Onto-Tools, the toolkit of the modern biologist: Onto-Express, Onto-Compare, Onto-Design and Onto-Translate

By Sorin Draghici, Purvesh Khatri, Pratik Bhavsar, Abhik Shah, Stephen A. Krawetz, M. Tainsky. Nucleic Acids Res., 2003

368 citations recorded by the source corpus.

View Paper: https://www.semanticscholar.org/paper/60305a22946851978901a27362baa6e87cf59afc

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Citations in the corpus

GO: : TermFinder--open source software for accessing Gene Ontology information and finding significantly enriched Gene Ontology terms associated with a list of genes (2004, methodology): “These include FunSpec (Robinson et al., 2002), Onto-Express (Draghici et al., 2003a,b; Khatri et al., 2002) and FatiGO (Al-Shahrour et al., 2004) which are web applications; GoMiner (Zeeberg et al., 03), a Java application; GeneMerge (Castillo Davis and Hartl, 2003), which is a standalone Perl…”
g:Profiler—a web-based toolset for functional profiling of gene lists from large-scale experiments (2007, methodology): “Most proﬁling tools mentioned in (10) provide either Bonferroni or independent FDR correction, other tools as Onto-Express (8) or FatiGO (23), for example, allow the user to select from multiple schemas, leaving the whole responsibility to the end user, who often prefers to apply the default…”
Pathways to the analysis of microarray data. (2005, background): “Many other types of annotations could also be used, such as promoter elements [35,36], chromosome position [ 37 ], protein structure or interaction data, and text enrichment in the literature [27].”
Automated genome annotation and pathway identification using the KEGG Orthology (KO) as a controlled vocabulary (2005, methodology): “TheGeneOntologyhasbeenusedintheannota-tion of many genome databases, including SGD, CGD, FlyBase, MGI, TAIR, ZFIN, DictyBase, WormBase and RGD. Researchers annotating these databases use a combination of automation and manual curation to assign GO terms to genes in these genomes.”
Enrichment Map: A Network-Based Method for Gene-Set Enrichment Visualization and Interpretation (2010, methodology): “Tools such as Onto-Express [25], the Cytoscape [26] plugin BiNGO [27] and WebGestalt [28] display the hierarchical structure of enriched GO terms.”
Ontological analysis of gene expression data: current tools, limitations, and open problems (2005, methodology): “3 When it is known that dependencies exist, methods such as false discovery rate (FDR) are more appropriate (Benjamini and Hochberg, 1995; Benjamini and Yekutieli, 2001; Drăghici, 2003).”