skm-pss-adapters

Export adapters from PSS neo4j db to other (flatfile) formats

PSS database

For testing, a snapshot of the PSS database is available at: https://github.com/NIB-SI/skm-neo4j

Connection to Neo4j settings

You can pass the connection settings (uri, username, password) to the CLI using command-line arguments:

  --neo4j-uri TEXT       Neo4j connection URI.
  --neo4j-user TEXT      Neo4j username.
  --neo4j-password TEXT  Neo4j password.

Alternatively, you can set these in an .env file in the current directory. The file should contain the following variables:

MY_NEO4J_URI=bolt://localhost:7687
MY_NEO4J_USER=neo4j
MY_NEO4J_PASSWORD=password

If you used the defaults in the skm-neo4j repo, you can use the .env.example file as provided.

mv .env.example .env

Usage

Create environment with dependencies:

mamba create -n pss-sbml conda-forge::neo4j-python-driver conda-forge::python-libsbml conda-forge::pyyaml conda-forge::click python-dotenv

If using the model fixes module, also install the following dependecies:

pip install pandas networkx rich matplotlib

SBML:

To view the CLI options:

python pss_adapter_cli.py to-sbml --help

Create the SBML file using the CLI:

python pss_adapter_cli.py to-sbml output.sbml --access public

Using the model-fixing functions:

python pss_adapter_cli.py to-sbml output-model-fixes.sbml --access public --model-fixes-identify  --model-fixes-apply

To add equations to the SBML file, you can use SBMLsqueezer from https://github.com/draeger-lab/SBMLsqueezer, e.g.

java -jar  /path..to..jar/SBMLsqueezer-2.2.jar --sbml-in-file output.sbml  --sbml-out-file output-squeezed

Known limitations and issues:

• The SBML file does not contain equations for the reactions.
  • See https://github.com/R4d0slav/ThesisRepository
  • You can add the equations using SBMLsqueezer as described above.
• Continuous updates to the PSS database means that the model may not be connected or completely consistent with modelling.
• Some molecules may be disconnected in the SBML file, for example if:
  • They occur in multiple compartments, but are not connected by a transport reaction.
  • A protein is formed by a translation reaction, but the protein is not "activated" by an "activation" reaction.
  • A complex is formed by a reaction, but the complex is not "activated" by an "activation" reaction.

TODOs

• Make a TOML file for installing from pip and a requirements file with fixed dependency version for testing