An intuitive R-based web application. Genes2GO uses the biomaRt package of Bioconductor in order to retrieve custom sets of gene ontology annotations for any list of genes from organisms covered by the Ensembl database.
The tool is now decommissioned
WordVis lets you find words in the English dictionary, see synonyms grouped by meaning, and browse them in a fluid, interactive web of words and meanings. With WordVis you can explore the English language and perfect your language skills.
An exhaustive collection of TFs annotated according to experimental and other evidence on their function as true DbTFs. TFcheckpoint.org provides a high-quality and comprehensive knowledge source for genome-scale regulatory network studies.
OLSVis is an interactive visualisation of EBI’s Ontology Lookup Service (OLS). It is an application of WordVis’ visualiser.
VSM is a tool that lets people manually create computable information, with both high ease of use, and high expressive power.
We aimed for VSM to be applicable to the widest range of use-cases, i.e.: it works for diverse, heterogeneous information. Simultaneously, VSM keeps any inherent complexity in the captured information manageable for humans, i.e.: we focused on high user-friendliness towards curators.
BioGateway 2.0 endpoint
A semantically integrated resource comprising the entire set of the OBO foundry candidate ontologies, the GO annotation files, the SWISS-PROT protein set, the NCBI taxonomy and several in-house ontologies. BioGateway provides a single entry point to query these resources through SPARQL. It constitutes a key component for a Semantic Systems Biology approach to generate new hypotheses concerning systems properties.
BioGateway Cytoscape App
The BioGateway App is a Cytoscape plugin designed to provide easy query access to the BioGateway RDF triple store, which contains functional and interaction information for proteins from several curated resources. For explorative network building, we have added a comprehensive dataset with regulatory relationships of mammalian DNA binding transcription factors and their target genes, compiled both from curated resources and from a text mining effort. Query results are visualised using the inherent flexibility of the Cytoscape framework, and network links can be checked against curated database records or against the original publication.
BioGateway 3.0 endpoint
Cell Cycle Ontology
GeXO, ReXO and ReTO are nested, each ontologies connected to top nodes from the upper level ontology (ULO) the common root of the three ontologies. Black and red edges depict ‘is_a’ and ‘part_of’ relations, respectively. The three ontologies cover an increasingly wider domain. Each GO sub-domain term (e.g. GO:0010467; denoting ‘gene expression’) and its descendants are linked to the ULO as a subclass of ‘Biological Process’ represented by the ‘dotted edges’.
Standards and Ontologies
Semantic Systems Biology