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Protein Ontology Publications:

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Please use the following reference to cite PRO:
Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. "Protein Ontology (PRO): enhancing and scaling up the representation of protein entities." Nucleic Acids Res. 2017, 45(D1): D339-D346.

Natale DA, Arighi CN, Blake JA, Bona J, Chen C, Chen SC, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Duncan WD, Huang H, Ren J, Ross K, Ruttenberg A, Shamovsky V, Smith B, Wang Q, Zhang J, El-Sayed A, Wu CH. "Protein Ontology (PRO): enhancing and scaling up the representation of protein entities." Nucleic Acids Res. 2017, 45(D1): D339-D346.
Natale DA, Arighi CN, Blake JA, Bult CJ, Christie KR, Cowart J, D'Eustachio P, Diehl AD, Drabkin HJ, Helfer O, Huang H, Masci AM, Ren J, Roberts NV, Ross K, Ruttenberg A, Shamovsky V, Smith B, Yerramalla MS, Zhang J, AlJanahi A, Çelen I, Gan C, Lv M, Schuster-Lezell E, Wu CH. "Protein Ontology: a controlled structured network of protein entities." Nucleic Acids Res.. 2014, 42(Database issue):D415-21. doi: 10.1093/nar/gkt1173.
Ross KE, Arighi CN, Ren J, Huang H, Wu CH. "Construction of protein phosphorylation networks by data mining, text mining and ontology integration:analysis of the spindle checkpoint." Database (Oxford) 2013:bat038. doi: 10.1093/database/bat038. [12].
Ross KE, Arighi CN, Ren J, Natale DA, Huang H, Wu CH. "Use of the protein ontology for multi-faceted analysis of biological processes: a case study of the spindle checkpoint." Front Genet. 2013, 4:62. doi: 10.3389/fgene.2013.00062.eCollection 2013. [13].
Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A,D'Eustachio P, Smith B, Blake JA, Wu C. "The representation of protein complexesin the Protein Ontology (PRO)." BMC Bioinformatics. 2011 Sep 19;12:371. doi:10.1186/1471-2105-12-371. [14].
Natale DA, Arighi CN, Barker WC, Blake JA, Bult CJ, Caudy M, Drabkin HJ, D'Eustachio P, Evsikov AV, Huang H, Nchoutmboube J, Roberts NV, Smith B, Zhang J, Wu CH, "The Protein Ontology: a structured representation of protein forms and complexes", Nucleic Acids Res. 39(Database issue):D539-45. 2011.
Cecilia Arighi. "A Tutorial on Protein Ontology Resources for Proteomic Studies." Methods Mol Biol. 2011, 694:77-90.
Anna M. Masci, Cecilia N. Arighi, Alexander D. Diehl, Anne E. Lieberman, Chris Mungall, Richard H. Scheuermann, Barry Smith, and Lindsay G. Cowell, "An improved ontological representation of dendritic cells as a paradigm for all cell types", BMC Bioinformatics 10:70, 2009.
Cecilia Arighi, Hongfang Liu, Darren Natale, Winona Barker, Harold Drabkin, Judith Blake, Barry Smith and Cathy Wu, "TGF-beta Signaling Proteins and the Protein Ontology" BMC Bioinformatics 2009, 10, Suppl 5:S3.
Cecilia Arighi, Hongfang Liu, Darren Natale, Winona Barker, Harold Drabkin, Zhangzhi Hu, Judith Blake, Barry Smith and Cathy Wu, "TGF-beta Signaling Proteins and the Protein Ontology", Bio-Ontologies 2008, Special Interest Groups meeting at ISMB 2008, pp. 25-29.
Drabkin HJ., Arighi CN, Wu CH, Blake JA, "Functional Annotation of Protein Isoforms and Modified Forms", BioComp2008.
Darren A Natale, Cecilia N Arighi, Winona C Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H Wu, "Framework for a Protein Ontology", BMC Bioinformatics 2007, 8(Suppl 9):S1.
Darren A. Natale, Cecilia N. Arighi, Winona Barker, Judith Blake, Ti-Cheng Chang, Zhangzhi Hu, Hongfang Liu, Barry Smith, and Cathy H. Wu, "Framework for a Protein Ontology", Proceedings of the First International Workshop on Text Mining in Bioinformatics, 2006, pp. 29-36.