Sabrina Toro, PhD
Assistant Research Professor, Biomedical Informatics

Publications

• Putman TE, Schaper K, Matentzoglu N, Rubinetti VP, Alquaddoomi FS, Cox C, Caufield JH, Elsarboukh G, Gehrke S, Hegde H, Reese JT, Braun I, Bruskiewich RM, Cappelletti L, Carbon S, Caron AR, Chan LE, Chute CG, Cortes KG, De Souza V, Fontana T, Harris NL, Hartley EL, Hurwitz E, Jacobsen JOB, Krishnamurthy M, Laraway BJ, McLaughlin JA, McMurry JA, Moxon SAT, Mullen KR, O'Neil ST, Shefchek KA, Stefancsik R, Toro S, Vasilevsky NA, Walls RL, Whetzel PL, Osumi-Sutherland D, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC. The Monarch Initiative in 2024: an analytic platform integrating phenotypes, genes and diseases across species. Nucleic Acids Res. 2024 Jan 5;52(D1):D938-D949. PubMed PMID: 38000386
• Gargano MA, Matentzoglu N, Coleman B, Addo-Lartey EB, Anagnostopoulos AV, Anderton J, Avillach P, Bagley AM, Bakštein E, Balhoff JP, Baynam G, Bello SM, Berk M, Bertram H, Bishop S, Blau H, Bodenstein DF, Botas P, Boztug K, Cady J, Callahan TJ, Cameron R, Carbon SJ, Castellanos F, Caufield JH, Chan LE, Chute CG, Cruz-Rojo J, Dahan-Oliel N, Davids JR, de Dieuleveult M, de Souza V, de Vries BBA, de Vries E, DePaulo JR, Derfalvi B, Dhombres F, Diaz-Byrd C, Dingemans AJM, Donadille B, Duyzend M, Elfeky R, Essaid S, Fabrizzi C, Fico G, Firth HV, Freudenberg-Hua Y, Fullerton JM, Gabriel DL, Gilmour K, Giordano J, Goes FS, Moses RG, Green I, Griese M, Groza T, Gu W, Guthrie J, Gyori B, Hamosh A, Hanauer M, Hanušová K, He YO, Hegde H, Helbig I, Holasová K, Hoyt CT, Huang S, Hurwitz E, Jacobsen JOB, Jiang X, Joseph L, Keramatian K, King B, Knoflach K, Koolen DA, Kraus ML, Kroll C, Kusters M, Ladewig MS, Lagorce D, Lai MC, Lapunzina P, Laraway B, Lewis-Smith D, Li X, Lucano C, Majd M, Marazita ML, Martinez-Glez V, McHenry TH, McInnis MG, McMurry JA, Mihulová M, Millett CE, Mitchell PB, Moslerová V, Narutomi K, Nematollahi S, Nevado J, Nierenberg AA, Cajbiková NN, Nurnberger JI Jr, Ogishima S, Olson D, Ortiz A, Pachajoa H, Perez de Nanclares G, Peters A, Putman T, Rapp CK, Rath A, Reese J, Rekerle L, Roberts AM, Roy S, Sanders SJ, Schuetz C, Schulte EC, Schulze TG, Schwarz M, Scott K, Seelow D, Seitz B, Shen Y, Similuk MN, Simon ES, Singh B, Smedley D, Smith CL, Smolinsky JT, Sperry S, Stafford E, Stefancsik R, Steinhaus R, Strawbridge R, Sundaramurthi JC, Talapova P, Tenorio Castano JA, Tesner P, Thomas RH, Thurm A, Turnovec M, van Gijn ME, Vasilevsky NA, Vlcková M, Walden A, Wang K, Wapner R, Ware JS, Wiafe AA, Wiafe SA, Wiggins LD, Williams AE, Wu C, Wyrwoll MJ, Xiong H, Yalin N, Yamamoto Y, Yatham LN, Yocum AK, Young AH, Yüksel Z, Zandi PP, Zankl A, Zarante I, Zvolský M, Toro S, Carmody LC, Harris NL, Munoz-Torres MC, Danis D, Mungall CJ, Köhler S, Haendel MA, Robinso... The Human Phenotype Ontology in 2024: phenotypes around the world. Nucleic Acids Res. 2024 Jan 5;52(D1):D1333-D1346. PubMed PMID: 37953324
