1. Wikidata for biomedical
knowledge integration and
curation
Benjamin Good
The Scripps Research Institute
@bgood
bgood@scripps.edu

2. “knowledge”
• A lot
• Important
• Text

3. What are the
functions of
Fibronectin?
37186 articles
What are the functions of
the 238 ‘significant’ genes
that came up in my high
throughput screen??

4. What are the
functions of
Fibronectin?
37186 articles
…
Gene Property Value
Fibronectin Biological
Process
Angiogenesis
Fibronectin Cellular
Localization
Extracellular
matrix
Fibronectin Related
Disease
Glomerulopathy
“knowledge integration”
“curation”
“knowledge base”
Answers

5. Knowledge Bases
5
1,500+ listed at http://www.oxfordjournals.org/nar/database/a/

6. Applications of knowledge bases
• Find information
• Plan research
• ”Known unknowns?”
• Interpret data
• Gene Ontology
Enrichment Analysis

7. Interesting Gene List
Gene Ontology, Pathway,
Network interpretation

8. Knowledge bases are important tools
and will only grow more important
over time

9. 9
Great!

10. 10
BUT

11. 11
1. Knowledge bases are not complete
2. Will get to later..

12. Annotation
missing from
human GO
annotation.
Should be here!
(‘5 HT Receptor’ means ‘Serotonin Receptor’)
Circa 2010

13. Added to GO
Jan. 2016
First characterized 1996
(Kohen et al J Neurochem)

14. Interesting Gene List
Gene Ontology, Pathway,
Network interpretation

15. We don’t know what we are missing
15
inflammatory
response
defense
response
Serotonin
receptor
activity?
?
response to
wounding
immune
response
Interesting Gene List

16. “Gene Ontology, its great right ?”
• “It sucks”
• “I only use it out of desperation”

17. WHY?!

18. Process of building knowledge bases
1. do science 2. publish it 3. Manually extract
the knowledge
Gene Property Value
Fibronectin Biological
Process
Angiogenesis
Fibronectin Cellular
Localization
Extracellular
matrix
Fibronectin Related
Disease
Glomerulopathy

19. why does he look so down?

20. Many scientists, powerful tools,
comparatively little reward for
curating knowledge
100’s of thousands 100’s

21. More than 2 articles
published/minute

22. Professional biocuration does not scale
up to the rate of production
1. do science 2. publish it 3. Manually extract
the knowledge
Gene Property Value
Fibronectin Biological
Process
Angiogenesis
Fibronectin Cellular
Localization
Extracellular
matrix
Fibronectin Related
Disease
Glomerulopathy

23. 23
1. Knowledge bases are not complete
2. Knowledge needs integration

24. Knowledge is scattered,
integration brings it together

25. Merging knowledge bases:
the language barrier
“Methadone”
Interacts with:
“Moxifloxacin”May treat:
Opioid-Related Disorders
ID:
N0000000174
ID:
4095
Molecular Weight:
309.44518 g/mol
…
= ?
= ?
= ?
= ?
= ?
= ?
ID:
DB00333
Manufactured by:
Roxane laboratories inc

26. Good for business, bad for science
Google Scholar search shows 469 papers about
“identifier mapping” in bioinformatics

27. What can we do?

28. Global Knowledge Platform
What would happen if everyone
was literally working on the same
database?
1. Split up work more effectively
2. Make integration the default
behavior

29. Is to data
as Wikipedia is to text
“Giving more people more access to more knowledge”
A free and open repository of knowledge
Managed by the MediaWiki foundation
that operates Wikipedia

30. It’s a
knowledge
base!
• Anyone
can edit
• Anyone
can use

31. Item: Q84

32. Item: Q414043
RELN
Genomic start: 103471784
GenLoc assembly:
GRCh38
Stated in:
Ensembl Release 83
Retrieved:
19 January 2016
Value (numeric)
Property
Claim Qualifiers
References
https://www.wikidata.org/wiki/Q414043
Statement

33. Item: Q414043
RELN
Encodes: Reelin (protein) Stated in:
NCBI homo sapiens
annotation release 107
Retrieved:
19 January 2016
Value (item)
Property
Claim Qualifiers
References
https://www.wikidata.org/wiki/Q414043
Statement

34. A Giant Global Graph
These statements link together into a queryable graph
https://query.wikidata.org

35. We are seeding it with
biomedical data
• All human, mouse genes
and proteins
• All Gene Ontology terms
• All FDA approved drugs
• 9,000+ human diseases
Burgstaller et al (2016) Database (preprint in BioRxiv)
Mitraka et al (2015) Semantic Web Applications for the Life Sciences (best paper) (preprint in BioRxiv)

