PyMeSHSim: an integrative python package for biomedical named entity recognition, normalization, and comparison of MeSH terms.

ABSTRACT:

Background

Many disease causing genes have been identified through different methods, but there have been no uniform annotations of biomedical named entity (bio-NE) of the disease phenotypes of these genes yet. Furthermore, semantic similarity comparison between two bio-NE annotations has become important for data integration or system genetics analysis.

Results

The package pyMeSHSim recognizes bio-NEs by using MetaMap which produces Unified Medical Language System (UMLS) concepts in natural language process. To map the UMLS concepts to Medical Subject Headings (MeSH), pyMeSHSim is embedded with a house-made dataset containing the main headings (MHs), supplementary concept records (SCRs), and their relations in MeSH. Based on the dataset, pyMeSHSim implemented four informati

SUBMITTER: Luo ZH 

PROVIDER: S-EPMC7301509 | biostudies-literature | 2020 Jun

REPOSITORIES: biostudies-literature