CoPub is a text mining tool that detects co-occuring biomedical concepts in abstracts from the Medline literature database. The biomedical concepts included in CoPub are all human, mouse and rat genes, furthermore biological processes, molecular functions and cellular components from Gene Ontology, and also liver pathologies, diseases, drugs and pathways. Altogether more than 250,000 search strings are linked with CoPub.
Special attention was given to genes and proteins. For all human, mouse and rat genes not only long forms of names were used, but also their symbols and aliases, which increases recall. Symbols not referring to genes or proteins are a well known problem, but sophisticated scripts detect these homonyms and neglect the abstracts in which they occur thereby increasing precision.
* Fast and easy access to relevant abstracts
* Single gene search in all categories
* Multiple gene search in all categories
* Single keyword search in gene category
* Categories of biomedical concepts: genes (human, mouse, rat), liver pathologies, biological processes, molecular functions, cellular components, diseases, drugs, pathways
* Use of long forms, symbols and aliases of genes
* Homonym detection
* Statistical filter to display only significant biomedical concepts
* Based on Medline abstracts till February 2008