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# Linked Data Browser at Knetminer/Data | ||
# Knetminer/Lodestar, Linked Data Browser at Knetminer/Data | ||
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*This branch is to manage a LODEStar version of [Knetminer Data Site](https://knetminer.org/data). You find more explanations on that web site. The original LODEStar text follows below.* | ||
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# Lodestar | ||
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Lodestar is a Linked Data Browser and SPARQL endpoint. Lodestar is a Java based web app that can wrap any existing SPARQL endpoint to provide a set of additional SPARQL and Linked Data services. Lodestar was developed to provide a consistent set of SPARQL and Linked Data services across the European Bioinformatics Institute (EBI). Some of the service provided by Lodestar: | ||
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* Javascript based SPARQL endpoint with configurable example queries and paginated results table | ||
* Read only SPARQL endpoint for protection from write operations | ||
* A single SPARQL endpoint that provides a UI, the service and a SPARQL 1.1 service description | ||
* SPARQL syntax highlighting provided by CodeMirror | ||
* Works with any SPARQL endpoint (Includes Virtuoso JDBC connection option) | ||
* Linked data browser for navigating data from a SPARQL endpoint | ||
* Configurable resource description/linked data pages: | ||
* Renders resources by label where possible | ||
* Grouping of related resource by type | ||
* Set top facts to display, such as labels and descriptions | ||
* Configurable limits for how many related resources to render in the browser | ||
* Renders depictions of resources | ||
* Handles content negotiation for both SPARQL queries and linked data pages | ||
* CORS enabled for cross domain scripting | ||
* Basic REST API for accessing data in simplified JSON format | ||
- Javascript based SPARQL endpoint with configurable example queries and paginated results table | ||
- Read only SPARQL endpoint for protection from write operations | ||
- A single SPARQL endpoint that provides a UI, the service and a SPARQL 1.1 service description | ||
- SPARQL syntax highlighting provided by CodeMirror | ||
- Works with any SPARQL endpoint (Includes Virtuoso JDBC connection option) | ||
- Linked data browser for navigating data from a SPARQL endpoint | ||
- Configurable resource description/linked data pages: | ||
- Renders resources by label where possible | ||
- Grouping of related resource by type | ||
- Set top facts to display, such as labels and descriptions | ||
- Configurable limits for how many related resources to render in the browser | ||
- Renders depictions of resources | ||
- Handles content negotiation for both SPARQL queries and linked data pages | ||
- CORS enabled for cross domain scripting | ||
- Basic REST API for accessing data in simplified JSON format | ||
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To see a demonstration of the Lodestar linked data browser please see the [Expression Atlas RDF website](http://www.ebi.ac.uk/rdf/services/atlas/sparql). Lodestar has been primarily developed as an internal tool for EBI services deploying RDF, however, the application should be sufficiently generic that others can use it. I can't guarantee any support for the software at this time, but please feel free to use it or adapt for your own purposes and let me know how you get on. | ||
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Documentation and stable release at http://ebispot.github.io/lodestar/. | ||
Documentation and stable release at [http://ebispot.github.io/lodestar/](http://ebispot.github.io/lodestar/). | ||
