. Ensuring Adherence to Standards in Experiment-Related Metadata Entered Via Spreadsheets. Scientific Data, 2025.

2022

Musen, M.A., O’Connor, M.J., Schultes, E., Martínez-Romero, M., Hardi, J., Graybeal, J. Modeling Community Standards for Metadata as Templates Makes Data FAIR. Scientific Data 9:696, 2022.

2020

Martin J O’Connor, Marcos Martínez-Romero, and the CEDAR Team CEDAR Template Model V1.6.0

2019

Miron, L., Gonçalves, R. S., Musen, M. A. (2019) Obstacles to the Reuse of Study Metadata in ClinicalTrials.gov. doi:10.1101/850578

O’Connor, M. J., Warzel, D. B., Martínez-Romero, M., Hardi, J., Willrett, D., Egyedi, A. L., Efekhari, A., Graybeal, J., Musen, M. A. (2019) Unleashing the value of Common Data Elements through the CEDAR Workbench. Proceedings of AMIA 2019 Annual Symposium, 681-690.

Martínez-Romero M, O’Connor MJ, Egyedi AL, Willrett D, Hardi J, Graybeal J, Musen MA. Using association rule mining and ontologies to generate metadata recommendations from multiple biomedical databases. Database. Volume 2019, 10 June 2019.  https://doi.org/10.1093/database/baz059.

Gonçalves RS, Kamdar MR, Musen MA. Aligning Biomedical Metadata with Ontologies Using Clustering and Embeddings.  Extended Semantic Web Conference (ESWC), Portorož, Slovenia. https://link.springer.com/chapter/10.1007/978-3-030-21348-0_10

Gonçalves RS, Musen MA. The variable quality of metadata about biological samples used in biomedical experiments. Scientific Data. 2019;(6):1-15. doi:10.1038/sdata.2019.21.

2018

Egyedi AL, O’Connor MJ, Martínez-Romero M, Willrett D, Hardi J, Graybeal J, Musen MA. 2018. Using Semantic Technologies to Enhance Metadata Submissions to Public Repositories in Biomedicine. Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS), Antwerp, Netherlands.

Stathias V, Koleti A, Vidovic´ D, Cooper DJ, Jagodnik KM, Terryn R, Forlin M, Chung C, Torre D, Ayad N et al.. 2018. Sustainable data and metadata management at the BD2K-LINCS Data Coordination and Integration Center. Scientific Data – Nature. 5(180117)
Bukhari SAC, O’Connor MJ, Martínez-Romero M, Egyedi AL, Willrett D, Graybeal J, Musen MA, Rubelt F, Cheung K-H, Kleinstein SH. 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)
Bukhari S Ahmad Chan, Martínez-Romero M, O’Connor MJ, Egyedi AL, Willrett D, Graybeal J, Musen MA, Cheung K-H, Kleinstein SH. 2018. CEDAR OnDemand: a browser extension to generate ontology-based scientific metadata. BMC Bioinformatics. 19:268

Moodley K, Hardi J​, Graybeal J​​, Musen MA​, Dumontier M. 2018. Assessing Schema.org’s Coverage of Terms from Key Biomedical Datasets. Intelligent Systems for Molecular Biology Conference.

2017

Gonçalves RS, O’Connor MJ, Martínez-Romero M, Egyedi AL, Willrett D, Graybeal J, Musen MA. 2017. The CEDAR Workbench: An Ontology-Assisted Environment for Authoring Metadata that Describe Scientific Experiments. International Semantic Web Conference.
Gonçalves RS, O’Connor MJ, Martínez-Romero M, Graybeal J, Musen MA. 2017. Metadata in the BioSample Online Repository are Impaired by Numerous Anomalies. 1st International Workshop SemSci: Enabling Open Semantic Science.
Martínez-Romero M, Jonquet C, O’Connor MJ, Graybeal J, Pazos A, Musen MA. 2017. NCBO Ontology Recommender 2.0: an enhanced approach for biomedical ontology recommendation. Journal of Biomedical Semantics. 8(21)
Egyedi AL, O’Connor MJ, O’Connor MJ, Martínez-Romero M, Willrett D, Hardi J, Graybeal J, Musen MA. 2017. Embracing Semantic Technology for Better Metadata Authoring in Biomedicine. Semantic Web Applications and Tools for Health Care and Life Sciences (SWAT4LS), Rome, Italy.
Martínez-Romero M, O’Connor MJ, Shankar R, Panahiazar M, Willrett D, Egyedi AL, Gevaert O, Graybeal J, Musen MA. 2017. Fast and Accurate Metadata Authoring Using Ontology-Based Recommendations. AMIA-American Medical Informatics Association 2017 Annual Symposium.
Panahiazar M, Dumontier M, Gevaert O. 2017. Predicting Biomedical Metadata in CEDAR: a study of gene expression metadata in GEO. Journal of Biomedical Informatics.
Martínez-Romero M, O’Connor MJ, Dorf M, Vendetti J, Willrett D, Egyedi AL, Graybeal J, Musen MA. 2017. Supporting Ontology-Based Standardization of Biomedical Metadata in the CEDAR Workbench. ICBO-International Conference on Biomedical Ontology.

2016

O’Connor MJ, Martínez-Romero M, Egyedi AL, Willrett D, Graybeal J, Musen MA. 2016. An Open Repository Model for Acquiring Knowledge about Scientific Experiments.  20th International Conference on Knowledge Engineering and Knowledge Management.
Haynes WA, Vallania F, Liu C, Bongen E, Tomczak A, Andres-Terrè M, Lofgren S, Tam A, Deisseroth CA, Li MD et al.. 2016. Empowering Multi-Cohort Gene Expression Analysis to Increase Reproducibility. Pacific Symposium on Biocomputing. 22:144–153.
Wilkinson MD. 2016. The FAIR Guiding Principles for scientific data management and stewardship. Scientific Data-Nature. 3:160018
Sweeney TE, Braviak L, Tato CM, Khatri P. 2016. Genome-wide expression for diagnosis of pulmonary tuberculosis: a multicohort analysis. The Lancet Respiratory Medicine. 4(3):213–224.
Posch L, Panahiazar M, Dumontier M, Gevaert O. 2016. Predicting Structured Metadata from Unstructured Metadata. Database. 2016

2015

Musen MA, Bean CA, Cheung K-H, Dumontier M, Durante KA, Gevaert O, Gonzalez-Beltran A, Khatri P, Kleinstein SH, O’Connor MJ et al.. 2015. The Center for Expanded Data Annotation and Retrieval. Journal of the American Medical Informatics Association, JAMIA. 22 (6) 1148-1152

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