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Items: 1 to 20 of 250

1.

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.

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 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 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.

5.

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.

6.

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.

PMID:
28792687
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.

E-MSD: an integrated data resource for bioinformatics.

Golovin A, Oldfield TJ, Tate JG, Velankar S, Barton GJ, Boutselakis H, Dimitropoulos D, Fillon J, Hussain A, Ionides JM, John M, Keller PA, Krissinel E, McNeil P, Naim A, Newman R, Pajon A, Pineda J, Rachedi A, Copeland J, Sitnov A, Sobhany S, Suarez-Uruena A, Swaminathan GJ, Tagari M, Tromm S, Vranken W, Henrick K.

Nucleic Acids Res. 2004 Jan 1;32(Database issue):D211-6.

9.

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
10.

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.

11.

Achieving maximum ROI from corporate databases: exploiting your databases with integrated querying for better decision-making.

Jardine LF, Krassavine AO, Payne AW, Porter S.

Comb Chem High Throughput Screen. 2006 Feb;9(2):87-93.

PMID:
16475966
12.

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.

13.

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
14.
15.

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.

16.

Submit your interaction data the IMEx way: a step by step guide to trouble-free deposition.

Orchard S, Kerrien S, Jones P, Ceol A, Chatr-Aryamontri A, Salwinski L, Nerothin J, Hermjakob H.

Proteomics. 2007 Sep;7 Suppl 1:28-34.

PMID:
17893861
17.

JAFA: a protein function annotation meta-server.

Friedberg I, Harder T, Godzik A.

Nucleic Acids Res. 2006 Jul 1;34(Web Server issue):W379-81.

18.

Linked data and provenance in biological data webs.

Zhao J, Miles A, Klyne G, Shotton D.

Brief Bioinform. 2009 Mar;10(2):139-52. doi: 10.1093/bib/bbn044. Epub 2008 Dec 6.

PMID:
19060306
19.

ATDB: a uni-database platform for animal toxins.

He QY, He QZ, Deng XC, Yao L, Meng E, Liu ZH, Liang SP.

Nucleic Acids Res. 2008 Jan;36(Database issue):D293-7. Epub 2007 Oct 11.

20.

AmiGO: online access to ontology and annotation data.

Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S; AmiGO Hub; Web Presence Working Group.

Bioinformatics. 2009 Jan 15;25(2):288-9. doi: 10.1093/bioinformatics/btn615. Epub 2008 Nov 25.

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