A software toolkit for the interconversion of standard data models for phenotypic data
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**Documentation**: https://cnag-biomedical-informatics.github.io/convert-pheno
**CLI Source Code**: https://github.com/cnag-biomedical-informatics/convert-pheno
**Web APP Playground**: https://convert-pheno.cnag.cat
**Web App Source Code**: https://github.com/cnag-biomedical-informatics/convert-pheno-ui
# NAME
convert-pheno - A script to interconvert common data models for phenotypic data
# SYNOPSIS
convert-pheno \[-i input-type\] <infile> \[-o output-type\] <outfile> \[-options\]
Arguments:
(input-type):
-ibff Beacon v2 Models ("individuals" JSON|YAML) file
-iomop OMOP-CDM CSV files or PostgreSQL dump
-ipxf Phenopacket v2 (JSON|YAML) file
-iredcap (experimental) REDCap (raw data) export CSV file
-icdisc (experimental) CDISC-ODM v1 XML file
(Wish-list)
#-openehr openEHR
#-ifhir HL7/FHIR
(output-type):
-obff Beacon v2 Models ("invididuals" JSON|YAML) file
-opxf Phenopacket v2 (JSON|YAML) file
(Wish-list)
#-oomop OMOP-CDM PostgreSQL dump
Options:
-exposures-file CSV file with a list of 'concept_id' considered to be exposures (with -iomop)
-mapping-file Fields mapping YAML (or JSON) file
-max-lines-sql Maximum number of lines read from SQL dump [500]
-min-text-similarity-score Minimum score for cosine similarity (or Sorensen-Dice coefficient) [0.8] (to be used with --search mixed)
-ohdsi-db Use Athena-OHDSI database (~2.2GB) with -iomop
-omop-tables (Only valid with -iomop) OMOP-CDM tables to be processed. Tables and are always included.
-out-dir Output (existing) directory
-O Overwrite output file
-path-to-ohdsi-db Directory for the file
-phl|print-hidden-labels Print original values (before DB mapping) of text fields <_labels>
-rcd|redcap-dictionary REDCap data dictionary CSV file
-schema-file Alternative JSON Schema for mapping file
-search Type of search [>exact|mixed]
-svs|self-validate-schema Perform a self-validation of the JSON schema that defines mapping
-sep|separator Delimiter character for CSV files [;] e.g., --sep $'\t'
-stream Enable incremental processing with -iomop and -obff [>no-stream|stream]
-sql2csv Print SQL TABLES (only valid with -iomop). Mutually exclusive with --stream
-test Does not print time-changing-events (useful for file-based cmp)
-text-similarity-method The method used to compare values to DB [>cosine|dice]
-u|username Set the username
Generic Options:
-debug Print debugging level (from 1 to 5, being 5 max)
-h|help Brief help message
-log Save log file (JSON). If no argument is given then the log is named [convert-pheno-log.json]
-man Full documentation
-no-color Don't print colors to STDOUT [>color|no-color]
-v|verbose Verbosity on
-V|version Print Version
# DESCRIPTION
`convert-pheno` is a command-line front-end to the CPAN's module [Convert::Pheno](https://metacpan.org/pod/Convert%3A%3APheno).
The module will be uploaded to CPAN once the paper is submitted.
# SUMMARY
A script that uses [Convert::Pheno](https://metacpan.org/pod/Convert%3A%3APheno) to interconvert common data models for phenotypic data
# INSTALLATION
## Containerized
### Method 1: From Docker Hub
Download a docker image (latest version) from [Docker Hub](https://hub.docker.com/r/manuelrueda/convert-pheno) by executing:
docker pull manuelrueda/convert-pheno:latest
docker image tag manuelrueda/convert-pheno:latest cnag/convert-pheno:latest
See additional instructions below.
### Method 2: With Dockerfile
Please download the `Dockerfile` from the repo:
wget https://raw.githubusercontent.com/cnag-biomedical-informatics/convert-pheno/main/Dockerfile
And then run:
docker build -t cnag/convert-pheno:latest .
### Additional instructions for Methods 1 and 2
To run the container (detached) execute:
docker run -tid --name convert-pheno cnag/convert-pheno:latest
To enter:
docker exec -ti convert-pheno bash
The command-line executable can be found at:
/usr/share/convert-pheno/bin/convert-pheno
The default container user is `root` but you can also run the container as `$UID=1000` (`dockeruser`).
docker run --user 1000 -tid --name convert-pheno cnag/convert-pheno:latest
Alternatively, you can use `make` to perform all the previous steps:
wget https://raw.githubusercontent.com/cnag-biomedical-informatics/convert-pheno/main/Dockerfile
wget https://raw.githubusercontent.com/cnag-biomedical-informatics/convert-pheno/main/makefile.docker
make -f makefile.docker install
make -f makefile.docker run
make -f makefile.docker enter
### Mounting volumes
Docker containers are fully isolated. If you need the mount a volume to the container please use the following syntax (`-v host:container`).
