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Page 1
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: wagner ah. Database (Oxford). 2022 May 25;2022:baac035. doi: 10.1093/database/baac035. Database (Oxford). 2022. PMID: 35616100 Free PMC article.
GA4GH: International policies and standards for data sharing across genomic research and healthcare.
Rehm HL, Page AJH, Smith L, Adams JB, Alterovitz G, Babb LJ, Barkley MP, Baudis M, Beauvais MJS, Beck T, Beckmann JS, Beltran S, Bernick D, Bernier A, Bonfield JK, Boughtwood TF, Bourque G, Bowers SR, Brookes AJ, Brudno M, Brush MH, Bujold D, Burdett T, Buske OJ, Cabili MN, Cameron DL, Carroll RJ, Casas-Silva E, Chakravarty D, Chaudhari BP, Chen SH, Cherry JM, Chung J, Cline M, Clissold HL, Cook-Deegan RM, Courtot M, Cunningham F, Cupak M, Davies RM, Denisko D, Doerr MJ, Dolman LI, Dove ES, Dursi LJ, Dyke SOM, Eddy JA, Eilbeck K, Ellrott KP, Fairley S, Fakhro KA, Firth HV, Fitzsimons MS, Fiume M, Flicek P, Fore IM, Freeberg MA, Freimuth RR, Fromont LA, Fuerth J, Gaff CL, Gan W, Ghanaim EM, Glazer D, Green RC, Griffith M, Griffith OL, Grossman RL, Groza T, Auvil JMG, Guigó R, Gupta D, Haendel MA, Hamosh A, Hansen DP, Hart RK, Hartley DM, Haussler D, Hendricks-Sturrup RM, Ho CWL, Hobb AE, Hoffman MM, Hofmann OM, Holub P, Hsu JS, Hubaux JP, Hunt SE, Husami A, Jacobsen JO, Jamuar SS, Janes EL, Jeanson F, Jené A, Johns AL, Joly Y, Jones SJM, Kanitz A, Kato K, Keane TM, Kekesi-Lafrance K, Kelleher J, Kerry G, Khor SS, Knoppers BM, Konopko MA, Kosaki K, Kuba M, Lawson J, Leinonen R, Li S… See abstract for full author list ➔ Rehm HL, et al. Among authors: wagner ah. Cell Genom. 2021 Nov 10;1(2):100029. doi: 10.1016/j.xgen.2021.100029. Cell Genom. 2021. PMID: 35072136 Free PMC article.
The GA4GH Phenopacket schema defines a computable representation of clinical data.
Jacobsen JOB, Baudis M, Baynam GS, Beckmann JS, Beltran S, Buske OJ, Callahan TJ, Chute CG, Courtot M, Danis D, Elemento O, Essenwanger A, Freimuth RR, Gargano MA, Groza T, Hamosh A, Harris NL, Kaliyaperumal R, Lloyd KCK, Khalifa A, Krawitz PM, Köhler S, Laraway BJ, Lehväslaiho H, Matalonga L, McMurry JA, Metke-Jimenez A, Mungall CJ, Munoz-Torres MC, Ogishima S, Papakonstantinou A, Piscia D, Pontikos N, Queralt-Rosinach N, Roos M, Sass J, Schofield PN, Seelow D, Siapos A, Smedley D, Smith LD, Steinhaus R, Sundaramurthi JC, Swietlik EM, Thun S, Vasilevsky NA, Wagner AH, Warner JL, Weiland C; GAGH Phenopacket Modeling Consortium; Haendel MA, Robinson PN. Jacobsen JOB, et al. Among authors: wagner ah. Nat Biotechnol. 2022 Jun;40(6):817-820. doi: 10.1038/s41587-022-01357-4. Nat Biotechnol. 2022. PMID: 35705716 Free PMC article. No abstract available.
GA4GH Phenopackets: A Practical Introduction.
Ladewig MS, Jacobsen JOB, Wagner AH, Danis D, El Kassaby B, Gargano M, Groza T, Baudis M, Steinhaus R, Seelow D, Bechrakis NE, Mungall CJ, Schofield PN, Elemento O, Smith L, McMurry JA, Munoz-Torres M, Haendel MA, Robinson PN. Ladewig MS, et al. Among authors: wagner ah. Adv Genet (Hoboken). 2022 Aug 25;4(1):2200016. doi: 10.1002/ggn2.202200016. eCollection 2023 Mar. Adv Genet (Hoboken). 2022. PMID: 36910590 Free PMC article.
Phenopacket-tools: Building and validating GA4GH Phenopackets.
Danis D, Jacobsen JOB, Wagner AH, Groza T, Beckwith MA, Rekerle L, Carmody LC, Reese J, Hegde H, Ladewig MS, Seitz B, Munoz-Torres M, Harris NL, Rambla J, Baudis M, Mungall CJ, Haendel MA, Robinson PN. Danis D, et al. Among authors: wagner ah. PLoS One. 2023 May 17;18(5):e0285433. doi: 10.1371/journal.pone.0285433. eCollection 2023. PLoS One. 2023. PMID: 37196000 Free PMC article.
The GA4GH Variation Representation Specification: A computational framework for variation representation and federated identification.
Wagner AH, Babb L, Alterovitz G, Baudis M, Brush M, Cameron DL, Cline M, Griffith M, Griffith OL, Hunt SE, Kreda D, Lee JM, Li S, Lopez J, Moyer E, Nelson T, Patel RY, Riehle K, Robinson PN, Rynearson S, Schuilenburg H, Tsukanov K, Walsh B, Konopko M, Rehm HL, Yates AD, Freimuth RR, Hart RK. Wagner AH, et al. Cell Genom. 2021 Nov 10;1(2):100027. doi: 10.1016/j.xgen.2021.100027. Cell Genom. 2021. PMID: 35311178 Free PMC article.
A harmonized meta-knowledgebase of clinical interpretations of somatic genomic variants in cancer.
Wagner AH, Walsh B, Mayfield G, Tamborero D, Sonkin D, Krysiak K, Deu-Pons J, Duren RP, Gao J, McMurry J, Patterson S, Del Vecchio Fitz C, Pitel BA, Sezerman OU, Ellrott K, Warner JL, Rieke DT, Aittokallio T, Cerami E, Ritter DI, Schriml LM, Freimuth RR, Haendel M, Raca G, Madhavan S, Baudis M, Beckmann JS, Dienstmann R, Chakravarty D, Li XS, Mockus S, Elemento O, Schultz N, Lopez-Bigas N, Lawler M, Goecks J, Griffith M, Griffith OL, Margolin AA; Variant Interpretation for Cancer Consortium. Wagner AH, et al. Nat Genet. 2020 Apr;52(4):448-457. doi: 10.1038/s41588-020-0603-8. Epub 2020 Apr 3. Nat Genet. 2020. PMID: 32246132 Free PMC article.
123 results