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Items: 1 to 20 of 202


TGF-beta signaling proteins and the Protein Ontology.

Arighi CN, Liu H, Natale DA, Barker WC, Drabkin H, Blake JA, Smith B, Wu CH.

BMC Bioinformatics. 2009 May 6;10 Suppl 5:S3. doi: 10.1186/1471-2105-10-S5-S3.


Framework for a protein ontology.

Natale DA, Arighi CN, Barker WC, Blake J, Chang TC, Hu Z, Liu H, Smith B, Wu CH.

BMC Bioinformatics. 2007 Nov 27;8 Suppl 9:S1.


A tutorial on protein ontology resources for proteomic studies.

Arighi CN.

Methods Mol Biol. 2011;694:77-90. doi: 10.1007/978-1-60761-977-2_6.


Tutorial on Protein Ontology Resources.

Arighi CN, Drabkin H, Christie KR, Ross KE, Natale DA.

Methods Mol Biol. 2017;1558:57-78. doi: 10.1007/978-1-4939-6783-4_3.


The Gene Ontology in 2010: extensions and refinements.

Gene Ontology Consortium.

Nucleic Acids Res. 2010 Jan;38(Database issue):D331-5. doi: 10.1093/nar/gkp1018. Epub 2009 Nov 17.


The representation of protein complexes in the Protein Ontology (PRO).

Bult CJ, Drabkin HJ, Evsikov A, Natale D, Arighi C, Roberts N, Ruttenberg A, D'Eustachio P, Smith B, Blake JA, Wu C.

BMC Bioinformatics. 2011 Sep 19;12:371. doi: 10.1186/1471-2105-12-371.


The ontology of biological sequences.

Hoehndorf R, Kelso J, Herre H.

BMC Bioinformatics. 2009 Nov 18;10:377. doi: 10.1186/1471-2105-10-377.


The Protein Ontology: a structured representation of protein forms and complexes.

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.

Nucleic Acids Res. 2011 Jan;39(Database issue):D539-45. doi: 10.1093/nar/gkq907. Epub 2010 Oct 8.


Relations as patterns: bridging the gap between OBO and OWL.

Hoehndorf R, Oellrich A, Dumontier M, Kelso J, Rebholz-Schuhmann D, Herre H.

BMC Bioinformatics. 2010 Aug 31;11:441. doi: 10.1186/1471-2105-11-441.


Ontology annotation: mapping genomic regions to biological function.

Thomas PD, Mi H, Lewis S.

Curr Opin Chem Biol. 2007 Feb;11(1):4-11. Epub 2007 Jan 5. Review.


GO-Elite: a flexible solution for pathway and ontology over-representation.

Zambon AC, Gaj S, Ho I, Hanspers K, Vranizan K, Evelo CT, Conklin BR, Pico AR, Salomonis N.

Bioinformatics. 2012 Aug 15;28(16):2209-10. doi: 10.1093/bioinformatics/bts366. Epub 2012 Jun 27.


An evaluation of GO annotation retrieval for BioCreAtIvE and GOA.

Camon EB, Barrell DG, Dimmer EC, Lee V, Magrane M, Maslen J, Binns D, Apweiler R.

BMC Bioinformatics. 2005;6 Suppl 1:S17. Epub 2005 May 24.


Semi-automated ontology generation within OBO-Edit.

W├Ąchter T, Schroeder M.

Bioinformatics. 2010 Jun 15;26(12):i88-96. doi: 10.1093/bioinformatics/btq188.


KaBOB: ontology-based semantic integration of biomedical databases.

Livingston KM, Bada M, Baumgartner WA Jr, Hunter LE.

BMC Bioinformatics. 2015 Apr 23;16:126. doi: 10.1186/s12859-015-0559-3.


Protein Ontology (PRO): enhancing and scaling up the representation of protein entities.

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.

Nucleic Acids Res. 2017 Jan 4;45(D1):D339-D346. doi: 10.1093/nar/gkw1075. Epub 2016 Nov 28.


Logical development of the cell ontology.

Meehan TF, Masci AM, Abdulla A, Cowell LG, Blake JA, Mungall CJ, Diehl AD.

BMC Bioinformatics. 2011 Jan 5;12:6. doi: 10.1186/1471-2105-12-6.


A top-level ontology of functions and its application in the Open Biomedical Ontologies.

Burek P, Hoehndorf R, Loebe F, Visagie J, Herre H, Kelso J.

Bioinformatics. 2006 Jul 15;22(14):e66-73.


A drug target slim: using gene ontology and gene ontology annotations to navigate protein-ligand target space in ChEMBL.

Mutowo P, Bento AP, Dedman N, Gaulton A, Hersey A, Lomax J, Overington JP.

J Biomed Semantics. 2016 Sep 27;7(1):59.


Toll-like receptor signaling in vertebrates: testing the integration of protein, complex, and pathway data in the protein ontology framework.

Arighi C, Shamovsky V, Masci AM, Ruttenberg A, Smith B, Natale DA, Wu C, D'Eustachio P.

PLoS One. 2015 Apr 20;10(3):e0122978. doi: 10.1371/journal.pone.0122978. eCollection 2015. Erratum in: PLoS One. 2015;10(6):e0131148.

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