A 10 minute introduction to Wikidata, the Gene Wiki project, and the Semantic Web. Presented at IC-Foods inaugural conference at UC Davis

1. Benjamin Good, TSRI
IC-Foods, UC Davis, 2016
@bgood
bgood@scripps.edu
http://www.slideshare.net/goodb
and the
Semantic Web of Food

2. Outline
• What Wikidata is
• What we are doing with it
• How you could use it to help build the Semantic Web of Food.

3. Is to data
as Wikipedia is to text
“Giving more people more access to more knowledge”
A free and open repository of knowledge
• Run by the Wikimedia Foundation
• Not a grant funded ‘project’… as stable as Wikipedia

4. It’s a knowledge
base!
• Anyone can edit
(human or robot)
• Anyone can use
(CC0)

5. Deeply integrated

6. Elements of the kb are called ‘items’
https://www.wikidata.org/wiki/Q146

7. Items are described by “statements” that link
together to form the language-independent
wikidata knowledge graph
Cat
Domesticated
Animal
Animal
Subclass Of
Subclass Of
Animalia
Taxon name
Kingdom
Taxon rank

8. Item: Q84

9. Inter-item links form a giant knowledge graph
Everything is connected
Reelin, Heart disease,
Barack Obama,
everything..
https://query.wikidata.org
SPARQL endpoint for Wikidata

10. Example question: repurposing Metformin
http://tinyurl.com/zem3oxz
Metformin
?disease
interacts
with
protein
geneencoded by genetic
association
Might
treat ?
Solute carrier
family 22
member 3
SLC22A3
prostate
cancer

11. Example biomedical content
• All human, mouse, rat, yeast, macaque, 120+
microbes genes and proteins
• All Gene Ontology terms
• All Human Disease Ontology terms
• 120,000+ chemicals
Burgstaller-Muelbacher et al (2016) Database
Mitraka et al (2015) Semantic Web Applications for the Life Sciences
Putman et al (2016) Database

12. Application #1 Wikipedia enhancement
Burgstaller et al (2016)

13. http://wikigenomes.org
Application #2 Wikigenomes

14. 1 requirement for any Semantic Web
• Unambiguous, accessible way of naming and defining things

15. You say Tomato,
I say:
https://www.wikidata.org/wiki/Q23501
NYT topic ID
TAXREF ID
iNaturalist taxon ID
EPPO Code
Tela Botanica ID
Great Aragonese Encyclopedia ID
New Zealand Organisms Register ID
GND ID
Encyclopedia of Life ID
200+ human language labels, definitions

16. You say Furaneol..
Dimethylhydroxy furanone
Pineapple ketone
2,5-Dimethyl-4-hydroxy-3(2H)-furanone
2,5-Dimethyl-4-hydroxy-2,3-dihydrofuran-3-one
2,5-Dimethyl-3-hydroxy-4-oxo-4,5-dihydrofuran
4-hydroxy-2,5-dimethyl-3(2H)-furanone
HDMF
4-hydroxy-2,5-dimethylfuran-3-one
CAS registry number
PubChem ID (CID)
InChI
InChIKey
ChemSpider ID
UNII
ChEMBL ID
ChEBI ID
ECHA InfoCard ID
Beilstein Registry Number
HMDB ID
Database ids..
Labels, definitions, article links
I say Q250455

17. Acknowledgements
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
@bgood on twitter
Adapted logo
Su Laboratory at TSRI The 16,950 other active editors of
Wikidata and especially the 693 that
joined last month and the 809 that
joined the month before that and
the 721 that joined the month
before that..
This work was supported by the US National Institute of Health
(grants GM089820 and U54GM114833) and by the Scripps
Translational Science Institute with an NIH-NCATS Clinical and
Translational Science Award (CTSA; 5 UL1 TR001114).