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Protein Ontology Dissemination:

PRO is part of the OBO foundry ontologies
PRO is included in BioPortal
iProClass database links to PRO
Cell Ontology links to PRO
Collaborations in PRO Community Portal
IUPHAR-DB links to PRO
OBI links to PRO
GO links to PRO
NCBI LinkOut links to PRO
UniProt links to PRO
EcoCyc links to PRO
MGI links to PRO
IDO links to PRO
OCA links to PRO
NIF links to PRO
SALO links to PRO
HPO links to PRO

 
  How to link to PRO:

https://pir17.georgetown.edu/confluence/display/PROWIKI/PRO+URI+policy

 
  Publications:

     
Please use the following reference to cite PRO:
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, «elen 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.

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, «elen 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.

 
  Presentations:

Protein Ontology and its web resources, Cecilia Arighi, NCBO webminar, Sept 1, 2010. [14].
Proteins, Pathways, and Macromolecular Complexes. Harold J Drabkin, Alexei Evsikov, Peter DíEustachio, Cecilia Arighi, Darren A Natale,Cathy Wu, Judith A Blake, Carol J Bult., ISMB 2010, Boston, July 11-13, 2010.
Data Integration and Literature Mining for the Curation of Protein Forms in the Protein Ontology (PRO). Jules Nchoutmboube, Cecilia N. Arighi, Cathy Wu., BIBM09, IEEE International Conference on Bioinformatics & Biomedicine , Washington D.C., November 1-4 , 2009.
Protein Ontology Tutorial. Cecilia N. Arighi. Third International Biocurator conference, Berlin, Germany, April 17, 2009.
PRotein Ontology (PRO) Framework and the Building of the Prototype for TGF-beta Signaling Proteins. Cecilia N. Arighi. 2nd International Biocuration meeting, San Jose, CA, October 27, 2007.
Framework for a Protein Ontology. Darren Natale. ACM First International Workshop on Text Mining in Bioinformatics (TMBIO 2006), which is part of the ACM Fifteenth Conference on Information and Knowledge Management (CIKM), Arlington, VA, November 10, 2006.



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