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Page 1
Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework.
Bridges Y, de Souza V, Cortes KG, Haendel M, Harris NL, Korn DR, Marinakis NM, Matentzoglu N, McLaughlin JA, Mungall CJ, Osumi-Sutherland D, Robinson PN, Smedley D, Jacobsen JO. Bridges Y, et al. Among authors: osumi sutherland d. bioRxiv [Preprint]. 2024 Jun 16:2024.06.13.598672. doi: 10.1101/2024.06.13.598672. bioRxiv. 2024. PMID: 38915571 Free PMC article. Preprint.
OBO Foundry in 2021: operationalizing open data principles to evaluate ontologies.
Jackson R, Matentzoglu N, Overton JA, Vita R, Balhoff JP, Buttigieg PL, Carbon S, Courtot M, Diehl AD, Dooley DM, Duncan WD, Harris NL, Haendel MA, Lewis SE, Natale DA, Osumi-Sutherland D, Ruttenberg A, Schriml LM, Smith B, Stoeckert CJ Jr, Vasilevsky NA, Walls RL, Zheng J, Mungall CJ, Peters B. Jackson R, et al. Database (Oxford). 2021 Oct 26;2021:baab069. doi: 10.1093/database/baab069. Database (Oxford). 2021. PMID: 34697637 Free PMC article.
Cell type ontologies of the Human Cell Atlas.
Osumi-Sutherland D, Xu C, Keays M, Levine AP, Kharchenko PV, Regev A, Lein E, Teichmann SA. Osumi-Sutherland D, et al. Nat Cell Biol. 2021 Nov;23(11):1129-1135. doi: 10.1038/s41556-021-00787-7. Epub 2021 Nov 8. Nat Cell Biol. 2021. PMID: 34750578 Review.
Anatomical structures, cell types and biomarkers of the Human Reference Atlas.
Börner K, Teichmann SA, Quardokus EM, Gee JC, Browne K, Osumi-Sutherland D, Herr BW 2nd, Bueckle A, Paul H, Haniffa M, Jardine L, Bernard A, Ding SL, Miller JA, Lin S, Halushka MK, Boppana A, Longacre TA, Hickey J, Lin Y, Valerius MT, He Y, Pryhuber G, Sun X, Jorgensen M, Radtke AJ, Wasserfall C, Ginty F, Ho J, Sunshine J, Beuschel RT, Brusko M, Lee S, Malhotra R, Jain S, Weber G. Börner K, et al. Nat Cell Biol. 2021 Nov;23(11):1117-1128. doi: 10.1038/s41556-021-00788-6. Epub 2021 Nov 8. Nat Cell Biol. 2021. PMID: 34750582 Free PMC article. Review.
Ontology Development Kit: a toolkit for building, maintaining and standardizing biomedical ontologies.
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. Matentzoglu N, et al. Database (Oxford). 2022 Oct 8;2022:baac087. doi: 10.1093/database/baac087. Database (Oxford). 2022. PMID: 36208225 Free PMC article.
Brain Data Standards - A method for building data-driven cell-type ontologies.
Tan SZK, Kir H, Aevermann BD, Gillespie T, Harris N, Hawrylycz MJ, Jorstad NL, Lein ES, Matentzoglu N, Miller JA, Mollenkopf TS, Mungall CJ, Ray PL, Sanchez REA, Staats B, Vermillion J, Yadav A, Zhang Y, Scheuermann RH, Osumi-Sutherland D. Tan SZK, et al. Sci Data. 2023 Jan 24;10(1):50. doi: 10.1038/s41597-022-01886-2. Sci Data. 2023. PMID: 36693887 Free PMC article.
The Ontology of Biological Attributes (OBA) - Computational Traits for the Life Sciences.
Stefancsik R, Balhoff JP, Balk MA, Ball R, Bello SM, Caron AR, Chessler E, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. Stefancsik R, et al. bioRxiv [Preprint]. 2023 Jan 27:2023.01.26.525742. doi: 10.1101/2023.01.26.525742. bioRxiv. 2023. Update in: Mamm Genome. 2023 Sep;34(3):364-378. doi: 10.1007/s00335-023-09992-1 PMID: 36747660 Free PMC article. Updated. Preprint.
The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.
Stefancsik R, Balhoff JP, Balk MA, Ball RL, Bello SM, Caron AR, Chesler EJ, de Souza V, Gehrke S, Haendel M, Harris LW, Harris NL, Ibrahim A, Koehler S, Matentzoglu N, McMurry JA, Mungall CJ, Munoz-Torres MC, Putman T, Robinson P, Smedley D, Sollis E, Thessen AE, Vasilevsky N, Walton DO, Osumi-Sutherland D. Stefancsik R, et al. Among authors: osumi sutherland d. Mamm Genome. 2023 Sep;34(3):364-378. doi: 10.1007/s00335-023-09992-1. Epub 2023 Apr 19. Mamm Genome. 2023. PMID: 37076585 Free PMC article.
55 results