Publications

Found 19 results
Author Title Type [ Year(Asc)]
2019
O'Connor MJ, Musen MA.  2019.  Unleashing the value of Common Data Elements through the CEDAR Workbench. Proceedings of AMIA 2019 Annual Symposium.
2018
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.
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 SAhmad 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
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)
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. SWAT4LS.
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.
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.
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.
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)
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
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.
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.
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