These tools will no longer be maintained as of December 31, 2024. Archived webpage can be found here. Indexing Initiative Github repository under development. Contact NLM Customer Service if you have questions.

TOOLS

SemRep

SemRep is a UMLS-based program that extracts three-part propositions, called semantic predications, from sentences in biomedical text. Predications consist of a subject argument, an object argument, and the relation that binds them. For example, from the sentence in (1), SemRep extracts the predications in (2).

  1. We used hemofiltration to treat a patient with digoxin overdose that was complicated by refractory hyperkalemia.
  2. Hemofiltration-TREATS-Patients
    Digoxin overdose-PROCESS_OF-Patients
    hyperkalemia-COMPLICATES-Digoxin overdose
    Hemofiltration-TREATS(INFER)-Digoxin overdose
The subject and object arguments of each predication are concepts from the UMLS Metathesaurus and their binding relationship (in uppercase) is a relation from the UMLS Semantic Network. For a detailed description of SemRep, see [1,2].

Holders of a UMLS license can run SemRep interactively or in batch mode using the SKR Scheduler. SemRep is also available as a stand-alone program on the Linux platform.

References

  1. Kilicoglu H, Rosemblat G, Fiszman M, Shin D. Broad-coverage biomedical relation extraction with SemRep. BMC Bioinformatics 2020;21:1-28.
  2. Rindflesch, T.C. and Fiszman, M. (2003). The interaction of domain knowledge and linguistic structure in natural language processing: interpreting hypernymic propositions in biomedical text. Journal of Biomedical Informatics, 36(6):462-477.