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Items: 1 to 20 of 99

1.

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.

2.

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.

3.

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.

4.

OLS Client and OLS Dialog: Open Source Tools to Annotate Public Omics Datasets.

Perez-Riverol Y, Ternent T, Koch M, Barsnes H, Vrousgou O, Jupp S, Vizcaíno JA.

Proteomics. 2017 Oct;17(19). doi: 10.1002/pmic.201700244.

5.

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.

6.

OLSVis: an animated, interactive visual browser for bio-ontologies.

Vercruysse S, Venkatesan A, Kuiper M.

BMC Bioinformatics. 2012 Jul 10;13:116. doi: 10.1186/1471-2105-13-116.

7.

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.

8.

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.

9.

OntoQuery: easy-to-use web-based OWL querying.

Tudose I, Hastings J, Muthukrishnan V, Owen G, Turner S, Dekker A, Kale N, Ennis M, Steinbeck C.

Bioinformatics. 2013 Nov 15;29(22):2955-7. doi: 10.1093/bioinformatics/btt514. Epub 2013 Sep 5.

10.

PRIDE: Data submission and analysis.

Vizcaíno JA, Reisinger F, Côté R, Martens L.

Curr Protoc Protein Sci. 2010 Apr;Chapter 25:Unit 25.4. doi: 10.1002/0471140864.ps2504s60.

PMID:
20393974
11.

The PRIDE proteomics identifications database: data submission, query, and dataset comparison.

Jones P, Côté R.

Methods Mol Biol. 2008;484:287-303. doi: 10.1007/978-1-59745-398-1_19.

PMID:
18592187
12.

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.

13.

BioPortal: ontologies and integrated data resources at the click of a mouse.

Noy NF, Shah NH, Whetzel PL, Dai B, Dorf M, Griffith N, Jonquet C, Rubin DL, Storey MA, Chute CG, Musen MA.

Nucleic Acids Res. 2009 Jul;37(Web Server issue):W170-3. doi: 10.1093/nar/gkp440. Epub 2009 May 29.

14.

Controlled vocabularies and ontologies in proteomics: overview, principles and practice.

Mayer G, Jones AR, Binz PA, Deutsch EW, Orchard S, Montecchi-Palazzi L, Vizcaíno JA, Hermjakob H, Oveillero D, Julian R, Stephan C, Meyer HE, Eisenacher M.

Biochim Biophys Acta. 2014 Jan;1844(1 Pt A):98-107. doi: 10.1016/j.bbapap.2013.02.017. Epub 2013 Feb 19. Review.

15.

IntAct: an open source molecular interaction database.

Hermjakob H, Montecchi-Palazzi L, Lewington C, Mudali S, Kerrien S, Orchard S, Vingron M, Roechert B, Roepstorff P, Valencia A, Margalit H, Armstrong J, Bairoch A, Cesareni G, Sherman D, Apweiler R.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D452-5.

16.

The Gene Ontology project in 2008.

Gene Ontology Consortium.

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

17.

SerbGO: searching for the best GO tool.

Mosquera JL, Sánchez-Pla A.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W368-71. doi: 10.1093/nar/gkn256. Epub 2008 May 14.

18.
19.

Data exploration tools for the Gene Ontology database.

Shoop E, Casaes P, Onsongo G, Lesnett L, Petursdottir EO, Donkor EK, Tkach D, Cosimini M.

Bioinformatics. 2004 Dec 12;20(18):3442-54. Epub 2004 Jul 22.

PMID:
15271779
20.

USAGE: a web-based approach towards the analysis of SAGE data. Serial Analysis of Gene Expression.

van Kampen AH, van Schaik BD, Pauws E, Michiels EM, Ruijter JM, Caron HN, Versteeg R, Heisterkamp SH, Leunissen JA, Baas F, van der Mee M.

Bioinformatics. 2000 Oct;16(10):899-905.

PMID:
11120679

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