Mining PubMed for Gene Relationships using Custom Ontologies

GeneCup is a tool to answer the question "What do we know about these genes and the topic I study?". GeneCup answers this question by searching PubMed to find sentences containing gene symbols and a custom list of keywords. Human GWAS findings from NHGRI-EBI GWAS catalog are also included in the search. These gene-keyword relationships are presented as a graph or a table. Here we present a curated ontology for drug addiction with over 300 keywords organized into seven categories. Deep learning is used to distinguish, for example, the sentences describing systemic stress from those describing cellular stress. A user account (free) is needed to create custom ontologies and save the search results. We do not track you.

Example: Rgma Penk.

By default, the addiction ontology is used. Custom ontologies can be created in user accounts.
Up to 200 gene symbols can be entered in the box above. Because we do not search for relationships between genes, a list with more items can be split into multiple searches without affecting the results. Gene symbols can be separated by a space, a comma or a semicolon.