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Items: 1 to 20 of 105

1.

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.

Bioinformatics. 2008 Dec 1;24(23):2767-72. doi: 10.1093/bioinformatics/btn528. Epub 2008 Oct 20.

2.

The Ontology Lookup Service: bigger and better.

Côté R, Reisinger F, Martens L, Barsnes H, Vizcaino JA, Hermjakob H.

Nucleic Acids Res. 2010 Jul;38(Web Server issue):W155-60. doi: 10.1093/nar/gkq331. Epub 2010 May 11.

3.

The Gene Ontology Annotation (GOA) project: implementation of GO in SWISS-PROT, TrEMBL, and InterPro.

Camon E, Magrane M, Barrell D, Binns D, Fleischmann W, Kersey P, Mulder N, Oinn T, Maslen J, Cox A, Apweiler R.

Genome Res. 2003 Apr;13(4):662-72. Epub 2003 Mar 12.

4.

OntoCAT--simple ontology search and integration in Java, R and REST/JavaScript.

Adamusiak T, Burdett T, Kurbatova N, Joeri van der Velde K, Abeygunawardena N, Antonakaki D, Kapushesky M, Parkinson H, Swertz MA.

BMC Bioinformatics. 2011 May 29;12:218. doi: 10.1186/1471-2105-12-218.

5.

The GOA database in 2009--an integrated Gene Ontology Annotation resource.

Barrell D, Dimmer E, Huntley RP, Binns D, O'Donovan C, Apweiler R.

Nucleic Acids Res. 2009 Jan;37(Database issue):D396-403. doi: 10.1093/nar/gkn803. Epub 2008 Oct 27.

6.

The Ontology Lookup Service: more data and better tools for controlled vocabulary queries.

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

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W372-6. doi: 10.1093/nar/gkn252. Epub 2008 May 8.

7.

OLS dialog: an open-source front end to the ontology lookup service.

Barsnes H, Côté RG, Eidhammer I, Martens L.

BMC Bioinformatics. 2010 Jan 17;11:34. doi: 10.1186/1471-2105-11-34.

8.

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.

9.

EDAM: an ontology of bioinformatics operations, types of data and identifiers, topics and formats.

Ison J, Kalas M, Jonassen I, Bolser D, Uludag M, McWilliam H, Malone J, Lopez R, Pettifer S, Rice P.

Bioinformatics. 2013 May 15;29(10):1325-32. doi: 10.1093/bioinformatics/btt113. Epub 2013 Mar 11.

10.

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.

11.

OntologyWidget - a reusable, embeddable widget for easily locating ontology terms.

Beauheim CC, Wymore F, Nitzberg M, Zachariah ZK, Jin H, Skene JH, Ball CA, Sherlock G.

BMC Bioinformatics. 2007 Sep 13;8:338.

12.

WSsas: a web service for the annotation of functional residues through structural homologues.

Talavera D, Laskowski RA, Thornton JM.

Bioinformatics. 2009 May 1;25(9):1192-4. doi: 10.1093/bioinformatics/btp116. Epub 2009 Feb 27.

PMID:
19251774
13.

Columba: an integrated database of proteins, structures, and annotations.

Trissl S, Rother K, Müller H, Steinke T, Koch I, Preissner R, Frömmel C, Leser U.

BMC Bioinformatics. 2005 Mar 31;6:81.

14.

QuickGO: a web-based tool for Gene Ontology searching.

Binns D, Dimmer E, Huntley R, Barrell D, O'Donovan C, Apweiler R.

Bioinformatics. 2009 Nov 15;25(22):3045-6. doi: 10.1093/bioinformatics/btp536. Epub 2009 Sep 10.

15.

The Gene Ontology Annotation (GOA) Database: sharing knowledge in Uniprot with Gene Ontology.

Camon E, Magrane M, Barrell D, Lee V, Dimmer E, Maslen J, Binns D, Harte N, Lopez R, Apweiler R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D262-6.

16.

The Sequence Ontology: a tool for the unification of genome annotations.

Eilbeck K, Lewis SE, Mungall CJ, Yandell M, Stein L, Durbin R, Ashburner M.

Genome Biol. 2005;6(5):R44. Epub 2005 Apr 29.

17.

The RESID Database of Protein Modifications as a resource and annotation tool.

Garavelli JS.

Proteomics. 2004 Jun;4(6):1527-33.

PMID:
15174122
18.

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.

19.

Human protein reference database as a discovery resource for proteomics.

Peri S, Navarro JD, Kristiansen TZ, Amanchy R, Surendranath V, Muthusamy B, Gandhi TK, Chandrika KN, Deshpande N, Suresh S, Rashmi BP, Shanker K, Padma N, Niranjan V, Harsha HC, Talreja N, Vrushabendra BM, Ramya MA, Yatish AJ, Joy M, Shivashankar HN, Kavitha MP, Menezes M, Choudhury DR, Ghosh N, Saravana R, Chandran S, Mohan S, Jonnalagadda CK, Prasad CK, Kumar-Sinha C, Deshpande KS, Pandey A.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D497-501.

20.

BioJava-ModFinder: identification of protein modifications in 3D structures from the Protein Data Bank.

Gao J, Prlic A, Bi C, Bluhm WF, Dimitropoulos D, Xu D, Bourne PE, Rose PW.

Bioinformatics. 2017 Jul 1;33(13):2047-2049. doi: 10.1093/bioinformatics/btx101.

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