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FYPO: the fission yeast phenotype ontology.
Harris MA, Lock A, Bähler J, Oliver SG, Wood V. Harris MA, et al. Bioinformatics. 2013 Jul 1;29(13):1671-8. doi: 10.1093/bioinformatics/btt266. Epub 2013 May 8. Bioinformatics. 2013. PMID: 23658422 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: harris ma. Bioinformatics. 2007 Aug 15;23(16):2198-200. doi: 10.1093/bioinformatics/btm112. Epub 2007 Jun 1. Bioinformatics. 2007. PMID: 17545183
Developing an ontology.
Harris MA. Harris MA. Methods Mol Biol. 2008;452:111-24. doi: 10.1007/978-1-60327-159-2_5. Methods Mol Biol. 2008. PMID: 18563371 Review.
The Protein Feature Ontology: a tool for the unification of protein feature annotations.
Reeves GA, Eilbeck K, Magrane M, O'Donovan C, Montecchi-Palazzi L, Harris MA, Orchard S, Jimenez RC, Prlic A, Hubbard TJ, Hermjakob H, Thornton JM. Reeves GA, et al. Among authors: harris ma. Bioinformatics. 2008 Dec 1;24(23):2767-72. doi: 10.1093/bioinformatics/btn528. Epub 2008 Oct 20. Bioinformatics. 2008. PMID: 18936051 Free PMC article.
How the gene ontology evolves.
Leonelli S, Diehl AD, Christie KR, Harris MA, Lomax J. Leonelli S, et al. Among authors: harris ma. BMC Bioinformatics. 2011 Aug 5;12:325. doi: 10.1186/1471-2105-12-325. BMC Bioinformatics. 2011. PMID: 21819553 Free PMC article.
PomBase: a comprehensive online resource for fission yeast.
Wood V, Harris MA, McDowall MD, Rutherford K, Vaughan BW, Staines DM, Aslett M, Lock A, Bähler J, Kersey PJ, Oliver SG. Wood V, et al. Among authors: harris ma. Nucleic Acids Res. 2012 Jan;40(Database issue):D695-9. doi: 10.1093/nar/gkr853. Epub 2011 Oct 28. Nucleic Acids Res. 2012. PMID: 22039153 Free PMC article.
Semantic integration of physiology phenotypes with an application to the Cellular Phenotype Ontology.
Hoehndorf R, Harris MA, Herre H, Rustici G, Gkoutos GV. Hoehndorf R, et al. Among authors: harris ma. Bioinformatics. 2012 Jul 1;28(13):1783-9. doi: 10.1093/bioinformatics/bts250. Epub 2012 Apr 26. Bioinformatics. 2012. PMID: 22539675 Free PMC article.
Canto: an online tool for community literature curation.
Rutherford KM, Harris MA, Lock A, Oliver SG, Wood V. Rutherford KM, et al. Among authors: harris ma. Bioinformatics. 2014 Jun 15;30(12):1791-2. doi: 10.1093/bioinformatics/btu103. Epub 2014 Feb 25. Bioinformatics. 2014. PMID: 24574118 Free PMC article.
A method for increasing expressivity of Gene Ontology annotations using a compositional approach.
Huntley RP, Harris MA, Alam-Faruque Y, Blake JA, Carbon S, Dietze H, Dimmer EC, Foulger RE, Hill DP, Khodiyar VK, Lock A, Lomax J, Lovering RC, Mutowo-Meullenet P, Sawford T, Van Auken K, Wood V, Mungall CJ. Huntley RP, et al. Among authors: harris ma. BMC Bioinformatics. 2014 May 21;15:155. doi: 10.1186/1471-2105-15-155. BMC Bioinformatics. 2014. PMID: 24885854 Free PMC article.
Representing kidney development using the gene ontology.
Alam-Faruque Y, Hill DP, Dimmer EC, Harris MA, Foulger RE, Tweedie S, Attrill H, Howe DG, Thomas SR, Davidson D, Woolf AS, Blake JA, Mungall CJ, O'Donovan C, Apweiler R, Huntley RP. Alam-Faruque Y, et al. Among authors: harris ma. PLoS One. 2014 Jun 18;9(6):e99864. doi: 10.1371/journal.pone.0099864. eCollection 2014. PLoS One. 2014. PMID: 24941002 Free PMC article.
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