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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. Among authors: haendel ma. Database (Oxford). 2021 Oct 26;2021:baab069. doi: 10.1093/database/baab069. Database (Oxford). 2021. PMID: 34697637 Free PMC article.
OBO-Edit--an ontology editor for biologists.
Day-Richter J, Harris MA, Haendel M; Gene Ontology OBO-Edit Working Group; Lewis S. Day-Richter J, et al. Among authors: haendel m. Bioinformatics. 2007 Aug 15;23(16):2198-200. doi: 10.1093/bioinformatics/btm112. Epub 2007 Jun 1. Bioinformatics. 2007. PMID: 17545183
Integrating phenotype ontologies across multiple species.
Mungall CJ, Gkoutos GV, Smith CL, Haendel MA, Lewis SE, Ashburner M. Mungall CJ, et al. Among authors: haendel ma. Genome Biol. 2010 Jan 8;11(1):R2. doi: 10.1186/gb-2010-11-1-r2. Genome Biol. 2010. PMID: 20064205 Free PMC article.
The teleost anatomy ontology: anatomical representation for the genomics age.
Dahdul WM, Lundberg JG, Midford PE, Balhoff JP, Lapp H, Vision TJ, Haendel MA, Westerfield M, Mabee PM. Dahdul WM, et al. Among authors: haendel ma. Syst Biol. 2010 Jul;59(4):369-83. doi: 10.1093/sysbio/syq013. Epub 2010 Mar 29. Syst Biol. 2010. PMID: 20547776 Free PMC article.
Uberon, an integrative multi-species anatomy ontology.
Mungall CJ, Torniai C, Gkoutos GV, Lewis SE, Haendel MA. Mungall CJ, et al. Among authors: haendel ma. Genome Biol. 2012 Jan 31;13(1):R5. doi: 10.1186/gb-2012-13-1-r5. Genome Biol. 2012. PMID: 22293552 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. Database (Oxford). 2012 Mar 20;2012:bar067. doi: 10.1093/database/bar067. Print 2012. Database (Oxford). 2012. PMID: 22434835 Free PMC article.
A unified anatomy ontology of the vertebrate skeletal system.
Dahdul WM, Balhoff JP, Blackburn DC, Diehl AD, Haendel MA, Hall BK, Lapp H, Lundberg JG, Mungall CJ, Ringwald M, Segerdell E, Van Slyke CE, Vickaryous MK, Westerfield M, Mabee PM. Dahdul WM, et al. Among authors: haendel ma. PLoS One. 2012;7(12):e51070. doi: 10.1371/journal.pone.0051070. Epub 2012 Dec 10. PLoS One. 2012. PMID: 23251424 Free PMC article.
An overview of the BioCreative 2012 Workshop Track III: interactive text mining task.
Arighi CN, Carterette B, Cohen KB, Krallinger M, Wilbur WJ, Fey P, Dodson R, Cooper L, Van Slyke CE, Dahdul W, Mabee P, Li D, Harris B, Gillespie M, Jimenez S, Roberts P, Matthews L, Becker K, Drabkin H, Bello S, Licata L, Chatr-aryamontri A, Schaeffer ML, Park J, Haendel M, Van Auken K, Li Y, Chan J, Muller HM, Cui H, Balhoff JP, Chi-Yang Wu J, Lu Z, Wei CH, Tudor CO, Raja K, Subramani S, Natarajan J, Cejuela JM, Dubey P, Wu C. Arighi CN, et al. Database (Oxford). 2013 Jan 17;2013:bas056. doi: 10.1093/database/bas056. Print 2013. Database (Oxford). 2013. PMID: 23327936 Free PMC article.
232 results