umlsmap2rdf

These python scripts take the Unified Medical Language System (UMLS) MRCONSO.RRF file and translates them into into RDF/OWL files for mapping.

Installation

You can install the development version directly from this repository with:

pip install git+https://github.com/KeironO/umlsmap2rdf --no-cache-dir

Usage

umlsmap2rdf has a really simple CLI. After installation type umlsmap2rdf --help to for help:

$ umlsmap2rdf --help
Usage: umlsmap2rdf [OPTIONS]

  --    _   _ __  __ _     ____    __  __    _    ____  ____ ___ _   _  ____
  --   | | | |  \/  | |   / ___|  |  \/  |  / \  |  _ \|  _ \_ _| \ | |/ ___|
  --   | | | | |\/| | |   \___ \  | |\/| | / _ \ | |_) | |_) | ||  \| | |  _
  --   | |_| | |  | | |___ ___) | | |  | |/ ___ \|  __/|  __/| || |\  | |_| |
  --    \___/|_|  |_|_____|____/  |_|  |_/_/   \_\_|   |_|  |___|_| \_|\____|
  --

  This python scripts collates the Unified Medical Language System (UMLS) maps
  into RDF/OWL files.

  If you have any issues, feel free to submit a bug report at:
  https://github.com/KeironO/umlsmap2rdf

      Thanks!

Options:
  --input_fp TEXT   The File Path of MRCONSO.RRF  [required]
  --output_fp TEXT  Number of greetings.  [required]
  --help            Show this message and exit.

Example Usage

To convert mapping from MRCONSO.RRF file to RDF, simply type:

umlsmap2rdf --input_fp /path/to/MRCONSO.RRF --output_fp /path/to/output.xml

Which will give you the following output:

<?xml version="1.0" encoding="utf-8"?>
<rdf:RDF
   xmlns:OWL="http://www.w3.org/2002/07/owl#"
   xmlns:RDF="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
   xmlns:RDFS="http://www.w3.org/2000/01/rdf-schema#"
   xmlns:rdf="http://www.w3.org/1999/02/22-rdf-syntax-ns#"
>
  <rdf:Description rdf:about="https://identifiers.org/umls:C0000511">
    <RDF:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>
    <OWL:sameAs rdf:resource="http://purl.bioontology.org/ontology/MESH/D015112"/>
    <OWL:sameAs rdf:resource="https://www.cancer.gov/publications/dictionaries/cancer-terms/def/CDR0000367450"/>
    <OWL:sameAs rdf:resource="https://purl.bioontology.org/ontology/NCI/C194"/>
  </rdf:Description>
  <rdf:Description rdf:about="https://identifiers.org/umls:C0000246">
    <RDF:type rdf:resource="http://www.w3.org/2002/07/owl#Class"/>

Currently supported mappings

DRUGBANK      = "http://purl.bioontology.org/ontology/DRUGBANK/"
GO            = "http://purl.obolibrary.org/obo/GO_"
HPO           = "http://purl.bioontology.org/ontology/HPO/"
ICD10         = "https://identifiers.org/icd10:"
ICD10CM       = "http://purl.bioontology.org/ontology/ICD10CM/"
ICD9CM        = "http://purl.bioontology.org/ontology/ICD9CM/"
MESH          = "http://purl.bioontology.org/ontology/MESH/"
NCBI          = "http://purl.bioontology.org/ontology/NCBITAXON/"
NCI           = "http://purl.bioontology.org/ontology/NCI/"
NCI_NCI_GLOSS = "https://www.cancer.gov/publications/dictionaries/cancer-terms/def/"
OWL           = "http://www.w3.org/2002/07/owl#"
RDF           = "http://www.w3.org/1999/02/22-rdf-syntax-ns#"
RDFS          = "http://www.w3.org/2000/01/rdf-schema#"
RDFS          = "http://www.w3.org/2000/01/rdf-schema#"
RXNORM        = "http://purl.bioontology.org/ontology/RXNORM/"
SKOS          = "http://www.w3.org/2004/02/skos/core#"
SNOMED        = "http://purl.bioontology.org/ontology/SNOMEDCT/"
UMLS          = "https://identifiers.org/umls:"
UMLS_STY      = "http://purl.bioontology.org/ontology/STY/"
WHO           = "http://purl.bioontology.org/ontology/WHO-ART/"

Bug reporting and feature suggestions

Please report all bugs or feature suggestions to the issues tracker. Please do not email me directly as I'm struggling to keep track of what needs to be fixed.

License

Code is proudly released under the terms of the MIT License.