The tools presented here have been developped within the framework of my PhD thesis entitled "Semantic methods for the cross-species metabolic pathways comparison : application to human, mice and chicken lipid metabolism". Some of these tools are still in development but all are functional.
GO2PUB is a bibliographic search tool using Gene Ontology. It is hosted on the Genouest platform and has been subject to an article in Journal of Biomedical Semantics. This tool operates PubMed queries expansion using the names, symbols an synonyms of the gene products annotated by the GO terms that the user chose.
GO2SiP is a tool that computes semantic similarities and particularities between gene products. It is still at a development stage. Currently, it supports the Wang semantic similarity measure, the particularity measure based on the Information Content and the particularity measure based on the semantic value. A node-based similarity method (probably Lin's) will be implemented soon. A click on a result show the corresponding GO graph. The particularity measure has been subject to an article in PLoS ONE.
GO2GRAPH is a tool of visualization of two gene products annotations in the GO graph. The gene products have to be put directly in the url as parameters. For example, to compare the mice gene Hsd17b3 (taxon n°10090) and the human gene SRD5A1 (taxon n°9606), we will use this url: http://bettembourg.fr/labo/go2graph/build.php?gene1=Hsd17b3&tax1=10090&gene2=SRD5A1&tax2=9606. The annotations specific to "gene1" are displayed in red, the annotations specific to "gene2" are displayed in green and the common annotations are displayed in blue.
CSPaCo (for Cross-Species Pathways Comparison) generates the metabolic pathways comparison graphes like those presented in the chapter 5 of my thesis. It currently consists in four numbered scripts. An integration work is yet to be done for an easier use. The first script has to be launched in a Protégé session (version 3.4.7, with the ScriptTab) in which we have first opened the rdf-owl file of a species provided by a metabolic pathway database. It generates the initial files required for the graphes creation. It has to be launched for each species that we want to compare. The second script writes the graphe files in dot format from the initial files. The third script combines these files with the similarity and particularity information provided by GO2SiP in gexf files. These files have to be opened with Gephi to organize the graphe layout (Yifan Hu spatialization) in order to export it in a gml file. The last script adds the coloured information relative to the similarity and the particularity to this graphe in a last gml file that can be opened in Gephi to be exported in an image.