36. Our seeds are largely
concepts linked to many
identifier systems
N identifiers per item
• Genes: 8
• Drugs: 18
• Diseases: 11
Burgstaller et al (2016) Database (preprint in BioRxiv)
Mitraka et al (2015) Semantic Web Applications for the Life Sciences (best paper) (preprint in BioRxiv)
Facilitate
integration
with key
external
knowledge
bases

37. Nurturing a multi-community
garden of biomedical knowledge
Gene DrugDisease

38. A Platform for knowledge integration and curation
38
Open data
Wikipedia(s)
Your Apps
Here!
Your Apps
Here!
Your Apps
Here!
Your Apps
Here!

39. Application #1 (of many)
Burgstaller et al (2016) Database (preprint in BioRxiv)

40. Impact of wikidata on Wikipedia
Gene Wiki
Version 1.
{{GNF_Protein_box | Name = Reelin| image = |
image_source = | PDB = {{PDB2|4AD9}} | HGNCid = 18512 |
MGIid = | Symbol = LACTB2 | AltSymbols =; CGI-83 |
IUPHAR = | ChEMBL = | OMIM = None | ECnumber = |
Homologene = 9349 | GeneAtlas_image1 = |
GeneAtlas_image2 = | GeneAtlas_image3 = |
Protein_domain_image = | Function =
{{GNF_GO|id=GO:0005515 |text = protein binding}}
{{GNF_GO|id=GO:0016787 |text = hydrolase activity}}
{{GNF_GO|id=GO:0046872 |text = metal ion binding}} |
Component = {{GNF_GO|id=GO:0005739 |text =
mitochondrion}} | Process = {{GNF_GO|id=GO:0008152
|text = metabolic process}} | Hs_EntrezGene = 51110 |
Hs_Ensembl = ENSG00000147592 | Hs_RefseqmRNA =
NM_016027 | Hs_RefseqProtein = NP_057111 |
Hs_GenLoc_db = hg38 | Hs_GenLoc_chr = 8 |
Hs_GenLoc_start = 70635318 | Hs_GenLoc_end = 70669174
| Hs_Uniprot = Q53H82 | Mm_EntrezGene = 212442 |
Mm_Ensembl = ENSMUSG00000025937 |
Mm_RefseqmRNA = NM_145381 | Mm_RefseqProtein =
NP_663356 | Mm_GenLoc_db = mm10 | Mm_GenLoc_chr =
1 | Mm_GenLoc_start = 13623330 | Mm_GenLoc_end =
13660546 | Mm_Uniprot = Q99KR3 | path = PBB/51110}}
=
Gene Wiki
Version 2.
{{Infobox gene}}
• All data in
Wikidata
• 1 Lua script works
for all genes
=
(1 of these for every gene)

41. Application #2 Web Apollo Genome Browser
41
• Genome annotation data retrieved
from wikidata via SPARQL queries
to https://query.wikidata.org
• Prototype achieved at recent San
Diego hackathon
1 Putman et al (2016) (under review) (preprint in BioRxiv)

42. Microbial Genetic Data
•Widely Distributed
•Difficult to query
•Not structured in meaningful way
•A lot of interest from this
community !

43. Microbial Genetic Data

44. Microbial genomes in Wikidata
• Loading genes,
proteins,
annotations for
120 reference
genomes.
• Completed 21
genomes so far
Putman et al (2016) (under review) (preprint in BioRxiv)

45. Microbiome modeling in Wikidata
Putman et al (2016) (under review) (preprint in BioRxiv)

46. 46
1. Knowledge bases are not complete
2. Knowledge needs integration
Can help

47. Centralizing content while distributing labor
47
Open data
Your Apps
Here!
Wikipedia(s)
Your Apps
Here!
Your Apps
Here!
Your Apps
Here!

48. Thanks!
Gene Wikidata Team
Andra Waagmeester (Micelio)
* Sebastian Burgstaller (Scripps)
* Tim Putman (Scripps)
* Elvira Mitraka (U Maryland)
Julia Turner (Scripps)
Justin Leong (UBC)
Lynn Schriml (U Maryland)
Paul Pavlidis (UBC)
Andrew Su (Scripps)
Ginger Tsueng (Scripps)
Contact
bgood@scripps.edu* First author on manuscript cited in this presentation
Ben Tim
Andra
Elvira
Sebastian
Some Gene Wiki team members
enjoying their best paper award
at SWAT4LS, Dec. 2015
Adapted logo