A docker image containing UMLS MetaMap and CrossMap between CUIs and SNOMED CT.
Sign up for an UMLS account (https://uts.nlm.nih.gov/home.html).
Then download the following files from UMLS/MetaMap Site and put them into context/data
MRCONSO.RRF (https://www.nlm.nih.gov/research/umls/licensedcontent/umlsknowledgesources.html)
public_mm_linux_main_2018.tar.bz2 (https://metamap.nlm.nih.gov/download/public_mm_linux_main_2018.tar.bz2)
public_mm_data_usabase_2018aa_base.tar.bz2 (https://metamap.nlm.nih.gov/download/DataSets/public_mm_data_base_2018ab_base.tar.bz2)
public_mm_data_dblexicon_2018.tar.bz2 (https://metamap.nlm.nih.gov/download/DataSets/public_mm_data_dblexicon_2018.tar.bz2)
public_mm_data_usabase_2018aa_relaxed.tar.bz2 (https://metamap.nlm.nih.gov/download/DataSets/public_mm_data_base_2018ab_relaxed.tar.bz2)
Execute the following commands:
docker build --tag metamap .
docker create -p 80:80 metamap
To run the container use
docker start metamap
Now you can visit localhost:80 to get started.
If using the service from a program, use post requests, e.g. with curl
curl -d "data=HIV" -X POST http://localhost:80/metamap
curl -d "data=C0022885" -X POST http://localhost:80/crosswalk
You can alse provide options using the options field.
- /root/bin - contains the tools
- /opt/public_mm - contains metamap installation
- /opt/MRCONSO.RRF - location of the mapping file
- MRCONSO: the location of the MRCONSO.RRF file.