Assigning factuality values to semantic relations extracted from biomedical research literature

Halil Kilicoglu, Graciela Rosemblat, Thomas C. Rindflesch

Research output: Contribution to journalArticlepeer-review


Biomedical knowledge claims are often expressed as hypotheses, speculations, or opinions, rather than explicit facts (propositions). Much biomedical text mining has focused on extracting propositions from biomedical literature. One such system is SemRep, which extracts propositional content in the form of subject-predicate-object triples called predications. In this study, we investigated the feasibility of assessing the factuality level of SemRep predications to provide more nuanced distinctions between predications for downstream applications. We annotated semantic predications extracted from 500 PubMed abstracts with seven factuality values (FACT, PROBABLE, POSSIBLE, DOUBTFUL, COUNTERFACT, UNCOMMITTED, and CONDITIONAL). We extended a rule-based, compositional approach that uses lexical and syntactic information to predict factuality levels. We compared this approach to a supervised machine learning method that uses a rich feature set based on the annotated corpus. Our results indicate that the compositional approach is more effective than the machine learning method in recognizing the factuality values of predications. The annotated corpus as well as the source code and binaries for factuality assignment are publicly available. We will also incorporate the results of the better performing compositional approach into SemMedDB, a PubMed-scale repository of semantic predications extracted using SemRep.

Original languageEnglish (US)
Article numbere0179926
JournalPloS one
Issue number7
StatePublished - Jul 2017
Externally publishedYes

ASJC Scopus subject areas

  • General Biochemistry, Genetics and Molecular Biology
  • General Agricultural and Biological Sciences


Dive into the research topics of 'Assigning factuality values to semantic relations extracted from biomedical research literature'. Together they form a unique fingerprint.

Cite this