To allow adapt the graph query especially (which is cached in Virtuoso)

Explore metrics about RDF datasets in web UI: http://loupe.linkeddata.es/loupe/index.jsp

Use Virtuoso and ElasticSearch

• Ontoloy github: https://github.com/nandana/loupe-ontology
• Paper: http://ceur-ws.org/Vol-1824/ldq_paper_1.pdf
• API github: https://github.com/oeg-upm/loupe-api

The API is down: http://api.loupe.linkeddata.es/

API down + last commit in 2017

Try contact [email protected] for the website source code

At the moment we use: https://github.com/reactjs/react-tabs
Should we improve its CSS?

Or switch for material-ui tabs?

• Example: https://bit.dev/mui-org/material-ui/tabs

Much heavier to implement

https://callstack.github.io/react-native-paper

https://react-native-elements.github.io/react-native-elements

Open a paper with list of results in overlay:

https://stackoverflow.com/questions/42130822/display-a-overlay-when-input-is-clicked-in-react

into-the-graph fail querying Wikidata endpoint due to the GRAPH ?graph { part, not supported in Blazegraph triple mode.

See https://query.wikidata.org/sparql

PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
SELECT * WHERE {
  graph ?g {
  <http://www.wikidata.org/entity/Q45> ?pred ?obj .
  } } LIMIT 10

For temporal SPARQL query over HDT (Memento) and GraphQL-LD

http://query.linkeddatafragments.org/
https://github.com/comunica/Tutorial-Comunica-Querying-Data/wiki/Comunica-tutorial:-Querying-Data#5-setting-up-a-web-client

The actual data table lib is quite good, but not optimized for React and the display get out of the grid cell

MD bootstrap data tables do multi sort and are easy to deploy:

https://mdbootstrap.com/docs/react/tables/datatables/

Virtuoso LDP generates a lots of graphs

See http://trek.semanticscience.org/describe?uri=http://w3id.org/FAIR_Training_LDP/DAV/home/LDP/Training/Murcia/marks_resource.ttl&endpoint=http://w3id.org/FAIR_COVID19/sparql/

A good way to navigate LDP for this use-case:

PREFIX ldp: <http://www.w3.org/ns/ldp#> 
PREFIX schema: <http://schema.org/> 
SELECT ?crateContainer WHERE { 
  GRAPH ?crateContainer { 
    ?crateContainer ldp:contains ?crate .
  } 
  GRAPH ?crate { ?s schema:studyDesign "Cohort" .} 
}

Should we have a switch to allow to get all triples in graphs instead of just classes?

We need to split the SPARQL query calls to get 500 as subject, 500 as predicate and 500 as object

issue with http://localhost:3000/describe?uri=http://bio2rdf.org/mesh:D001172

With lock icon in navbar and password access

Allow to change:

• SPARQL endpoint URL
• SPARQL query for full text search
• Prefix/namespaces defined. The use can choose between:
  • directly add in the file (easy to implement)
  • use a central service, such as PrefixCommons (to implement later)

Those variables are stored in the React Context API store

https://github.com/reactjs/react-tabs
https://reactcommunity.org/react-tabs/

Tutorial to use the new React Context API store: https://www.toptal.com/react/react-context-api

Most complete tutorial, with all solutions (classic, redux, context API): https://towardsdatascience.com/passing-data-between-react-components-parent-children-siblings-a64f89e24ecf

Clean tutorial without using Redux: https://medium.com/@ruthmpardee/passing-data-between-react-components-103ad82ebd17

Fix issue with describe not reloading when URI param changes at the same time

So that users can browse those URIs directly on the browser

The Yasr plugin might be interesting: https://triply.cc/docs/yasgui-api#writing-a-yasr-plugin

The data pulled could be stored as RDF, then the visualization would be built directly using rdflib

See documentation: https://zazuko.com/get-started/developers/

We should be able to click on a switch button to switch between the graphical representation of triples (current) and just a datatable with 4 columns: subject, predicate, object, graph

