SARS-CoV-2-WikiPathways

Temporary repository of RDF of selected pathways from WikiPathways, supporting the Wikidata bot. If you like this work and want to cite it, for now, please cite this paper. If you use specific pathways, please cite that pathway according to the guidelines.

The following steps can be taken to update the content of this repository.

Step 1: Update the GPML files

make fetch

Step 2: Update the author information

This is currently a manual step. Check all pathways and see if the authors are updated, and update or create the appropriate files in the authors/ folder. Even the order of the authors can have changed.

Step 3: Make sure to have the BridgeDb ID mapping databases

To download the BridgeDb identifier mapping files, download them from here and save them in the /path/to/where/the/bridge/files/are folder, mathching what you entered in the config.properties file above with the bridgefiles= parameter. You also want to download the identifier mapping database for coronavirus genes and proteins.

Step 4: Create the RDF (Turtle)

The Turtle in the wp/Human folder is created with WPRDF from the SARS-CoV-2-WikiPathways branch. The RDF is generated with the following command:

make

If wished, the Turtle can be validated using the method proposed in this Open PHACTS specification:

find wp -name "*ttl" | xargs cat | rapper -i turtle -t -q - . > /dev/null

Step 5: Update the SBML

make sbml
make svg

Step 6: Run the validation and create the reports

make check

Step 7: Update the JSON/SVG for Wikidata (automatic)

The JSON/SVG used on Scholia needs updating. A hook on this repository has been put in place and each time a commit is made, the JSON and SVG needed by Scholia are automatically updated. Thanks to Anders!

Step 8: Summary statistics (optional)

If you have the Debian/Ubuntu rasqal-utils package installed, you can run the following queries to get some statistics:

cat wp/Human/WP*.ttl > all.ttl
echo "## Reactions"
roqet sparql/reactions.rq -D all.ttl > /dev/null
echo "## Publications"
roqet sparql/publications.rq -D all.ttl > /dev/null
echo "## Genes"
roqet sparql/genes.rq -D all.ttl > /dev/null
echo "## Proteins"
roqet sparql/proteins.rq -D all.ttl > /dev/null
echo "## Metabolites"
roqet sparql/metabolites.rq -D all.ttl > /dev/null
echo "## DataNodes"
roqet sparql/datanodes.rq -D all.ttl > /dev/null
rm all.ttl

Step 9: run the Wikidata bot (optional)

Before you attempt to run the bot, make sure all publications are in Wikidata and with statements to list their PubMed identifiers.

The bot is an adaption of the WikiPathways bot in the github.com/SuLab/scheduled-bots/ repository. You need, however, the sars-cov-2-wikipathways-2 branch:

git clone https://github.com/SuLab/scheduled-bots.git
cd scheduled-bots
git checkout -b sars-cov-2-wikipathways-2

In the scheduled_bots/wikipathways folder in that repository you will find the bot:

python3 bot.py