GeneCup: mining PubMed and GWAS catalog for gene-keyword relationships.

ABSTRACT: Interpreting and integrating results from omics studies typically requires a comprehensive and time consuming survey of extant literature. GeneCup is a literature mining web service that retrieves sentences containing user-provided gene symbols and keywords from PubMed abstracts. The keywords are organized into an ontology and can be extended to include results from human genome-wide association studies. We provide a drug addiction keyword ontology that contains over 300 keywords as an example. The literature search is conducted by querying the PubMed server using a programming interface, which is followed by retrieving abstracts from a local copy of the PubMed archive. The main results presented to the user are sentences where gene symbol and keywords co-occur. These sentences are present

SUBMITTER: Gunturkun MH 

PROVIDER: S-EPMC9073678 | biostudies-literature | 2022 May

REPOSITORIES: biostudies-literature