Wikidata as a FAIR knowledge graph for the life sciences

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Talk given at the Workshop on Advanced Knowledge Technologies for Science in a FAIR World (AKTS) https://www.isi.edu/ikcap/akts/akts2019/

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

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

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

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

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
Qualifiers
References

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

Small data to big data
10
?

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

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

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

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

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

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

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

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Wikidata as a FAIR knowledge graph for the life sciences

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

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

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