ABRoad-KG-store (demo)

Setting up the KG

Docker image

Pull the image

docker pull openlink/virtuoso-opensource-7

Download the demo data

You can find the demo data at link. The directory contains all the triples and loading files to mount the Virtuoso triple-store.

Save the data into a directory like /path/to/data/dir This directory should contain the sub-directory import containing the data and the loading files, like:

/path/to/data/dir

├── import
│   ├── vocabularies
│   │   ├── abroad.owl
│   │   ├── chebi_lite.owl
│   │   ├── cheminf.owl
│   │   ChunkNPR
│   │   │   supp-test-hits
│   │   │   ├── chunks_re.ttl.gz
│   │   │   ├── void.ttl
│   │   Chemical-activity-evidences
│   │   │   supp-test-hits
│   │   │   ├── activity_evidence.ttl.gz
│   │   │   ├── void.ttl
│   ├── load_voc.sh
│   ├── settings.sh
│   ├── upload_Resource-1_version-X1.sh
│   ├── upload_Resource-2_version-X2.sh
│   ├── ...
│   ├── update.sh

Mount the Virutoso triple-store

To mount the Virtuoso triple-store, please use the following bash command:

-d indicates the path to the directory containing the data downloaded before. -c: start to mount the triple-store and clean to unmount the triple-store. After -c, when using start all loading files are presented sequentially. Note that settings.sh and load_voc.sh should be on top the list, and, update.sh at the end.

bash workflow/w_virtuoso.sh -d  /path/to/data/dir/ \
    -c start settings.sh load_voc.sh upload_PubMed_supp-test-hits.sh upload_LOTUS_2023-01-06.sh upload_TiabFetchedDocumentDiscusses_supp-test-hits.sh upload_TiabNPR_supp-test-hits.sh upload_ChunkNPR_supp-test-hits.sh upload_gbif-taxonomy_28-08-2023.sh upload_identification_test-hits-supp.sh upload_PubMed_only-lotus.sh upload_Chemical-activity-evidences_supp-test-hits.sh upload_Organism-activity-evidences_supp-test-hits.sh update.sh

To stop the triple-store, use the following:

bash workflow/w_virtuoso.sh -d /path/to/data/dir -c clean

Checking before using.

Before launching the web-interface (see repository: abroad-demo-webapp), check the following:

Check the CORS (for the UI)

In the Virtuoso conductor panel accessible by default at http://localhost:8890/

• Go to conductor
• Log with Account: dba and password: abroad
• Go to Web Application Server > Virtual Domains & Directories
• Select the Default Web Site at port 8890 (by default)
• Go to /sparql > Edit
• Check that Cross-Origin Resource Sharing is with "*"

Done ! The server should be now on and ready !

Go to repository: abroad-demo-webapp to see now how to launch the web-app.