Validating Candidate Gene-Mutation Relations in MEDLINE Abstracts via CrowdsourcingMarch 2012
Topics: Diseases, Genetics, Informatics
We describe an experiment to elicit judgments on the validity of gene-mutation relations in MEDLINE abstracts via crowdsourcing. The biomedical literature contains rich information on such relations, but the correct pairings are difficult to extract automatically because a single abstract may mention multiple genes and mutations. We ran an experiment presenting candidate gene-mutation relations as Amazon Mechanical Turk "HITs" (human intelligence tasks). We extracted candidate mutations from a corpus of 250 MEDLINE abstracts using EMU combined with curated gene lists from NCBI . The resulting document-level annotations were "projected" into the abstract text to highlight mentions of genes and mutations. Turkers returned results within 30 hours. We evaluated the aggregated weighted results against a gold standard of expert curated gene-mutation relations. Weighted accuracy was 82%, with the best Turker achieving over 95% accuracy. The experiment demonstrates feasibility of attracting proficient annotators and the success of the interface in facilitating these judgments.