From Knowledge Graphs via Lego Bricks to scientific conversations - Dennis Madsen, Scientific Director, Novo Nordisk

1. Novo Nordisk®
From knowledge graphs via
Lego bricks to scientific
conversations
Dennis Madsen
Roland Hangelbroek
Vinay Jethava
NN GraphDay May 7, 2024

2. Novo Nordisk®
From knowledge graphs via
Lego bricks to scientific
conversations
Dennis Madsen
Roland Hangelbroek
Vinay Jethava
NN GraphDay May 7, 2024

3. Novo Nordisk®
Our knowledge graph principles
Why Clear purpose with KG
Relevant Pipelines to update
Interoperability Entities and ontologies

4. Novo Nordisk®
Named Entity Recognition
Entity Linking
Relation Extraction
NovoLinker

5. Novo Nordisk®
Named Entity Recognition

6. Novo Nordisk®
Entity Linking
Ontology Vocabulary

7. Novo Nordisk®
Relation Extraction

8. Novo Nordisk®
Currently in NovoLinker - Entities
• Genes / Proteins – Linked to HGNC, Interpro and
Protein Ontology
• Chemicals & Drugs – Linked to Chebi and NCIT
• Diseases & Phenotypes – Linked to MONDO and
HPO
• Cell lines – Linked to cellosaurus
• Cell types – Linked to cell type ontology (CL)
• Geographical locations – Linked to Geonames
• Sequence features – Linked to sequence ontology
• Organizations – Linked to Wikidata, Crunchbase,
ROR
• Organisms - Linked to NCBITaxon
• Anatomy – Linked to Uberon
Gene ontology:
• Biological process
• Molecular function
• Cell component
Others:
• Assays, medical procedures, devices,
miRNA, sequence variants, persons

9. Novo Nordisk®
Currently in NovoLinker – Relations
• Protein – protein interactions
• Chemical – protein interactions
• Adverse drug effects
• Gene – disease relations
• Drug– drug interactions
• Causal relations

10. Novo Nordisk®
Use cases | Patents
 Long complex documents
 Rich relationships
• Patent Families
• CPC/IPCR classification hierarchy
• References (Patents/Articles)
• Inventors/Owners
 Additional information (figures, tables, sequences)

11. Novo Nordisk®
Use cases | Patents
11
• Basic schema
• Text-based embeddings
• Node embeddings
• Entity detection using
Novo Linker
• Enabling agentic
interaction with the
patent-graph

12. Novo Nordisk®
Patents (VNJE)
anansi (RLHB)
(Literature, news, conference notes,
pharma pipelines)
N L
Computational
Biology (NYYL)
N L
Clinical Data (KEGS)
NNRCO
Screening Data (VMNZ)
N
L
N
L
Lego bricks

13. Novo Nordisk®
Chat with data

14. Novo Nordisk®
14

15. Novo Nordisk®
LLM Functions - API
Patents (VNJE)
anansi (RLHB)
(Literature, news, conference
notes, pharma pipelines)
N L
Computational
Biology (NYYL)
N L
Clinical Data (KEGS)
NNRCO
Screening Data
(VMNZ)
N
L
N
L
A
P
I

16. Novo Nordisk®
Use cases

17. Novo Nordisk®