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A Simple Standard for Sharing Ontological Mappings (SSSOM).
Matentzoglu N, Balhoff JP, Bello SM, Bizon C, Brush M, Callahan TJ, Chute CG, Duncan WD, Evelo CT, Gabriel D, Graybeal J, Gray A, Gyori BM, Haendel M, Harmse H, Harris NL, Harrow I, Hegde HB, Hoyt AL, Hoyt CT, Jiao D, Jiménez-Ruiz E, Jupp S, Kim H, Koehler S, Liener T, Long Q, Malone J, McLaughlin JA, McMurry JA, Moxon S, Munoz-Torres MC, Osumi-Sutherland D, Overton JA, Peters B, Putman T, Queralt-Rosinach N, Shefchek K, Solbrig H, Thessen A, Tudorache T, Vasilevsky N, Wagner AH, Mungall CJ. Matentzoglu N, et al. Among authors: brush m. Database (Oxford). 2022 May 25;2022:baac035. doi: 10.1093/database/baac035. Database (Oxford). 2022. PMID: 35616100 Free PMC article.
The Monarch Initiative in 2019: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Shefchek KA, Harris NL, Gargano M, Matentzoglu N, Unni D, Brush M, Keith D, Conlin T, Vasilevsky N, Zhang XA, Balhoff JP, Babb L, Bello SM, Blau H, Bradford Y, Carbon S, Carmody L, Chan LE, Cipriani V, Cuzick A, Della Rocca M, Dunn N, Essaid S, Fey P, Grove C, Gourdine JP, Hamosh A, Harris M, Helbig I, Hoatlin M, Joachimiak M, Jupp S, Lett KB, Lewis SE, McNamara C, Pendlington ZM, Pilgrim C, Putman T, Ravanmehr V, Reese J, Riggs E, Robb S, Roncaglia P, Seager J, Segerdell E, Similuk M, Storm AL, Thaxon C, Thessen A, Jacobsen JOB, McMurry JA, Groza T, Köhler S, Smedley D, Robinson PN, Mungall CJ, Haendel MA, Munoz-Torres MC, Osumi-Sutherland D. Shefchek KA, et al. Among authors: brush m. Nucleic Acids Res. 2020 Jan 8;48(D1):D704-D715. doi: 10.1093/nar/gkz997. Nucleic Acids Res. 2020. PMID: 31701156 Free PMC article.
Research resources: curating the new eagle-i discovery system.
Vasilevsky N, Johnson T, Corday K, Torniai C, Brush M, Segerdell E, Wilson M, Shaffer C, Robinson D, Haendel M. Vasilevsky N, et al. Among authors: brush m. Database (Oxford). 2012 Mar 20;2012:bar067. doi: 10.1093/database/bar067. Print 2012. Database (Oxford). 2012. PMID: 22434835 Free PMC article.
The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species.
Mungall CJ, McMurry JA, Köhler S, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Lewis SE, NguyenXuan J, Shefchek K, Vasilevsky N, Yuan Z, Washington N, Hochheiser H, Groza T, Smedley D, Robinson PN, Haendel MA. Mungall CJ, et al. Among authors: brush m. Nucleic Acids Res. 2017 Jan 4;45(D1):D712-D722. doi: 10.1093/nar/gkw1128. Epub 2016 Nov 29. Nucleic Acids Res. 2017. PMID: 27899636 Free PMC article.
Navigating the Phenotype Frontier: The Monarch Initiative.
McMurry JA, Köhler S, Washington NL, Balhoff JP, Borromeo C, Brush M, Carbon S, Conlin T, Dunn N, Engelstad M, Foster E, Gourdine JP, Jacobsen JO, Keith D, Laraway B, Xuan JN, Shefchek K, Vasilevsky NA, Yuan Z, Lewis SE, Hochheiser H, Groza T, Smedley D, Robinson PN, Mungall CJ, Haendel MA. McMurry JA, et al. Among authors: brush m. Genetics. 2016 Aug;203(4):1491-5. doi: 10.1534/genetics.116.188870. Genetics. 2016. PMID: 27516611 Free PMC article.
Standardization of assay representation in the Ontology for Biomedical Investigations.
Vita R, Zheng J, Jackson R, Dooley D, Overton JA, Miller MA, Berrios DC, Scheuermann RH, He Y, McGinty HK, Brochhausen M, Lin AY, Jain SB, Chibucos MC, Judkins J, Giglio MG, Feng IY, Burns G, Brush MH, Peters B, Stoeckert CJ Jr. Vita R, et al. Among authors: brush mh. Database (Oxford). 2021 Jul 9;2021:baab040. doi: 10.1093/database/baab040. Database (Oxford). 2021. PMID: 34244718 Free PMC article. Review.
CLO: The cell line ontology.
Sarntivijai S, Lin Y, Xiang Z, Meehan TF, Diehl AD, Vempati UD, Schürer SC, Pang C, Malone J, Parkinson H, Liu Y, Takatsuki T, Saijo K, Masuya H, Nakamura Y, Brush MH, Haendel MA, Zheng J, Stoeckert CJ, Peters B, Mungall CJ, Carey TE, States DJ, Athey BD, He Y. Sarntivijai S, et al. J Biomed Semantics. 2014 Aug 13;5:37. doi: 10.1186/2041-1480-5-37. eCollection 2014. J Biomed Semantics. 2014. PMID: 25852852 Free PMC article.
Biolink Model: A universal schema for knowledge graphs in clinical, biomedical, and translational science.
Unni DR, Moxon SAT, Bada M, Brush M, Bruskiewich R, Caufield JH, Clemons PA, Dancik V, Dumontier M, Fecho K, Glusman G, Hadlock JJ, Harris NL, Joshi A, Putman T, Qin G, Ramsey SA, Shefchek KA, Solbrig H, Soman K, Thessen AE, Haendel MA, Bizon C, Mungall CJ; Biomedical Data Translator Consortium. Unni DR, et al. Among authors: brush m. Clin Transl Sci. 2022 Aug;15(8):1848-1855. doi: 10.1111/cts.13302. Epub 2022 Jun 6. Clin Transl Sci. 2022. PMID: 36125173 Free PMC article. Review.
Progress toward a universal biomedical data translator.
Fecho K, Thessen AE, Baranzini SE, Bizon C, Hadlock JJ, Huang S, Roper RT, Southall N, Ta C, Watkins PB, Williams MD, Xu H, Byrd W, Dančík V, Duby MP, Dumontier M, Glusman G, Harris NL, Hinderer EW, Hyde G, Johs A, Su AI, Qin G, Zhu Q; Biomedical Data Translator Consortium. Fecho K, et al. Clin Transl Sci. 2022 May 25;15(8):1838-47. doi: 10.1111/cts.13301. Online ahead of print. Clin Transl Sci. 2022. PMID: 35611543 Free PMC article. Review.
166 results