mgend-rdf

Usage

USAGE:
    mgend-rdf [FLAGS] <input> --assembly <assembly> --directory <directory> --format <format> --hgnc <hgnc>

FLAGS:
    -h, --help         Prints help information
        --rehearsal    Process only one line
    -V, --version      Prints version information

OPTIONS:
        --assembly <assembly>      Assembly [possible values: GRCh37, GRCh38]
        --directory <directory>    Path to output directory
        --format <format>          Output format [possible values: jsonld, turtle]
        --hgnc <hgnc>              Path to hgnc_complete_set.txt (wget
                                   ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt)

ARGS:
    <input>    Path to input file [*.tsv | *.tsv.gz]

1. Obtain hgnc_complete_set.txt

   $ wget ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt
   

2. Run converter

   $ mgend-rdf --assembly GRCh38 --format turtle --hgnc hgnc_complete_set.txt --directory output MGeND_hg38.tsv.gz
   

Usage (Docker version)

NOTE

• The data file location used by the container should be placed in ./data/ and accessed in the container by the path /data/.
• If you have an old version of the docker engine ($ docker version < 1.27.0), install docker-compose and use the docker-compose command instead of the docker compose command.

STEPS

1. Build container (at the first time or at the time of source code modification)

$ git clone https://github.com/med2rdf/mgend.git
$ cd mgend
$ docker compose build --no-cache
// output help
$ docker compose run --rm rust-app mgend-rdf --help

2. Obtain hgnc_complete_set.txt and save it in ./data/ directory

$ curl -o ./data/hgnc_complete_set.txt https://storage.googleapis.com/public-download-files/hgnc/tsv/tsv/hgnc_complete_set.txt

3. Copy input file to ./data/ directory

$ cp -a /your/path/MGeND_hg38.tsv.gz ./data/MGeND_hg38.tsv.gz

4. Run converter

$ docker compose run --rm rust-app mgend-rdf --assembly GRCh38 --format turtle --hgnc /data/hgnc_complete_set.txt --directory /data/output /data/MGeND_hg38.tsv.gz
// check the output files
$ ls ./data/output
mgend_variant.ttl.gz   mgend_case.ttl.gz   mgend_disease.ttl.gz   mgend_gene.ttl.gz  mgend_submission.ttl.gz

From this point onward, the instructions describe how to convert files (ttl to nt format) to remove backslashes from the local part of RDF URIs during loading.
This step is not necessarily required if you are not using Virtuoso as the database for loading RDF.

5. Extract .gz files

$ gunzip data/output/*.gz

7. Convert from ttl to nt format

$ docker compose run --rm raptor rapper -i turtle -o ntriples /data/output/mgend_case.ttl > ./data/output/mgend_case.nt 2> ./data/output/mgend_ttl2nt_convert.log
$ docker compose run --rm raptor rapper -i turtle -o ntriples /data/output/mgend_disease.ttl > ./data/output/mgend_disease.nt 2>> ./data/output/mgend_ttl2nt_convert.log
$ docker compose run --rm raptor rapper -i turtle -o ntriples /data/output/mgend_gene.ttl > ./data/output/mgend_gene.nt 2>> ./data/output/mgend_ttl2nt_convert.log
$ docker compose run --rm raptor rapper -i turtle -o ntriples /data/output/mgend_submission.ttl > ./data/output/mgend_submission.nt 2>> ./data/output/mgend_ttl2nt_convert.log
$ docker compose run --rm raptor rapper -i turtle -o ntriples /data/output/mgend_variant.ttl > ./data/output/mgend_variant.nt 2>> ./data/output/mgend_ttl2nt_convert.log
// check error
$ grep -i "Error" ./data/output/mgend_ttl2nt_convert.log

Schema

How to build

Prerequisites

• rustup

$ git clone https://github.com/med2rdf/mgend.git
$ cargo build --release
$ ./target/release/mgend-rdf --help