Find an example below (note that you need to change the paths to match yours):
docker run -tid --volume /media/mrueda/4TBT/data:/data --name convert-pheno-mount cnag/convert-pheno:latest
Then I will do something like this:
# First I create an alias to simplify invocation (from the host)
alias convert-pheno='docker exec -ti convert-pheno-mount /usr/share/convert-pheno/bin/convert-pheno'
# Now I use the alias to run the command (note that I use the flag --out-dir to specify the output directory)
convert-pheno -ibff /data/individuals.json -opxf pxf.json --out-dir /data
## Non containerized
The script runs on command-line Linux and it has been tested on Debian/RedHat based distributions (only showing commands for Debian's). Perl 5 is installed by default on Linux,
but we will install a few CPAN modules with `cpanminus`.
git clone https://github.com/cnag-biomedical-informatics/convert-pheno.git
cd convert-pheno
Now you have two choose between one of the 2 options below:
**Option 1:** Install dependencies (they're harmless to your system) as `sudo`:
make install # (Will ask for sudo passwd)
make test
**Option 2:** Install the dependencies in a "virtual environment" (i.e., install the CPAN modules in the directory of the application). We'll be using the module`Carton` for that:
# NB: We're installing cpanminus and Carton as sudo. That's why you will be asked to provide sudo password.
make install-carton
make test
### System requirements
* Ideally a Debian-based distribution (Ubuntu or Mint), but any other (e.g., CentOs, OpenSuse) should do as well.
* Perl 5 (>= 5.10 core; installed by default in most Linux distributions). Check the version with "perl -v".
* >= 4GB of RAM
* 1 core
* At least 16GB HDD
# HOW TO RUN CONVERT-PHENO
For executing convert-pheno you will need:
- Input file(s):
A text file in one of the accepted formats. With `--iomop` I/O files can be gzipped.
- Optional:
Athena-OHDSI database
The database file is available at this [link](https://drive.google.com/drive/folders/104_Bgl3IxM3U6u-wn-1LUvNZXevD2DRm?usp=sharing) (~2.2GB). The database may be needed when using `-iomop`.
Regardless if you're using the containerized or non-containerized version, the download procedure is the same. In Linux you can use `wget`, `curl` or `aria2c`:
$ wget 'https://drive.google.com/uc?export=download&id=104ciON3zRc3ScAzzrL_3GO14aCnBLh-c&confirm=t' -O ohdsi.db
or
$ curl -L 'https://drive.google.com/uc?export=download&id104ciON3zRc3ScAzzrL_3GO14aCnBLh-c' > ohdsi.db
or
$ aria2c -x2 'https://drive.google.com/uc?export=download&id=104ciON3zRc3ScAzzrL_3GO14aCnBLh-c&confirm=t' -o ohdsi.db
(you can install `wget`, `curl` or `aria2c` inside the container by typing `sudo apt install wget`, `sudo apt install curl` or `sudo apt install aria2`.
Once downloaded, you have two options:
a) Move the file `ohdsi.db` inside the `db/` directory.
or
b) Use the option `--path-to-ohdsi-db`
**Examples:**
$ bin/convert-pheno -ipxf phenopackets.json -obff individuals.json
$ $path/convert-pheno -ibff individuals.json -opxf phenopackets.yaml --out-dir my_out_dir
$ $path/convert-pheno -iredcap redcap.csv -opxf phenopackets.json --redcap-dictionary redcap_dict.csv --mapping-file mapping_file.yaml
$ $path/convert-pheno -iomop dump.sql -obff individuals.json
$ $path/convert-pheno -iomop dump.sql.gz -obff individuals.json.gz --stream -omop-tables measurement -verbose
$ $path/convert-pheno -cdisc cdisc_odm.xml -obff individuals.json --rcd redcap_dict.csv --mapping-file mapping_file.yaml --search mixed --min-text-similarity-score 0.6
$ $path/convert-pheno -iomop *csv -obff individuals.json -sep ','
$ carton exec -- $path/convert-pheno -ibff individuals.json -opxf phenopackets.json # If using Carton
## COMMON ERRORS AND SOLUTIONS
* Error message: CSV_XS ERROR: 2023 - EIQ - QUO character not allowed @ rec 1 pos 21 field 1
Solution: Make sure you use the right character separator for your data. The script tries to guess it from the file extension (e.g. comma for csv), but sometimes extension and actual separator do not match.
Example for tab separator in CLI.
--sep $'\t'
* Error message: Foo
Solution: Bar
# CITATION
The author requests that any published work that utilizes `Convert-Pheno` includes a cite to the the following reference:
Rueda, M et al., (2023). Convert-Pheno: A software toolkit for the interconversion of standard data models for phenotypic data \[Software\]. Available from https://github.com/cnag-biomedical-informatics/convert-pheno
# AUTHOR
Written by Manuel Rueda, PhD. Info about CNAG can be found at [https://www.cnag.crg.eu](https://www.cnag.crg.eu).
# COPYRIGHT AND LICENSE
Copyright (C) 2022-2023, Manuel Rueda - CNAG.
This program is free software, you can redistribute it and/or modify it under the terms of the [Artistic License version 2.0](https://metacpan.org/pod/perlartistic).