OC-2-KB: integrating crowdsourcing into an obesity and cancer knowledge base curation system

BMC Med Inform Decis Mak. 2018 Jul 23;18(Suppl 2):55. doi: 10.1186/s12911-018-0635-5.


Background: There is strong scientific evidence linking obesity and overweight to the risk of various cancers and to cancer survivorship. Nevertheless, the existing online information about the relationship between obesity and cancer is poorly organized, not evidenced-based, of poor quality, and confusing to health information consumers. A formal knowledge representation such as a Semantic Web knowledge base (KB) can help better organize and deliver quality health information. We previously presented the OC-2-KB (Obesity and Cancer to Knowledge Base), a software pipeline that can automatically build an obesity and cancer KB from scientific literature. In this work, we investigated crowdsourcing strategies to increase the number of ground truth annotations and improve the quality of the KB.

Methods: We developed a new release of the OC-2-KB system addressing key challenges in automatic KB construction. OC-2-KB automatically extracts semantic triples in the form of subject-predicate-object expressions from PubMed abstracts related to the obesity and cancer literature. The accuracy of the facts extracted from scientific literature heavily relies on both the quantity and quality of the available ground truth triples. Thus, we incorporated a crowdsourcing process to improve the quality of the KB.

Results: We conducted two rounds of crowdsourcing experiments using a new corpus with 82 obesity and cancer-related PubMed abstracts. We demonstrated that crowdsourcing is indeed a low-cost mechanism to collect labeled data from non-expert laypeople. Even though individual layperson might not offer reliable answers, the collective wisdom of the crowd is comparable to expert opinions. We also retrained the relation detection machine learning models in OC-2-KB using the crowd annotated data and evaluated the content of the curated KB with a set of competency questions. Our evaluation showed improved performance of the underlying relation detection model in comparison to the baseline OC-2-KB.

Conclusions: We presented a new version of OC-2-KB, a system that automatically builds an evidence-based obesity and cancer KB from scientific literature. Our KB construction framework integrated automatic information extraction with crowdsourcing techniques to verify the extracted knowledge. Our ultimate goal is a paradigm shift in how the general public access, read, digest, and use online health information.

Keywords: Biomedical named-entity recognition; Cancer; Crowdsourcing; Information extraction; Obesity; Relation extraction; Semantic web knowledge base.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Crowdsourcing*
  • Data Curation
  • Evidence-Based Medicine
  • Humans
  • Information Storage and Retrieval
  • Knowledge Bases*
  • Machine Learning
  • Neoplasms*
  • Obesity*
  • PubMed
  • Semantics
  • Software