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  2. Haendel M, Vasilevsky N, Unni D, Bologa C, Harris N, Rehm H, Hamosh A, Baynam G, Groza T, McMurry J, Dawkins H, Rath A, Thaxon C, Bocci G, Joachimiak MP, Köhler S, Robinson PN, Mungall C, Oprea TI. How many rare diseases are there? Nat Rev Drug Discov, 2019 Nov 5. https://www.nature.com/articles/d41573-019-00180-y
  3. Mabee PM, Balhoff JP, Dahdul WM, Lapp H, Mungall CJ, Vision TJ. A Logical Model of Homology for Comparative Biology. Syst. Biol. 2019, p. 588822. http://dx.doi.org/10.1093/sysbio/syz067
  4. Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou L-P, Good B, Gaudet P, Lewis SE, Mungall CJ. Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. Nat Genet, nature.com; 2019 Oct;51(10):1429–1433. http://dx.doi.org/10.1038/s41588-019-0500-1 PMID: 31548717
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  6. Jackson RC, Balhoff JP, Douglass E, Harris NL, Mungall CJ, Overton JA. ROBOT: A Tool for Automating Ontology Workflows. BMC Bioinformatics , 2019 Jul 29;20(1):407. http://dx.doi.org/10.1186/s12859-019-3002-3 PMID: 31357927
  7. Carbon S</b> Champieux R, McMurry JA, Winfree L, Wyatt LR, Haendel MA. An analysis and metric of reusable data licensing practices for biomedical resources. PLoS One. 2019 Mar 27;14(3):e0213090. http://dx.doi.org/10.1371/journal.pone.0213090 PMID: 30917137
  8. Dunn NA, Unni D, Diesh C, Munoz-Torres M, Harris NL, Yao E, Rasche H, Holmes IH, Elsik CG, Lewis SE. Apollo: Democratizing genome annotation. PLoS Comput Biol. 2019 Feb;15(2):e1006790. http://dx.doi.org/10.1371/journal.pcbi.1006790 PMCID: PMC6380598
  9. Mungall CJ, Koehler S, Robinson P, Holmes I, Haendel M. k-BOOM: A Bayesian approach to ontology structure inference, with applications in disease ontology construction. bioRxiv. 2019. https://www.biorxiv.org/content/10.1101/048843v3
  10. Giglio M, Tauber R, Nadendla S, Munro J, Olley D, Ball S, Mitraka E, Schriml LM, Gaudet P, Hobbs ET, Erill I, Siegele DA, Hu JC, Mungall C, Chibucos MC. ECO, the Evidence & Conclusion Ontology: community standard for evidence information. Nucleic Acids Res. 2019 Jan 8;47(D1):D1186–D1194. http://dx.doi.org/10.1093/nar/gky1036 PMCID: PMC6323956
  11. Haendel MA, McMurry JA, Relevo R, Mungall CJ, Robinson PN, Chute CG. A Census of Disease Ontologies. Annu Rev Biomed Data Sci. Annual Reviews; 2018 Jul 20;1(1):305–331. https://doi.org/10.1146/annurev-biodatasci-080917-013459
  12. Klopfenstein DV, Zhang L, Pedersen BS, Ramírez F, Warwick Vesztrocy A, Naldi A, Mungall CJ, Yunes JM, Botvinnik O, Weigel M, Dampier W, Dessimoz C, Flick P, Tang H. GOATOOLS: A Python library for Gene Ontology analyses. Sci Rep. 2018 Jul 18;8(1):10872. http://dx.doi.org/10.1038/s41598-018-28948-z PMCID: PMC6052049
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  14. Tang H, Mungall CJ, Mi H, Thomas PD. GOTaxon: Representing the evolution of biological functions in the Gene Ontology. arXiv [q-bio.PE]. 2018. http://arxiv.org/abs/1802.06004
  15. Matentzoglu N, Malone J, Mungall C, Stevens R. MIRO: guidelines for minimum information for the reporting of an ontology. J Biomed Semantics. 2018 Jan 18;9(1):6. http://dx.doi.org/10.1186/s13326-017-0172-7 PMCID: PMC5774126
  16. Cooper L, Meier A, Laporte M-A, Elser JL, Mungall C, Sinn BT, Cavaliere D, Carbon S, Dunn NA, Smith B, Qu B, Preece J, Zhang E, Todorovic S, Gkoutos G, Doonan JH, Stevenson DW, Arnaud E, Jaiswal P. The Planteome database: an integrated resource for reference ontologies, plant genomics and phenomics. Nucleic Acids Res. 2018 Jan 4;46(D1):D1168–D1180. http://dx.doi.org/10.1093/nar/gkx1152 PMCID: PMC5753347
  17. Haendel MA, Mcmurry JA, Relevo R, Mungall CJ, Robinson PN, Chute CG. Annual Review of Biomedical Data Science A Census of Disease Ontologies. 2018;(April):305–331.
  18. GO Consortium. Gene Ontology Resource: 20 years and still GOing strong. Nucleic Acids Res. Oxford University Press; 2018;47(D1):D330–D338.
  19. Köhler S, Carmody L, Vasilevsky N, Jacobsen JOB, Danis D, Gourdine J-P, Gargano M, Harris NL, Matentzoglu N, McMurry JA, Others. Expansion of the Human Phenotype Ontology (HPO) knowledge base and resources. Nucleic Acids Res. Oxford University Press; 2018;47(D1):D1018–D1027.
  20. Balhoff JP, Good BM, Carbon S, Mungall CJ. Arachne: an OWL RL reasoner applied to Gene Ontology Causal Activity Models (and beyond). Zenodo; 2018. http://dx.doi.org/10.5281/ZENODO.2397192
  21. 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 JOB, 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. The Monarch Initiative: an integrative data and analytic platform connecting phenotypes to genotypes across species. Nucleic Acids Res. 2017 Jan 4;45(D1):D712–D722. http://dx.doi.org/10.1093/nar/gkw1128 PMCID: PMC5210586
  22. Holmes IH, Mungall CJ. BioMake: a GNU make-compatible utility for declarative workflow management. Bioinformatics. 2017 Nov 1;33(21):3502–3504. http://dx.doi.org/10.1093/bioinformatics/btx306 PMCID: PMC5860158
  23. Osumi-Sutherland D, Courtot M, Balhoff JP, Mungall C. Dead simple OWL design patterns. J Biomed Semantics. 2017 Jun 5;8(1):18. http://dx.doi.org/10.1186/s13326-017-0126-0 PMCID: PMC5460348
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  51. Rubin GM, Yandell MD, Wortman JR, Gabor Miklos GL, Nelson CR, Hariharan IK, Fortini ME, Li PW, Apweiler R, Fleischmann W, Cherry JM, Henikoff S, Skupski MP, Misra S, Ashburner M, Birney E, Boguski MS, Brody T, Brokstein P, Celniker SE, Chervitz SA, Coates D, Cravchik A, Gabrielian A, Galle RF, Gelbart WM, George RA, Goldstein LS, Gong F, Guan P, Harris NL, Hay BA, Hoskins RA, Li J, Li Z, Hynes RO, Jones SJ, Kuehl PM, Lemaitre B, Littleton JT, Morrison DK, Mungall C, O’Farrell PH, Pickeral OK, Shue C, Vosshall LB, Zhang J, Zhao Q, Zheng XH, Lewis S. Comparative genomics of the eukaryotes. Science. 2000 Mar 24;287(5461):2204–2215. https://www.ncbi.nlm.nih.gov/pubmed/10731134 PMCID: PMC2754258
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