Monarch-BioCypher
This is a work in progress BioCypher adapter for the tsv files of the Monarch Initiative. It currently serves as an experimental platform for the conception of a mapping configuration and adapter structure template.
It currently relies on an experimental feature branch of a fork of the BioCypher project. The branch should get merged to the main project in the near future.
At the time being only the gene to phenotype file is mapped and the adapter retains only the lines for mice and men (taxon ids 10090 and 9606) to match the pipeline of the german center for diabetes research (see here).
The script assumes the presence of an uncompressed version of the tsv file in the data
folder (data/gene_phenotype.all.tsv). The latest version of the file can be obtained at:
https://data.monarchinitiative.org/latest/tsv/gene_associations/gene_phenotype.all.tsv.gz
The adapter (adapter.py) currently only generates neo4j-admin import-ready
files via the batch writer class (to biocypher-out or any specified location).
The process can be run using script.py. If all
goes well, the output folder will contain a neo4j-admin-import-call.sh
file which, when run in the terminal in the database folder, will create
a new database under the name specified in the db_name argument of the
BioCypherAdapter instantiation in script.py. The database does not
need to be running at this point (but it can). However, it is important
that the target database (in the current example the one named "import")
is either completely empty or does not exist yet.
After import, and in case the database in point did not exist yet, the
database can be created and activated in the Neo4j browser with :use system, create database monarch, :use monarch. At this point,
the DBMS needs to be running.
Installation
The project can be installed using poetry:
git clone https://github.com/vincentvialard/Monarch-BioCypher.git
cd Monarch-BioCypher
poetry install