seandavi/map_to_mesh_with_mti

Use the MTI tooling from NCBI to map UMLS and MESH terms to arbitrary text.

Run MTI in batch mode with Docker image

MTI is the main product of the Indexing Initiative project and has been providing indexing recommendations based on the Medical Subject Headings (MeSH®) vocabulary since 2002. See MTI Documentation and Home Page for details.

Build docker

docker build -t seandavi/mti_batch .
docker push seandavi/mti_batch

Running

• MTI documentation

1. Place file(s) to be analyzed into docker container with volume mount.
2. Run docker container specifying environment variables USERNAME and PASSWORD. Use your UMLS username and password here; ie., you need a UMLS account.
3. Capture stdout from container, as that will be the output

docker run -v input_dir:/data \
    -e USERNAME="UMLS_USERNAME" \
    -e PASSWORD="UMLS_PASSWORD" \
    seandavi/mti_batch [OPTIONS] inputFile

Options include:

  allowed options:
    --email <address> : set email address. (required option)
    --command <name> : batch command: metamap, semrep, etc. (default: MTI -opt1L_DCMS -E)
    --note <notes> : batch notes
    --silent : don't send email after job completes.
    --silent-errors : Silent on Errors
    --singleLineInput : Single Line Delimited Input
    --singleLinePMID : Single Line Delimited Input w/ID
    --priority : request a Run Priority Level: 0, 1, or 2