biothings/semmeddb

SemMedDB Predication Parser

Source Data Files

There are four files required by this parser:

1. semmedVER43_2022_R_PREDICATION.csv.gz, the PREDICATION CSV file
   • Version: 43
   • Download page (UMLS login required)
2. SemanticTypes_2018AB.txt, the Semantic Type Mappings file
   • Version: 2018AB
   • Download page
3. MRCUI.RRF, the Retired CUI Mapping file
   • Version: 2022AA
   • Download page: this file is part of the 2022AA UMLS Metathesaurus Full Subset (UMLS login required); no direct download link is available.
   • Description page
4. UMLS_CUI_Semtype.tsv, the Preferred CUI Names & Semtypes file.
   • Github Repo: https://github.com/erikyao/UMLS_CUI_Semtype
   • How to Generate:
     • Source data files:
       1. MRCUI.RRF (see above)
       2. MRCONSO.RRF, the Concept Names and Sources file
          • Version: 2022AA
          • Download page (UMLS login required)
          • Description page
       3. MRSTY.RRF, the Semantic Types file
          • Version: 2022AA
          • Download page: this file is part of the 2022AA UMLS Metathesaurus Full Subset (UMLS login required); no direct download link is available.
          • Description page
       4. SemanticTypes_2018AB.txt (see above)
     • Script: parser.py
       • Filename is as hardcoded here.