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Create BridgeDb Identity Mapping files

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

The script will be tested with Wikidata [3,4] from November 2019, and is based on the create_bridgedb_metabolites repository

We're greatfull for all that worked on identifier mappings in this/these project(s):

Everyone can contribute ID mappings to Wikidata.

Releases

The files are released via the BridgeDb Website: https://www.bridgedb.org/data/gene_database/

The mapping files are also archived on Figshare: https://figshare.com/search?q=diseases+bridgedb+mapping+database&quick=1

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

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

  1. make sure the Wikidata files are saved

2.1 ID mappings

A set of SPARQL queries have been compiled and saved in the wikidata/ folder. These queries can be manually executed at http://query.wikidata.org/. These queries download mappings from Wikidata for OMIM (omim.rq), Disease Ontology (do.rq), UMLS CUI (cui.rq), Orphanet (orpha.rq), MeSH descriptor IDs (mesh.rq)-> coming soon.

However, you can also use the below curl command line operations.

curl -H "Accept: text/csv" --data-urlencode query@wikidata/omim.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o omim2wikidata.csv
curl -H "Accept: text/csv" --data-urlencode query@wikidata/do.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o do2wikidata.csv
curl -H "Accept: text/csv" --data-urlencode query@wikidata/cui.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o cui2wikidata.csv
curl -H "Accept: text/csv" --data-urlencode query@wikidata/orpha.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o orpha2wikidata.csv
curl -H "Accept: text/csv" --data-urlencode query@wikidata/mesh.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o mesh2wikidata.csv  
curl -H "Accept: text/csv" --data-urlencode query@wikidata/icd9.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o icd92wikidata.csv
curl -H "Accept: text/csv" --data-urlencode query@wikidata/icd10.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o icd102wikidata.csv
curl -H "Accept: text/csv" --data-urlencode query@wikidata/icd11.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o icd112wikidata.csv
curl -H "Accept: text/csv" --data-urlencode query@wikidata/mondo.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o mondo2wikidata.csv

4.2 Get Disease Labels

With a similar SPARQL query (names.rq) the disease labels (English only) can be downloaded as simple TSV and saved as "names2wikidata.tsv" (note that this file is TAB separated):

curl -H "Accept: text/tab-separated-values" --data-urlencode query@wikidata/names.rq -G https://query.wikidata.org/bigdata/namespace/wdq/sparql -o names2wikidata.tsv
  1. Update the createDerby.groovy file with the new version numbers ("DATASOURCEVERSION" field) and run the script with Groovy: #Update line
export CLASSPATH=`ls -1 *.jar | tr '\n' ':'`
groovy createDerby.groovy

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

  2. 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
  1. Upload the data to Figshare and update the following pages:
  1. 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.

  1. 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. Mietchen D, Hagedorn G, Willighagen E, Rico M, Gómez-Pérez A, Aibar E, Rafes K, Germain C, Dunning A, Pintscher L, Kinzler D (2015) Enabling Open Science: Wikidata for Research (Wiki4R). Research Ideas and Outcomes 1: e7573. https://doi.org/10.3897/rio.1.e7573