Presented via video at Wikimedia Research Showcase August 23, 2017. Video available at https://www.youtube.com/watch?v=Fa0Ztv2iF4w&t=33m

1. The Gene Wiki: Using
Wikipedia and Wikidata to
organize biomedical
knowledge
Andrew Su, Ph.D.
@andrewsu
[[User:Andrew Su]]
http://sulab.org
August 23, 2017
WMF Research
Slides: slideshare.net/andrewsu

2. 2
Crowd volunteers
and partners
Andra
Waagmeester
(andrawaag)
Lynn
Schriml
Elvira
Mitraka
(emitraka)
U. Maryland, Baltimore
MicelioUBC
Paul Pavlidis
Ben Good
(i9606)
Greg Stupp
(gstupp)
Sebastian
Burgstaller
(sebotic)
Tim Putman
(putmantime)
Ginger
Tsueng
Nuria
Queralt
Rosinach
bit.ly/genewikidata
sulab.org
We are recruiting!
U. Washington
Kevin Hybiske

3. The biomedical literature is massive…
3
0
200,000
400,000
600,000
800,000
1,000,000
1,200,000
1,400,000
1985 1990 1995 2000 2005 2010 2015
Number of new PubMed-indexed articles

4. Filtering, extracting, and summarizing PubMed
Documents
Concepts Review article
about fibronectin

5. Filtering, extracting, and summarizing PubMed
Documents
Concepts

6. The Gene Wiki project, circa 2008
6
Huss, PLoS Biol, 2008
Data imported
from structured
biomedical
databases
Summarized
knowledge via
crowdsourcing

7. 7

8. 8
Biomedical
databases
Applications

9. 9
Biomedical
databases
Applications
1. Text mining biological annotations
https://www.ncbi.nlm.nih.gov/pubmed/22165947

10. 10
Biomedical
databases
Applications
1. Text mining biological annotations
2. Editor engagement via peer-
review dual publication model
https://www.ncbi.nlm.nih.gov/pubmed/24012870

11. 11
Biomedical
databases
Applications
1. Text mining biological annotations
2. Editor engagement via peer-
review dual publication model
3. Embedding structured data using
Wikipedia templates
https://www.ncbi.nlm.nih.gov/pubmed/22434829
The expression of the protein has been found to be
significantly lower in [[schizophrenia]] and
psychotic...
The expression of the protein has been found to be
significantly lower in {{SWL|type=decreased
expression|target=schizophrenia}} and psychotic...

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

13. 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

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

15. 15
Qualifiers
References

16. 16
Biomedical
databases
Applications
1. Text mining biological annotations
2. Editor engagement via peer-
review dual publication model
3. Embedding structured data using
Wikipedia templates

17. 17
EMA
GWAS CentralPubChem

18. 18
Biomedical
databases
Applications
1. Text mining biological annotations
2. Editor engagement via peer-
review dual publication model
3. Embedding structured data using
Wikipedia templates
Applications
1. Demonstrating integrative
biomedical queries

19. Simple data retrieval
19
39 genes
gene geneLabel gene geneLabel gene geneLabel gene geneLabel
Q5013317 COL22A1 Q18027370 IGSF3 Q18053559 CDHR3 Q14903974 SMAD3
Q14912759 SLC22A5 Q18045382 HPSE2 Q18045669 ATG3 Q18033889 IL1RL1
Q14914243 PSAP Q18048437 IL33 Q18035037 RAD50 Q17917202 ERBB4
Q14907990 SLC30A8 Q18051900 PYHIN1 Q18036984 FBXL7 Q18027836 IL6R
Q18025002 GAB1 Q17709208 ACO1 Q18033919 XPR1 Q18030185 NOTCH4
Q18035589 C6orf10 Q18027822 IL2RB Q15326496 RORA Q18030409 PDE4D
Q18054256 GSDMA Q18030364 PBX2 Q18042132 GSDMB Q18045645 IKZF4
Q18058487 C5orf56 Q18037773 ABI3BP Q18029145 MKLN1 Q18039979 KLHL5
Q18030785 PRKG1 Q18039623 CTNNA3 Q18036729 RAP1GAP2 Q18026947 HLA-DQA1
Q18033424 IL18R1 Q18046350 ZNF665 Q14878303 IL13
“Retrieve genes with
genetic association
with asthma”
http://bit.ly/bosc2017_wikidata

