SPARQL endpoint over STRING database Web APIs and its related ontology.
To set up the SPARQL endpoint please first deploy the SPARQL micro-service (SPARQL-MS), instructions are available in SPARQL-MS git repository. For an ease deployment, we recommend the SPARQL-MS docker container setup. Then, if a folder services does not exist, copy the folder services in this git repository into the SPARQL-MS directory where you have run docker-compose, else just copy stringdb folder into the existing services directory. The stringdb folder contains configuration files, mostly access details to the STRING Web API functions and mappings (i.e. SPARQL construct queries) to populate the ontology.
For a quick test of the deployed SPARQL-MS endpoints, run the shell script test_sparqlms_stringdb.sh. Please change the variable server_sparqlms=http://localhost, if the SPARQL-MS is deployed in a URL different from localhost. A report cotaining the test results is generated and saved (i.e. test_output.log) in the current directory of the script execution.
A performace evaluation was done with several queries that are fully described in query_evaluation.
The ontology used to structure the STRING database Web API responses are fully described and available in STRING DB ontology documentation.
The official persitent URL of this ontology is http://purl.org/stringdb .
The files in this repository are under CC0 1.0 Universal. However, note that terms that are not prefixed with http://purl.org/stringdb# at the STRING database Web API ontology may be subject to another license, please refer to the original ontology of the term for further license details (often metioned within the "Is defined by" subsection / property).
Tarcisio Mendes de Farias, Christophe Dessimoz, Aaron Ayllon Benitez, Chen Yang, Jiao Long, & Ana-Claudia Sima. (2022, August 2). Federating and querying heterogeneous and distributed Web APIs and triple stores. In proceedings of ISMB 2022 Bio-ontologies COSI, 2022. https://doi.org/10.5281/zenodo.6952236