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Items: 1 to 20 of 101


An ontology-neutral framework for enrichment analysis.

Tirrell R, Evani U, Berman AE, Mooney SD, Musen MA, Shah NH.

AMIA Annu Symp Proc. 2010 Nov 13;2010:797-801.


Chapter 9: Analyses using disease ontologies.

Shah NH, Cole T, Musen MA.

PLoS Comput Biol. 2012;8(12):e1002827. doi: 10.1371/journal.pcbi.1002827. Epub 2012 Dec 27.


Enabling enrichment analysis with the Human Disease Ontology.

LePendu P, Musen MA, Shah NH.

J Biomed Inform. 2011 Dec;44 Suppl 1:S31-8. doi: 10.1016/j.jbi.2011.04.007. Epub 2011 Apr 29.


How to learn about gene function: text-mining or ontologies?

Soldatos TG, Perdigão N, Brown NP, Sabir KS, O'Donoghue SI.

Methods. 2015 Mar;74:3-15. doi: 10.1016/j.ymeth.2014.07.004. Epub 2014 Aug 1. Review.


NCBO Technology: Powering semantically aware applications.

Whetzel PL; NCBO Team.

J Biomed Semantics. 2013 Apr 15;4 Suppl 1:S8. doi: 10.1186/2041-1480-4-S1-S8. Epub 2013 Apr 15.


Utilizing a structural meta-ontology for family-based quality assurance of the BioPortal ontologies.

Ochs C, He Z, Zheng L, Geller J, Perl Y, Hripcsak G, Musen MA.

J Biomed Inform. 2016 Jun;61:63-76. doi: 10.1016/j.jbi.2016.03.007. Epub 2016 Mar 14.


Investigating the concordance of Gene Ontology terms reveals the intra- and inter-platform reproducibility of enrichment analysis.

Zhang L, Zhang J, Yang G, Wu D, Jiang L, Wen Z, Li M.

BMC Bioinformatics. 2013 Apr 29;14:143. doi: 10.1186/1471-2105-14-143.


Visual annotation display (VLAD): a tool for finding functional themes in lists of genes.

Richardson JE, Bult CJ.

Mamm Genome. 2015 Oct;26(9-10):567-73. doi: 10.1007/s00335-015-9570-2. Epub 2015 Jun 6.


BioPortal: enhanced functionality via new Web services from the National Center for Biomedical Ontology to access and use ontologies in software applications.

Whetzel PL, Noy NF, Shah NH, Alexander PR, Nyulas C, Tudorache T, Musen MA.

Nucleic Acids Res. 2011 Jul;39(Web Server issue):W541-5. doi: 10.1093/nar/gkr469. Epub 2011 Jun 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.


Annotation concept synthesis and enrichment analysis: a logic-based approach to the interpretation of high-throughput experiments.

Jiline M, Matwin S, Turcotte M.

Bioinformatics. 2011 Sep 1;27(17):2391-8. doi: 10.1093/bioinformatics/btr337. Epub 2011 Jul 9.


Building a biomedical ontology recommender web service.

Jonquet C, Musen MA, Shah NH.

J Biomed Semantics. 2010 Jun 22;1 Suppl 1:S1. doi: 10.1186/2041-1480-1-S1-S1.


GOrilla: a tool for discovery and visualization of enriched GO terms in ranked gene lists.

Eden E, Navon R, Steinfeld I, Lipson D, Yakhini Z.

BMC Bioinformatics. 2009 Feb 3;10:48. doi: 10.1186/1471-2105-10-48.


Onto-CC: a web server for identifying Gene Ontology conceptual clusters.

Romero-Zaliz R, Del Val C, Cobb JP, Zwir I.

Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W352-7. doi: 10.1093/nar/gkn323. Epub 2008 Jun 10.


IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools.

Carazzolle MF, de Carvalho LM, Slepicka HH, Vidal RO, Pereira GA, Kobarg J, Meirelles GV.

PLoS One. 2014 Jun 20;9(6):e100385. doi: 10.1371/journal.pone.0100385. eCollection 2014. Erratum in: PLoS One. 2014;9(9):e108101.


Logical Gene Ontology Annotations (GOAL): exploring gene ontology annotations with OWL.

Jupp S, Stevens R, Hoehndorf R.

J Biomed Semantics. 2012 Apr 24;3 Suppl 1:S3. doi: 10.1186/2041-1480-3-S1-S3.


Comparing gene annotation enrichment tools for functional modeling of agricultural microarray data.

van den Berg BH, Thanthiriwatte C, Manda P, Bridges SM.

BMC Bioinformatics. 2009 Oct 8;10 Suppl 11:S9. doi: 10.1186/1471-2105-10-S11-S9.


STOP using just GO: a multi-ontology hypothesis generation tool for high throughput experimentation.

Wittkop T, TerAvest E, Evani US, Fleisch KM, Berman AE, Powell C, Shah NH, Mooney SD.

BMC Bioinformatics. 2013 Feb 14;14:53. doi: 10.1186/1471-2105-14-53.

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