Speaker: Jesús Barrasa, Sales Engineering Director EMEA, Neo4j

1. Using public (life sciences &
healthcare) RDF resources
in Neo4j
Dr. Jesús Barrasa
Director Sales Engineering EMEA - Neo4j

2. Based in London UK.
With Neo4j for 5 years (but a life of graphs)
Head of Sales Engineering in Europe.
Lead the Neosemantics (n10s) Labs project.
Me

3. Data practitioners with some basic
understanding of both RDF and Neo4j
Who is this talk for?

4. What are RDF resources?
Databases
Annotated Datasets
Public Vocabularies
Ontologies
Constraints
RDF

5. Which RDF resources?

6. How to access them?
● Bulk download
● API
○ URI deref
○ SPARQL
■ CONSTRUCT
■ DESCRIBE
■ SELECT
https://www.nlm.nih.gov/databases/download/mesh.html

7. What is RDF?
• A Model : URIs and Triples
• A query language: SPARQL (Uris and Triples… and variables)
• A number of serialisation formats: JSON-LD, Turtle, RDF/XML,...
“RDF is a standard model for data interchange
on the Web”
RDF Spec (https://www.w3.org/RDF/)

8. RDF triples form a graph
<http://www.wikidata.org/entity/Q84263196> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.wikidata.org/category/Disease> .
<http://www.wikidata.org/entity/Q84263196> <http://www.w3.org/2000/01/rdf-schema#label> "COVID-19" .
<http://www.wikidata.org/entity/Q84263196> <http://www.w3.org/2000/01/rdf-schema#subClassOf> <http://www.wikidata.org/entity/Q2633267> .
<http://www.wikidata.org/entity/Q2633267> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://www.wikidata.org/category/Disease> .
<http://www.wikidata.org/entity/Q2633267> <http://www.w3.org/2000/01/rdf-schema#label> "Atypical pneumonia" .

9. What is RDF? The Serialisation Formats
JSON-LD
N-Triples
RDF/XML
Turtle

10. ● object is a Literal
↳ a node property●
● object is a resource
↳ a relationship●
● predicate is rdf:type
↳ a node label
RDF fits nicely into a Property Graph
https://jbarrasa.com/2016/06/07/importing-rdf-data-into-neo4j/

11. n10s does it for you

12. Neo4j-RDF integration
URL DEREF → RDF → n10s
SPARQL DESCRIBE → RDF → n10s
SPARQL CONSTRUCT → RDF → n10s
RDF DUMP → RDF → n10s
SPARQL SELECT → TABLE → LOAD CSV,
APOC

13. Let’s build a MVG for :
• Semantic search
• Knowledge discovery
• Knowledge reconciliation
Let’s do it… in 20 minutes!
https://www.gartner.com/en/documents/3985680

14. Demo
Diseases
Chemicals
and drugs
Infectious
Diseases
Virus
taxonomy
Virus
taxonomy
Diseases
Scientific
Literature

15. Next Steps
● Add more datasources
● Use Graph Algorithms
● Advanced Ontology/Schema usage:
○ Inferencing / Validation

16. COVID-19 Knowledge Graph Project
https://covidgraph.org/

17. Your turn!
Download Neo4j + n10s
https://neo4j.com/labs/neosemantics-rdf/
Link to sources from today’s session
https://github.com/jbarrasa/connections-lifesci

18. Using public (life sciences &
healthcare) RDF resources
in Neo4j
Dr. Jesús Barrasa
Director Sales Engineering EMEA - Neo4j
Questions?