20. Data integration
20
“Retrieve genes with
genetic association
with asthma and gene
product is localized to
cell membrane”
gene geneLabel gene geneLabel gene geneLabel gene geneLabel
Q14912759 SLC22A5 Q18027370 IGSF3 Q18035037 RAD50 Q18027836 IL6R
Q14914243 PSAP Q18033424 IL18R1 Q18033919 XPR1 Q18030409 PDE4D
Q14907990 SLC30A8 Q18045382 HPSE2 Q18042132 GSDMB Q18030185 NOTCH4
Q18035589 C6orf10 Q18027822 IL2RB Q18036729 RAP1GAP2 Q18026947 HLA-DQA1
Q18054256 GSDMA Q18053559 CDHR3 Q18033889 IL1RL1
Q18030785 PRKG1 Q14903974 SMAD3 Q17917202 ERBB4
22 genes
http://bit.ly/bosc2017_wikidata

21. Leveraging the Disease Ontology structure
21
“Retrieve genes with
genetic association with any
respiratory disease and
gene product is localized to
cell membrane”
31 genes / 8 diseases
diseaseGALabel gene_counts geneList
asthma 15
SMAD3, RAP1GAP2, IL18R1, HPSE2,
SLC30A8, SLC22A5, PSAP, ERBB4, HLA-
DQA1, IGSF3, IL2RB, IL6R, NOTCH4, PDE4D,
RAD50
chronic obstructive pulmonary
disease 5 HLA-C, SFTPD, ANXA5, ANXA11, ATP2C2
lung cancer 3 TGM5, VTI1A, PHACTR2
interstitial lung disease 2 DSP, ATP11A
non-small-cell lung carcinoma 2 NALCN, DLST
nasopharynx carcinoma 2 ITGA9, TNFRSF19
adenocarcinoma of the lung 1 BTNL2
pulmonary emphysema 1 BICD1
http://bit.ly/bosc2017_wikidata

22. Opportunistic integration
22
diseaseGALabel exposureLabel
lung cancer arsenic pentoxide exposure
lung cancer HN1 exposure
lung cancer mechlorethamine exposure
lung cancer HN3 exposure
asthma Phenacyl chloride exposure
pulmonary emphysema phosgene exposure
“Retrieve genes with
genetic association with any
respiratory disease and
gene product is localized to
cell membrane and show
causative chemical
hazards”
4 diseases / 6 chemical hazards
http://bit.ly/bosc2017_wikidata

23. 23
Biomedical
databases
Applications
1. Text mining biological annotations
2. Editor engagement via peer-
review dual publication model
3. Embedding structured data using
Wikipedia templates
Applications
1. Demonstrating integrative
biomedical queries
2. Building domain-specific web
applications

24. Small data to big data
24
?

25. Chlambase.org for the Chlamydia research community
25
Community-specific
structured knowledge
Genetic mutants, gene
expression, host-pathogen
interactions, orthologs, ….

26. Domain-specific applications based on Wikidata
26
Chlambase

27. Thoughts for the future
(TFTF)
27
https://www.pexels.com/photo/telescope-view-binoculars-viewpoint-4754/

28. TFTF #1: Need incentives for data owners → data contributors
28
Circular
Diagram
Direct measures of usage
• SPARQL query logs
• Network interconnectedness
• Other ideas?

29. TFTF #2: Need functional integration of WP and WD edit histories
1. Statement-level filtering
2. Across all sourced WD items
(arbitrary access)
29
https://en.wikipedia.org/wiki/Wikipedia_talk:WikiProject_Medicine/Archive_92

30. TFTF #3: Need more expressive data modeling and reporting
• Defining data models and constraints
(ShEx?)
• Visualizing and disseminating models
• Reporting violations and auto-suggesting
fixes
30
https://github.com/SuLab/Genewiki-ShEx

31. 31
Crowd volunteers
and partners
Andra
Waagmeester
(andrawaag)
Lynn
Schriml
Elvira
Mitraka
(emitraka)
U. Maryland, Baltimore
MicelioUBC
Paul Pavlidis
Ben Good
(i9606)
Greg Stupp
(gstupp)
Sebastian
Burgstaller
(sebotic)
Tim Putman
(putmantime)
Ginger
Tsueng
Nuria
Queralt
Rosinach
bit.ly/genewikidata
sulab.org
We are recruiting!
U. Washington
Kevin Hybiske

32. 32

33. Open source
33
github.com/SuLab/GeneWikiCentral
github.com/SuLab/wikidataintegrator – python module for Wikidata
github.com/SuLab/scheduled-bots – bot automation framework
github.com/SuLab/WikiGenomes.org
github.com/SuLab/ChlamBase.org
github.com/SuLab/Genewiki-ShEx – data models
github.com/SuLab/wdbiothings – wrapper for BioThings APIs
Expert interfaces
License