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Results: 1 to 20 of 93

1.

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.

PMID:
20935045
[PubMed - indexed for MEDLINE]
Free PMC Article
2.

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.

PMID:
21929785
[PubMed - indexed for MEDLINE]
Free PMC Article
3.

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.

PMID:
19426460
[PubMed - indexed for MEDLINE]
Free PMC Article
4.

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.

PMID:
21082429
[PubMed - indexed for MEDLINE]
5.

Protein Ontology: a controlled structured network of protein entities.

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.

Nucleic Acids Res. 2014 Jan;42(Database issue):D415-21. doi: 10.1093/nar/gkt1173. Epub 2013 Nov 21.

PMID:
24270789
[PubMed - indexed for MEDLINE]
Free PMC Article
6.

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.

PMID:
18047702
[PubMed - indexed for MEDLINE]
Free PMC Article
7.

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.

PMID:
19920128
[PubMed - indexed for MEDLINE]
Free PMC Article
8.

The Ontology Lookup Service, a lightweight cross-platform tool for controlled vocabulary queries.

Côté RG, Jones P, Apweiler R, Hermjakob H.

BMC Bioinformatics. 2006 Feb 28;7:97.

PMID:
16507094
[PubMed - indexed for MEDLINE]
Free PMC Article
9.

SynDB: a Synapse protein DataBase based on synapse ontology.

Zhang W, Zhang Y, Zheng H, Zhang C, Xiong W, Olyarchuk JG, Walker M, Xu W, Zhao M, Zhao S, Zhou Z, Wei L.

Nucleic Acids Res. 2007 Jan;35(Database issue):D737-41. Epub 2006 Nov 10.

PMID:
17098931
[PubMed - indexed for MEDLINE]
Free PMC Article
10.

The Gene Ontology project in 2008.

Gene Ontology Consortium.

Nucleic Acids Res. 2008 Jan;36(Database issue):D440-4. Epub 2007 Nov 4.

PMID:
17984083
[PubMed - indexed for MEDLINE]
Free PMC Article
11.

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.

PMID:
19919720
[PubMed - indexed for MEDLINE]
Free PMC Article
12.

The Protein Information Resource: an integrated public resource of functional annotation of proteins.

Wu CH, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu ZZ, Ledley RS, Lewis KC, Mewes HW, Orcutt BC, Suzek BE, Tsugita A, Vinayaka CR, Yeh LS, Zhang J, Barker WC.

Nucleic Acids Res. 2002 Jan 1;30(1):35-7.

PMID:
11752247
[PubMed - indexed for MEDLINE]
Free PMC Article
13.

The Protein Information Resource.

Wu CH, Yeh LS, Huang H, Arminski L, Castro-Alvear J, Chen Y, Hu Z, Kourtesis P, Ledley RS, Suzek BE, Vinayaka CR, Zhang J, Barker WC.

Nucleic Acids Res. 2003 Jan 1;31(1):345-7.

PMID:
12520019
[PubMed - indexed for MEDLINE]
Free PMC Article
14.

GOChase: correcting errors from Gene Ontology-based annotations for gene products.

Park YR, Park CH, Kim JH.

Bioinformatics. 2005 Mar;21(6):829-31. Epub 2004 Oct 28.

PMID:
15513987
[PubMed - indexed for MEDLINE]
Free Article
15.

PINdb: a database of nuclear protein complexes from human and yeast.

Luc PV, Tempst P.

Bioinformatics. 2004 Jun 12;20(9):1413-5. Epub 2004 Apr 15.

PMID:
15087322
[PubMed - indexed for MEDLINE]
Free Article
16.

CORUM: the comprehensive resource of mammalian protein complexes.

Ruepp A, Brauner B, Dunger-Kaltenbach I, Frishman G, Montrone C, Stransky M, Waegele B, Schmidt T, Doudieu ON, Stümpflen V, Mewes HW.

Nucleic Acids Res. 2008 Jan;36(Database issue):D646-50. Epub 2007 Oct 26.

PMID:
17965090
[PubMed - indexed for MEDLINE]
Free PMC Article
17.

Organelle DB: an updated resource of eukaryotic protein localization and function.

Wiwatwattana N, Landau CM, Cope GJ, Harp GA, Kumar A.

Nucleic Acids Res. 2007 Jan;35(Database issue):D810-4. Epub 2006 Nov 27.

PMID:
17130152
[PubMed - indexed for MEDLINE]
Free PMC Article
18.

PDBML: the representation of archival macromolecular structure data in XML.

Westbrook J, Ito N, Nakamura H, Henrick K, Berman HM.

Bioinformatics. 2005 Apr 1;21(7):988-92. Epub 2004 Oct 27.

PMID:
15509603
[PubMed - indexed for MEDLINE]
Free Article
19.

Unintended consequences of existential quantifications in biomedical ontologies.

Boeker M, Tudose I, Hastings J, Schober D, Schulz S.

BMC Bioinformatics. 2011 Nov 24;12:456. doi: 10.1186/1471-2105-12-456.

PMID:
22115278
[PubMed - indexed for MEDLINE]
Free PMC Article
20.

A UML profile for the OBO relation ontology.

Guardia GD, Vêncio RZ, de Farias CR.

BMC Genomics. 2012;13 Suppl 5:S3. doi: 10.1186/1471-2164-13-S5-S3. Epub 2012 Oct 19.

PMID:
23095840
[PubMed - indexed for MEDLINE]
Free PMC Article

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