The document discusses the use of Wikidata as a fair knowledge graph for life sciences, highlighting its potential in biomedical applications such as integrative queries, drug repurposing, and community curation. It emphasizes the importance of crowdsourced knowledge in improving data curation and mentions a high acceptance rate for crowdsourced edits. Key advantages of Wikidata-backed applications include enhanced application development and data persistence beyond the typical lifecycle of web projects.

1. Wikidata as a FAIR
knowledge graph for the
life sciences
September 24, 2019
Slides: slideshare.net/andrewsu
Andrew Su, Ph.D.
@andrewsu
http://sulab.org
Q19857262

2. The Gene Wiki project, circa 2008
2
Huss, PLoS Biol, 2008
Data imported
from structured
databases
Summarized
knowledge via
crowdsourcing

3. 3

4. is to data
is to text
biomedical
Provide a database of the world’s
knowledge that anyone can edit
- Denny Vrandečić

5. Subclass of
Regulates
Physically
interacts with
Protein
Neural
development
Property:P279
Property:P128
Property:P129
Q8054
Q1345738
VLDL receptor Q1979313
Amyloid
beta A4 Q423510
Q13561329
http://www.wikidata.org/wiki/Q13561329
Decreased
expression in
Property:P1910
Schizophrenia Q41112
Bipolar disorder Q131755

6. Property:P279
Property:P128
Property:P129
Q8054
Q1345738
Q1979313
Q423510
Q13561329
Property:P1910
Q41112
Q131755
https://www.wikidata.org/wiki/Special:EntityData/Q13561329.json

7. 7
Qualifiers
References

8. 8

9. Biomedical use cases
• ID translation (aka Rosetta Stone)
• Integrative queries
• Graph mining for drug repurposing
• Generalized back-end database for customized front-
end applications
9

10. Small data to big data
10
?

11. Chlambase.org for the Chlamydia research community
11
Community-specific
knowledge
Genetic mutants, gene
expression, host-pathogen
interactions, orthologs, ….

12. Key advantages of Wikidata-backed applications
• Application development can focus on front-end
interface
• Data persistence extends beyond the life of the web
application / grant
12

13. Biomedical use cases
• ID translation
• Integrative queries
• Graph mining for drug repurposing
• Generalized back-end database for customized front-
end applications
• Community curation of ontologies
13

14. Curated
Knowledge
Crowd-sourced
Knowledge
Wikidata Crowdsourcing Model for Enhancing DO Curation
• Github issues
• Github pull requests
• CSVs

15. Wikidata Crowdsourced Edits on Disease Items
98% acceptance
rate after expert
curation

16. 16
https://commons.wikimedia.org/wiki/File:FAIR_data_principles.jpg
=

17. Acknowledgements
• Andra Waagmeester (Micelio)
• Sabah Ul-Hasan
• Ginger Tsueng
• Mike Mayers
• Roger Tu
• Lynn Schriml (Univ. Maryland)
• Chunlei Wu (Scripps Research
• Kevin Hybiske (Univ. Washington)
17
Past team members
• Ben Good
• Greg Stupp
• Tim Putman
• Sebastian Burgstaller-Muehlbacher
• Núria Queralt Rosinach
• Elvira Mitraka
• Derek Jow
• Paul Pavlidis
Funding