The user can them filter and sort the triples as he wants

On http://ld-browser.137.120.31.101.nip.io/
CORS issues only on icons

axios/axios#853

Subjects:
http://localhost:3000/describe?uri=http://bio2rdf.org/drugbank:DB00001

Object:
http://localhost:3000/describe?uri=http://bio2rdf.org/drugbank_resource:FASTA

In GraphsOverviews.js

SELECT DISTINCT ?g WHERE { GRAPH ?g {?s ?p ?o} }

Works really fast on Virtuoso, but not GraphDB

This was a easy way to fix it, but could be improved later

I was thinking about putting the current SPARQL endpoint on the top navbar right

Hum, and a Autocomplete directly at this place
So the top bar would be:

• which URI you describe
• In which SPARQL endpoint

If it is too packed, I can just put under the URI in current UI

And add the dropdown for graph query in graph overview?

It will be better to refactor a bit to define a specific component for our different Autocomplete

At the moment we try to get only the classes of the graph

A few issues when resolving a graph URI:

• Not all classes are always retrieved on big graph: the query needs to be optimized. But this kind of query can be quite expensive to run, so we are using limit at the moment
• If the graph has no classes then the UI shows nothing (add fallback query which get any statement?)

Use HCLS metadata from the SPARQL endpoint when present

Also provide user with the option to provide HCLS metadata by uploading a RDF turtle file

https://maastrichtu-ids.github.io/into-the-graph/describe?uri=http://bio2rdf.org/clinicaltrials:NCT00209495

Use typescript instead of javascript

Conversion started here: https://github.com/MaastrichtU-IDS/into-the-graph/tree/typescript-conversion

Links

Convert to typescript:

• https://www.typescriptlang.org/docs/handbook/react-&-webpack.html
• https://www.typescriptlang.org/docs/handbook/migrating-from-javascript.html
• https://github.com/microsoft/TypeScript-React-Conversion-Guide
• Babel + ts + MaterialUI : https://medium.com/@rajeshpriyadarshinimishra/basic-react-app-setup-with-typescript-babel-webpack-and-material-ui-installation-38ff0829206c
• ts + mui + withStyles : https://material-ui.com/guides/typescript/#usage-of-withstyles
• Fix CSS import in ts: https://medium.com/@sapegin/css-modules-with-typescript-and-webpack-6b221ebe5f10
• Example of mui app in ts: https://github.com/mui-org/material-ui/tree/master/examples/create-react-app-with-typescript

If the user access the describe with an endpoint provided then we should show a snackbar asking him if he wants to update it.

e.g.
http://192.168.1.70:19006/describe?uri=http://rdf.disgenet.org/v5.0.0/void/disgenetv5.0nanopub&endpoint=http://rdf.disgenet.org/sparql/

All comes from dependencies

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npm WARN deprecated [email protected]: cross-spawn no longer requires a build toolchain, use it instead
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List here: https://github.com/OpenLinkSoftware/general-turtle-doc-collection/blob/master/LODCloud_SPARQL_Endpoints.ttl

We could also parse it automatically

Biomedical SPARQL: https://yummydata.org/

See the search query

• At the moment we only do a simple search via SPARQL using contains on label, but still really slow for big datasets such as ncats-red-kg
• A customize search query have been written for GraphDB using its homemade search index
• Virtuoso and Blazegraph also allows to index statements

We should be able to easily switch from a search query to another, through an Admin UI?
See #8

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:

• COVID-19
• DBpedia

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 🚫

Add more tables to describe a dataset:

• Dataset-Property-Dataset List
• Property and Object Type
• Same Type-Property-Type List as theirs (with unique and not unique)

Propose tables similar to what is proposed in Bio2RDF: http://download.bio2rdf.org/files/release/3/affymetrix/affymetrix.html

Using YASGUI widget to query http://dbpedia.org/sparql:

You are trying to query an HTTP endpoint (http://dbpedia.org/sparql) from an HTTPS website (https://trek.semanticscience.org/sparql).
This is not allowed in modern browsers, see https://developer.mozilla.org/en-US/docs/Web/Security