• Carmody LC, Gargano MA, Toro S, Vasilevsky NA, Adam MP, Blau H, Chan LE, Gomez-Andres D, Horvath R, Kraus ML, Ladewig MS, Lewis-Smith D, Lochmüller H, Matentzoglu NA, Munoz-Torres MC, Schuetz C, Seitz B, Similuk MN, Sparks TN, Strauss T, Swietlik EM, Thompson R, Zhang XA, Mungall CJ, Haendel MA, Robinson PN. The Medical Action Ontology: A tool for annotating and analyzing treatments and clinical management of human disease. Med. 2023 Dec 8;4(12):913-927.e3. PubMed PMID: 37963467
• Toro, S., Anagnostopoulos, A. V., Bello, S., Blumberg, K., Cameron, R., Carmody, L., Diehl, A. D., Dooley, D., Duncan, W., Fey, P., Gaudet, P., Harris, N. L., Joachimiak, M., Kiani, L., Lubiana, T., Munoz-Torres, M. C., O’Neil, S., Osumi-Sutherland, D., Puig, A., … Mungall, C. J. (2023). Dynamic Retrieval Augmented Generation of Ontologies using Artificial Intelligence (DRAGON-AI). In arXiv [cs.AI]. arXiv. http://arxiv.org/abs/2312.10904
• Sabrina Toro, Nicole Vasilevsky, Sarah Gehrke, Monica Munoz-Torres. "The Mondo Disease Ontology: Highlights from 2023" Monarch Initiative, December 20, 2023, https://monarchinit.medium.com/the-mondo-disease-ontology-highlights-from-2023-1f37363c7ff1
• Matentzoglu N, Goutte-Gattat D, Tan SZK, Balhoff JP, Carbon S, Caron AR, Duncan WD, Flack JE, Haendel M, Harris NL, Hogan WR, Hoyt CT, Jackson RC, Kim H, Kir H, Larralde M, McMurry JA, Overton JA, Peters B, Pilgrim C, Stefancsik R, Robb SM, Toro S, Vasilevsky NA, Walls R, Mungall CJ, Osumi-Sutherland D. Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies. Database (Oxford). 2022 Oct 8;2022. PubMed PMID: 36208225
• Dhombres F, Morgan P, Chaudhari BP, Filges I, Sparks TN, Lapunzina P, Roscioli T, Agarwal U, Aggarwal S, Beneteau C, Cacheiro P, Carmody LC, Collardeau-Frachon S, Dempsey EA, Dufke A, Duyzend MH, El Ghosh M, Giordano JL, Glad R, Grinfelde I, Iliescu DG, Ladewig MS, Munoz-Torres MC, Pollazzon M, Radio FC, Rodo C, Silva RG, Smedley D, Sundaramurthi JC, Toro S, Valenzuela I, Vasilevsky NA, Wapner RJ, Zemet R, Haendel MA, Robinson PN. Prenatal phenotyping: A community effort to enhance the Human Phenotype Ontology. Am J Med Genet C Semin Med Genet. 2022 Jun;190(2):231-242. PubMed PMID: 35872606
• . Harmonizing model organism data in the Alliance of Genome Resources. Genetics. 2022 Apr 4;220(4). PubMed PMID: 35380658
• Toro, Sabrina, Vasilevsky, Nicole, Matentzoglu, Nicolas, Robinson, Peter N., & Mungall, Christopher. (2022). Axiomatization and refactoring of the 'chromosomal disorder' branch of Mondo. Zenodo. https://doi.org/10.5281/zenodo.6612070
• Nicole A Vasilevsky, Nicolas A Matentzoglu, Sabrina Toro, Joseph E Flack IV, Harshad Hegde, Deepak R Unni, Gioconda F Alyea, Joanna S Amberger, Larry Babb, James P Balhoff, Taylor I Bingaman, Gully A Burns, Orion J Buske, Tiffany J Callahan, Leigh C Carmody, Paula Carrio Cordo, Lauren E Chan, George S Chang, Sean L Christiaens, Louise C Daugherty, Michel Dumontier, Laura E Failla, May J Flowers, H. Alpha Garrett Jr., Jennifer L Goldstein, Dylan Gration, Tudor Groza, Marc Hanauer, Nomi L Harris, Jason A Hilton, Daniel S Himmelstein, Charles Tapley Hoyt, Megan S Kane, Sebastian Köhler, David Lagorce, Abbe Lai, Martin Larralde, Antonia Lock, Irene López Santiago, Donna R Maglott, Adriana J Malheiro, Birgit H M Meldal, Monica