Nanopub Query is the second-generation query service for nanopublications.
You can check out Nanopub Query at these instances:
See the JavaDocs for the API and source code documentation.
Each nanopublications is loaded into different repos in the form of RDF4J triple stores. There are these general repos:
meta: Stores some specific "admin-graph metadata" of the nanopublications (see below), but not the nanopublications themselvesfull: Stores all nanopublications in full and their admin-graph metadata (this is not scalable on the long term, so will be deprecated in the medium-term future)last30d: Stores all nanopublications of the last 30 days and their admin-graph metadatatext: Stores all nanopublications for full-text searchadmin: Stores some further admin info, such as the full pubkeys for their hash valuesempty: Empty repo from which other repos can be accessed via the SPARQLservicekeyword
On top of that, there are these specific repos:
pubkey: For each public key used to sign a nanopublication, a separate repo is createdtype: For each nanopub type, a separate repo is created too
Two admin graphs (npa:graph and npa:networkGraph) are created with metadata about the nanopublications.
The admin triple table shows the details.
Get pre-packaged data (optional):
$ wget https://zenodo.org/records/14260335/files/rdf4j-20241202.tar.gz
$ tar -xzf rdf4j-20241202.tar.gz
Init directories:
$ ./init-dirs.sh
Check docker-compose.yml and make any adjustments in a new file docker-compose.override.yml.
There is a deadlock problem with RDF4J (details), which requires some specific web server configuration to work around it. Specifically, concurrent requests per repo have to be avoided, with a configuration like in this nginx example.
Start with Docker Compose:
$ sudo docker compose up -d
This software is made available under the MIT license. See LICENSE.txt for the details.
For an overview of the dependencies and their licenses, run mvn project-info-reports:dependencies and then visit target/reports/dependencies.html.