Validating candidate gene-mutation relations in MEDLINE abstracts via crowdsourcing
DILS'12 Proceedings of the 8th international conference on Data Integration in the Life Sciences(2012)
摘要
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 for review. Reviewers returned results within 36 hours. Initial weighted results evaluated against a gold standard of expert curated gene-mutation relations achieved 85% accuracy, with the best reviewer achieving 91% accuracy. We expect performance to increase with further experimentation, providing a scalable approach for rapid manual curation of important biological relations.
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关键词
curated gene list,validating candidate gene-mutation relation,candidate mutation,biomedical literature,best reviewer,candidate gene-mutation relation,amazon mechanical turk hits,gene-mutation relation,correct pairings,abstract text,medline abstract
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