C Munoz-Torres, Tristan H Nelson, Frank W Nicholas, David Ochoa, Daniel P Olson, Tudor I Oprea, David Osumi-Sutherland, Helen Parkinson, Zoë May Pendlington, Ana Rath, Heidi L Rehm, Lyubov Remennik, Erin R Riggs, Paola Roncaglia, Justyne E Ross, Marion F Shadbolt, Kent A Shefchek, Morgan N Similuk, Nicholas Sioutos, Damian Smedley, Rachel Sparks, Ray Stefancsik, Ralf Stephan, Andrea L Storm, Doron Stupp, Gregory S Stupp, Jagadish Chandrabose Sundaramurthi, Imke Tammen, Darin Tay, Courtney L Thaxton, Eloise Valasek, Jordi Valls-Margarit, Alex H Wagner, Danielle Welter, Patricia L Whetzel, Lori L Whiteman, Valerie Wood, Colleen H Xu, Andreas Zankl, Xingmin Aaron Zhang, Christopher G Chute, Peter N Robinson, Christopher J Mungall, Ada Hamosh, Melissa A Haendel (2022). Mondo: Unifying diseases for the world, by the world. medRxiv 2022.04.13.22273750; doi: https://doi.org/10.1101/2022.04.13.22273750
• Toro, Sabrina and Vasilevsky, Nicole. "The Mondo Disease Ontology: Highlights from 2022" Monarch Initiative, December 1, 2022, https://monarchinit.medium.com/the-mondo-disease-ontology-highlights-from-2022-efa00dcf94d2
• Nicole Vasilevsky, Sabrina Toro, Nico A. Matentzoglu, Dazhi Jiao, Nomi L. Harris, Melissa A. Haendel, Peter N. Robinson, Chris Mungall, "Mondo Disease Ontology: Building a Community-Based Disease Resource" American Medical Informatics Association (AMIA) 2022 Informatics Summit, Chicago, IL | March, 2022
• Nicolas Matentzoglu, Joe Flack, John Graybeal, Nomi L. Harris, Harshad B. Hegde, Charles T. Hoyt, Hyeongsik Kim, Sabrina Toro, Nicole Vasilevsky, Christopher J. Mungall, "A Simple Standard for Ontological Mappings 2022: Updates of data model and outlook" OM-2022: The 17th International Workshop on Ontology Matching, | October, 2022
• Nicole Vasilevsky, Nico Matentzoglu, Sabrina Toro, Joe Flack, Ada Hamosh, Peter Robinson, Melissa Haendel, Chris Mungall, "Standardization of Cancer Terminology in the Mondo Disease Ontology." Cancer Genomics Consoritum 2022 Annual Meeting, Virtual | https://cgc.ezavconferences.com/129-standardization-of-cancer-terminology-in-the-mondo-disease-ontology/ | August, 2022
• James Overton, Rebecca Jackson, Sabrina Toro, Shawn Tan, Bradley Varner, David Osumi-Sutherland, Nicolas Matentzoglu, Nicole Vasilevsky, "OBO Academy: Training materials for Bio-ontologists." 13th International Conference for Biomedical Ontologies (ICBO 2022), Ann Arbor, MI | https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_9719.pdf | September, 2022
• Toro, Sabrina, Nicolas Matentzoglu, Kathleen R. Mullen, Nicole Vasilevsky, Halie M.Rando, Melissa Haendel, Christopher J. Mungall, Zhi-Liang Hu, Gregoire Leroy, Imke Tammen, and Frank W. Nicholas, "Classifying Animal Breeds with the Vertebrate Breed Ontology (VBO)" 13th International Conference for Biomedical Ontologies (ICBO 2022), Ann Arbor, MI | https://icbo-conference.github.io/icbo2022/papers/ICBO-2022_paper_1882.pdf | September, 2022
• Nicole Vasilevsky, James Overton, Rebecca Jackson, Sabrina Toro, Shawn Tan, Bradley Varner, David Osumi-Sutherland, Nicolas Matentzoglu, "OBO Academy: Training materials for Bio-ontologists." 15th Annual Biocuration Conference, Virtual | https://f1000research.com/posters/11-1144 | October, 2022
