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aiSee: Gene Symbol Disambiguation Graphs
Disambiguation graphs as generated by GeneIlluminator, an easy-to-use Web-based tool for disambiguation of gene nomenclature in PubMed abstracts. Images courtesy of François B. Alako, Wageningen University.
GeneIlluminator assigns biological functions to a gene symbol and
its alternative names. If a symbol is ambiguous, GeneIlluminator creates clusters
describing in which part of the tree of life a gene symbol unambiguously points
to the same gene.
When given a species in addition to a gene symbol, GeneIlluminator uses naïve Bayesian classification to predict which cluster this gene belongs to for the given species.
Hence GeneIlluminator can be used to enrich query terms unambiguously and effectively for searching the literature, starting solely with a gene symbol and optionally a species of interest.
GeneIlluminator relies on aiSee for visualization of disambiguation graphs.
aiSee has been a great asset at displaying the ambiguity flow across species kingdoms.
François B. Alako, Wageningen University
- See also
- Graph-based analysis of gene expression experiments
- Chilibot — mining PubMed for gene/protein/keyword relationships
- PubNet — Publication Network graph utility
- Apropos — database and annotation tool
- GenDB — genome annotation system
- DIMA — domain interaction map