Create BridgeDb Identity Mapping files

This groovy script creates a Derby file for BridgeDb [1,2] for use in PathVisio, etc.

The script uses Rhea [3] for each new version release (~monthly), and is based on the create_bridgedb_metabolites repository

Releases

The files are released via the BridgeDb Website: https://bridgedb.github.io/data/gene_database/

The mapping files are also archived on Figshare: https://figshare.com/projects/BridgeDb_interactions/37805

License

This repository: New BSD.

Derby License -> http://db.apache.org/derby/license.html BridgeDb License -> http://www.bridgedb.org/browser/trunk/LICENSE-2.0.txt

Run the script and test the results

1. Update the createDerby.groovy file with latest metadata, e.g. ("DATASOURCEVERSION" field) and change the version of the Rhea database in this line.

2. add the jars to your classpath, e.g. on Linux with:

export CLASSPATH=`ls -1 *.jar | tr '\n' ':'`

3. download Rhea tsv mapping file

• ID mappings

Use the below curl command line operations.

cd create-bridgedb-interactions/data
curl -o mappingsrhea.tsv ftp://ftp.expasy.org/databases/rhea/tsv/rhea2xrefs.tsv

4. Run the script with Groovy:

export CLASSPATH=`ls -1 *.jar | tr '\n' ':'`
groovy createDerby.groovy

5. Test the resulting Derby file by opening it in PathVisio

6. Use the BridgeDb QC tool to compare it with the previous mapping file

The BridgeDb repository has a tool to perform quality control (qc) on ID mapping files:

sh qc.sh old.bridge new.bridge

8. Upload the data to Figshare and update the following pages:

• http://www.bridgedb.org/mapping-databases/hmdb-metabolite-mappings/ #Update link
• http://bridgedb.org/data/gene_database/ #Update link

9. Tag this repository with the DOI of the latest release.

To ensure we know exactly which repository version was used to generate a specific release, the latest commit used for that release is tagged with the DOI on Figshare. To list all current tags:

git tag

To make a new tag, run:

git tag $DOR

where $DOI is replaced with the DOI of the release.

10. Inform downstream projects

At least the following projects need to be informed about the availability of the new mapping database:

• BridgeDb webservice
• WikiPathways RDF generation team (Jenkins server)
• WikiPathways indexer (supporting the WikiPathways web service)

References

1. http://bridgedb.org/
2. Van Iersel, M. P., Pico, A. R., Kelder, T., Gao, J., Ho, I., Hanspers, K., Conklin, B. R., Evelo, C. T., Jan. 2010. The BridgeDb framework: standardized access to gene, protein and metabolite identifier mapping services. BMC bioinformatics 11 (1), 5+. http://dx.doi.org/10.1186/1471-2105-11-5
3. Vrandečić, Denny. "Wikidata: a new platform for collaborative data collection." Proceedings of the 21st International Conference on World Wide Web. ACM, 2012. https://doi.org/10.1145/2187980.2188242
4. Morgat, Anne, et al. "Updates in rhea—an expert curated resource of biochemical reactions." Nucleic acids research, 2016. https://dx.doi.org/10.1093%2Fnar%2Fgkw990