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## Release Notes | ||
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See the [revision history file](revision-history.md). | ||
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## Testing the Knetminer branch locally | ||
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To test locally, ensure you are on the `knetminer-httpsparql` branch. Follow the steps below: | ||
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1. Clone the repository (or checkout knetminer-httpsparql): | ||
`git clone -b knetminer-httpsparql https://github.com/Rothamsted/knetminer-lodestar` | ||
2. Navigate to the test-utils directory: | ||
`cd knetminer-lodestar/test-utils` | ||
3. Run the build script: | ||
`./build-n-run-test.sh` | ||
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After the build is successful, you can access the application at localhost:8080. Here are the sites to check: | ||
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- http://localhost:8080/ | ||
- http://localhost:8080/sparql | ||
- http://localhost:8080/describe | ||
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As it is common, the describe endpoint shows a subject-centric description of a resource, given its URI. For example: | ||
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- http://localhost:8080/describe?uri=http%3A%2F%2Fknetminer.org%2Fdata%2Frdf%2Fresources%2Fpublication_23105158 | ||
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Links like this are created in the SPARQL query results, when your query returns a URI. | ||
For instance, try [one of the GXA examples][GXA-EX-1], and then click links under the 'gene' or 'study' column. | ||
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[GXA-EX-1]: http://localhost:8080/sparql?query=PREFIX+bk%3A+%3Chttp%3A%2F%2Fknetminer.org%2Fdata%2Frdf%2Fterms%2Fbiokno%2F%3E%09PREFIX+bkr%3A+%3Chttp%3A%2F%2Fknetminer.org%2Fdata%2Frdf%2Fresources%2F%3E%0D%0APREFIX+bka%3A+%3Chttp%3A%2F%2Fknetminer.org%2Fdata%2Frdf%2Fterms%2Fbiokno%2Fattributes%2F%3E%09PREFIX+bkg%3A+%3Chttp%3A%2F%2Fknetminer.org%2Fdata%2Frdf%2Fresources%2Fgraphs%2F%3E%0D%0APREFIX+rdf%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F1999%2F02%2F22-rdf-syntax-ns%23%3E%09PREFIX+rdfs%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2000%2F01%2Frdf-schema%23%3E%0D%0APREFIX+owl%3A+%3Chttp%3A%2F%2Fwww.w3.org%2F2002%2F07%2Fowl%23%3E%09PREFIX+dc%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Felements%2F1.1%2F%3E%0D%0APREFIX+dcterms%3A+%3Chttp%3A%2F%2Fpurl.org%2Fdc%2Fterms%2F%3E%09PREFIX+agri%3A+%3Chttp%3A%2F%2Fagrischemas.org%2F%3E%0D%0APREFIX+bioschema%3A+%3Chttp%3A%2F%2Fbioschemas.org%2F%3E%09PREFIX+schema%3A+%3Chttp%3A%2F%2Fschema.org%2F%3E%0D%0A%0D%0A%0D%0ASELECT+%3Fgene+%3FgeneAcc+%3FcondLabel+%3FstudyTitle+%3Fstudy+%3Fpub+%3FpubTitle+%3FpubYear+%3FcondTerm+%0D%0A%7B%0D%0A%09%3Fgene+a+bk%3AGene%3B%0D%0A%09%09dcterms%3Aidentifier+%3FgeneAcc.%0D%0A%09%09%0D%0A%09%3Fgene+bioschema%3AexpressedIn+%3Fcondition.%0D%0A%09%09%0D%0A%09%3FexpStatement+a+rdfs%3AStatement%3B%0D%0A%09%09rdf%3Asubject+%3Fgene%3B%0D%0A%09%09rdf%3Apredicate+bioschema%3AexpressedIn%3B%0D%0A%09%09rdf%3Aobject+%3Fcondition%3B%0D%0A%09%09agri%3Aevidence+%3Fstudy.%0D%0A%0D%0A%09%3Fgene+bk%3Aocc_in+%3Fpub.%0D%0A%09%09%0D%0A%09%3Fpub+a+bk%3APublication%3B%0D%0A%09%09bka%3AAbstractHeader+%3FpubTitle.%0D%0A%09OPTIONAL+%7B+%3Fpub+bka%3AYEAR+%3FpubYear+%7D%0D%0A%09%09%09%0D%0A%09%3Fcondition+schema%3Aname+%3FcondLabel.%0D%0A%09OPTIONAL+%7B+%3Fcondition+dc%3Atype+%3FcondTerm.+%7D%0D%0A%09%09%0D%0A%09%3Fstudy+%0D%0A%09%09dc%3Atitle+%3FstudyTitle%3B%0D%0A%7D%0D%0AORDER+BY+%3Fstudy+%3Fgene%0D%0A&render=HTML&limit=25&offset=0#loadstar-results-section | ||
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