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Publication for GoFish
Chapter 8: Biological Knowledge Assembly and Interpretation
[…] extual presentation helps users to understand biological semantics and contexts. A number of analysis tools with these steps have been introduced: ArrayXPath, Pathway Miner, EASE in pathway analysis, GOFish, GOTree Machine, FatiGO, GOAL, GOMIner, FuncAssociate in ontology analysis and GeneMerge, MAPPFinder, DAVID, GFINDer, OntoTools in both analyses . […]
User centered and ontology based information retrieval system for life sciences
[…] Indeed, it is then possible to select documents that are not indexed using exactly the same terms as the query and thus avoid silences. This strategy is used for instance by the IRSs of PubMed  and GoFish . However, since no distinction is made between the initial terms and those added, users may be puzzled by the set of documents retrieved. Indeed, since they are not aware their query has bee […]
GO Explorer: A gene ontology tool to aid in the interpretation of shotgun proteomics data
[…] ene is annotated with a term, it is also implicitly annotated with all (less specific) ancestors of that term.Currently, there are several GO-based tools; some examples are: DAVID , GOMiner , and GoFish . We refer the reader to for a more comprehensive listing. Even though such tools are frequently used to analyze microarray data, the ones specific for proteomics amount to very few . More […]
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