• Kathleen R. Mullen, Nicolas Matentzoglu, Halie M. Rando, Nicole Vasilevsky, Melissa Haendel, Christopher J. Mungall, Zhi-Liang Hu, Gregoire Leroy, Imke Tammen, Frank W. Nicholas, and Sabrina Toro, "Abyssinian to Zebu: Classifying Animal Breeds with the Vertebrate Breed Ontology (VBO)" International Society for Computational Biology (ISCB) Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, CO | December, 2022
• Sabrina Toro, Kathleen R. Mullen, Nicolas Matentzoglu, Joseph E. Flack IV, Harshad Hegde, Peter N. Robinson, Ada Hamosh, Melissa Haendel, Christopher J. Mungall, Nicole Vasilevsky , "The Mondo Disease Ontology: A Standardized Disease Terminology of Human and Animal Diseases" International Society for Computational Biology (ISCB) Rocky Mountain Bioinformatics Conference, Aspen/Snowmass, CO | December, 2022
• Nicole Vasilevsky, James Overton, Rebecca Jackson, Sabrina Toro, Shawn Tan, Bradley Varner, David Osumi-Sutherland, and Nicolas Matentzoglu, "OBO Academy: Training materials for bio-ontologists." 30th conference on Intelligent Systems For Molecular Biology (ISCB 2022), Madison, WI | July, 2022
• Sabrina Toro, Ada Hamosh, Nico Matentzoglu, Monica Munoz-Torres, Lauren Chan, Courtney Thaxton, Gioconda Alyea, Melissa Haendel, Chris Mungall, Peter N Robinson, & Nicole Vasilevsky. (2021). New view of the Mondo Disease Ontology High-level Classification According to Harrison's Principles of Internal Medicine textbook. Zenodo. https://doi.org/10.5281/zenodo.5273598
• Toro S, Matentzoglu N, Haendel M et al. Reclassification and axiomatization of chromosomal anomaly diseases in the mondo ontology [version 1; not peer reviewed]. F1000Research 2021, 10:986 (poster) (https://doi.org/10.7490/f1000research.1118805.1)
• Vasilevsky NA, Toro S, Ulschmid C and Siegel D. Curating clinical phenotypes in PHACE Syndrome to reveal disease mechanisms [version 1; not peer reviewed]. F1000Research 2021, 10:997 (poster) (https://doi.org/10.7490/f1000research.1118811.1)
• Reclassification of Infectious Disease in the Mondo Disease Ontology Nicole Vasilevsky, Sabrina Toro, Nico Matentzoglu, Dazhi Jiao, Melissa Haendel, Peter N Robinson, and Chris Mungall ICBO 2021
• Vasilevsky, Nicole and Toro, Sabrina. “Career paths and projections in biocuration: panel discussion from the biocuration2021 virtual conference” The ISB, July 26, 2021, https://www.biocuration.org/career-paths-and-projections-in-biocuration-panel-discussion-from-the-biocuration2021-virtual-conference/
• Nicole A. Vasilevsky, Sabrina Toro, Nico A. Matentzoglu, Dazhi Jiao, Nomi L. Harris, Melissa A. Haendel, Peter N. Robinson, Chris Mungall. 2022. “Mondo Disease Ontology: Building a Community-based Disease Resource” Presented at AMIA 2022 Informatics Summit, March 23.
• Toro, Sabrina and Vasilevsky, Nicole. “Mondo Disease Ontology Highlights from 2021” Monarch Initiative, December 1, 2021, https://monarchinit.medium.com/mondo-disease-ontology-highlights-from-2021-7f2e66baae0b