Interfaces

Interfaces to browse and consume Knowledge Graphs data.

Integrated interfaces#

d2s-api#

Web services described following the OpenAPI 3.0 specifications. The generated services enable the user to query a BioLink-compliant RDF knowledge graph using HTTP request following the Reasoner API Specifications.

d2s start api

docker run -it --rm -p 8080:8080 \
  --net d2s-core_network \
  -e ENDPOINT="http://graphdb:7200/repositories/test" \
  umids/d2s-api

Access on http://localhost:8080

into-the-graph#

into-the-graph is a lightweight RDF linked data browser supporting graphs.

Browse various SPARQL endpoints and their graphs by providing the endpoint URL. It includes a YASGUI editor and provide insights about the graphs content using precomputed HCLS descriptive statistics.

See an example deployment at trek.semanticscience.org. The SPARQL endpoint can be changed directly on the web app in /settings.

d2s start into-the-graph

docker run --rm -it -p 8082:80 umids/into-the-graph:latest

Access on http://localhost:8082

Comunica Widget#

A jQuery widget to query heterogeneous interfaces using Comunica SPARQL and GraphQL.

d2s start comunica

docker run -p 8084:80 -it --rm umids/comunica-sparql-widget

# Provide a local queries.json file
docker run -v $(pwd)/workspace/comunica-settings.json:/usr/share/nginx/html/queries.json -p 8080:80 -it --rm umids/comunica-sparql-widget

Access on http://localhost:8084

settings.json file and queries needs to be changed before docker build. See documentation.

TODO: improve how settings and queries pass (script to download them from URL before starting nginx?.

See documentation about Comunica's GraphQL-LD implementation.

BioThings Studio#

BioThings Studio enables to deploy a Docker container with all dependencies required to build BioThings APIs. See the BioThings Studio documentation.

d2s start biothings-studio

docker run -d --rm --name studio \
  -p 8001:8080 -p 8000:8000 -p 9000:9000 \
  -p 7022:7022 -p 7080:7080 -p 9200:9200 -p 27017:27017 \
  -v $(pwd)/workspace/biothings:/data \
  biothings/biothings-studio:0.2a

Access BioThings Studio web UI at http://localhost:8880

Access BioThings API at http://localhost:7080

Additional interfaces#

LinkedDataHub#

LinkedDataHub is an Open Source Knowledge Graph management system. You can use it to manage data, create visualizations and build apps on RDF Knowledge Graphs.

Clone the repository and prepare the environment file:

git clone https://github.com/AtomGraph/LinkedDataHub.git
cd LinkedDataHub
cp .env_sample .env

Start LinkedDataHub:

docker-compose up -d

Access LinkedDataHub web UI at https://localhost:4443

You will need to accept the risk due to self-signed certificates.

You can now follow the web UI instructions to create an account to login to your LinkedDataHub.

Access Fuseki admin UI at http://localhost:3030/ds

Access Fuseki end user UI at http://localhost:3031/ds

To stop LinkedDataHub, run from the LinkedDataHub folder:

docker-compose down

LinkedPipes#

LinkedPipes is a Suite for Linked Data, with ETL, Visualization services and Applications.

Try the ETL web UI to define data transformation pipelines to RDF:

git clone https://github.com/linkedpipes/etl linkedpipes-etl
cd linkedpipes-etl
LP_ETL_PORT=8091 docker-compose up -d

Access at http://localhost:8091

LinkedPipes proposes various visualisation services:

LinkedPipes Visualization Assistant: lets you configure interactive views based on Linked Data
LinkedPipes Applications: visualization web platform that allows the users to explore, visualize and publish LinkedData based visualizer applications

To stop the LinkedPipes ETL, run from the linkedpipes-etl folder:

docker-compose down

YASGUI#

The popular Yet Another Sparql Graphical User Interface. Integrated to into-the-graph.

docker run -it --rm --name yasgui -p 8088:80 \
    -e "DEFAULT_SPARQL_ENDPOINT=http://dbpedia.org/sparql" \
    -e "ENABLE_ENDPOINT_SELECTOR=true" \
    erikap/yasgui

Require the SPARQL endpoint to allow Cross-Origin Requests.

Access at http://localhost:8088

LODEstar#

SPARQL query and URI resolution, available through DockerHub.

docker run --rm -d --name lodestar -p 8082:8080 \
  -e ENDPOINT_URL=https://graphdb.dumontierlab.com/repositories/ncats-red-kg \
  -e TOP_RELATIONSHIP=http://w3id.org/biolink/vocab/id,http://w3id.org/biolink/vocab/name,http://w3id.org/biolink/vocab/description \
  -e LABEL=http://w3id.org/biolink/vocab/label \
  -e DESCRIPTION=http://w3id.org/biolink/vocab/description \
  -e MAX_OBJECTS=10 \
  -e SERVICE_BASE_URI=http://localhost:8080/ncats-red-kg netresearch/lodestar

Access at http://localhost:8082/lodestar/sparql

Does not support graphs 🚫

Trifid#

Linked Data Server: URI dereferencing, custom HTML render, YASGUI SPARQL endpoint.

git clone https://github.com/vemonet/trifid.git
docker build -t trifid ./trifid

docker run --rm -ti --name trifid -p 8080:8080 trifid --sparql-endpoint-url=https://graphdb.dumontierlab.com/repositories/test --dataset-base-url=https://w3id.org/d2s/

docker run --rm -ti --name trifid -v /home/vemonet/sandbox/trifid:/data -p 8080:8080 trifid --config=/data/config-ncats-red-kg.json

Go to http://localhost:8080/dataset/huri/ to resolve https://w3id.org/d2s/dataset/huri/

Modified version on GitHub.

Original project available on DockerHub. But config not working.

docker run -ti -p 8080:8080 zazuko/trifid
# Not working, provide env config file?
docker run -ti -p 8080:8080 -e TRIFID_CONFIG=config-ncats-red-kg.json zazuko/trifid
docker run -ti -p 8080:8080 -e SPARQL_ENDPOINT_URL=https://graphdb.dumontierlab.com/repositories/test -e DATASET_BASE_URL=https://w3id.org/d2s/ zazuko/trifid

Access default example on http://localhost:8080/data/person/mary-cooper to resolve URI.

Does not support graphs 🚫

brwsr#

Lightweight Linked Data Browser.

git clone https://github.com/Data2Semantics/brwsr.git
docker-compose up

Go to http://localhost:5000.

Change the SPARQL endpoint in the docker-compose.yml.

Does not support graphs 🚫

RhizomerEye#

RhizomerEye is a tool to expose a SPARQL endpoint as REST API and deploy a Web UI to browse the triplestore.

See the source code for the RhizomerAPI and RhizomerEye.

The Web UI has been deployed publicly for a few triplestores:

TriplyDB#

See official documentation. It allows to deploy the following services over a triplestore:

YASGUI SPARQL endpoint
Search index using ElasticSearch.
Web UI to resolve and browse a triplestore
Supports graphs in the TPF table browser (not in the browser)

TriplyDB is hosted centrally and cannot be deployed locally 🚫