Tools

Genes2GO

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. 

Link: http://norstore-trd-bio0.hpc.ntnu.no:8080/Genes2GO/

TFCheckpoint

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.

Link: http://www.tfcheckpoint.org/

WordVis

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.

Link: http://wordvis.com/

OLSVis

OLSVis is an interactive visualisation of EBI’s Ontology Lookup Service (OLS). It is an application of WordVis’ visualiser.

Link: http://ols.wordvis.com/

VSM

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.

Link: http://scicura.org/vsm/intro.html

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. 

Link: http://www.semantic-systems-biology.org/biogateway

BioGateway 3.0 endpoint

 

Link: 

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.

Link: https://www.biogateway.eu/

Datasets

Cell Cycle Ontology

An application ontology integrating knowledge about the eukaryotic cell cycle.

Link: https://bioportal.bioontology.org/ontologies/CCO

GEXKB graphs

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’.

GEXO: http://bioportal.bioontology.org/ontologies/GEXO

REXO: http://bioportal.bioontology.org/ontologies/REXO

RETO: http://bioportal.bioontology.org/ontologies/RETO

CCKR Map

Gastrin is a hormone whose main function is to stimulate secretion of hydrochloric acid by the gastric mucosa, which results in gastrin formation inhibition. This hormone also acts as a mitogenic factor for gastrointestinal epithelial cells. Gastrin has two biologically active peptide forms, G34 and G17.Gastrin gene expression is upregulated in both a number of pre-malignant conditions and in established cancer through a variety of mechanisms. Depending on the tissue where it is expressed and the level of expression, differential processing of the polypeptide product leads to the production of different biologically active peptides. In turn, acting through the classical gastrin cholecystokinin B receptor CCK-BR, its isoforms and alternative receptors, these peptides trigger signalling pathways which influence the expression of downstream genes that affect cell survival, angiogenesis and invasion.

Link: http://www.pantherdb.org/pathway/pathwayDiagram.jsp?catAccession=P06959

Main publications

Systems Biology
 

 

Tools
 

 

Semantic Systems Biology
 

 

Crossover