Benjamin Good, TSRIIC-Foods, UC Davis, 2016

@bgoodbgood@scripps.eduhttp://www.slideshare.net/goodb

and the

Semantic Web of Food

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

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

It’s a knowledge base!

• Anyone can edit (human or robot)

• Anyone can use (CC0)

Deeply integrated

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

Items are described by “statements” that link together to form the language-independent wikidata knowledge graph

Cat

Domesticated Animal

Animal

Subclass Of

Subclass Of

AnimaliaTaxon name

KingdomTaxon rank

Item: Q84

Inter-item links form a giant knowledge graph

Everything is connectedReelin, Heart disease, Barack Obama, everything..

https://query.wikidata.orgSPARQL endpoint for Wikidata

Example question: repurposing Metformin

http://tinyurl.com/zem3oxz

Metformin

?disease

interacts with

protein

geneencoded by genetic association

Mighttreat ?

Solute carrier family 22

member 3

SLC22A3

prostate cancer

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) DatabaseMitraka et al (2015) Semantic Web Applications for the Life Sciences

Putman et al (2016) Database

Application #1 Wikipedia enhancement

Burgstaller et al (2016)

http://wikigenomes.org

Application #2 Wikigenomes

1 requirement for any Semantic Web

• Unambiguous, accessible way of naming and defining things

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

You say Furaneol..Dimethylhydroxy furanonePineapple ketone2,5-Dimethyl-4-hydroxy-3(2H)-furanone2,5-Dimethyl-4-hydroxy-2,3-dihydrofuran-3-one2,5-Dimethyl-3-hydroxy-4-oxo-4,5-dihydrofuran4-hydroxy-2,5-dimethyl-3(2H)-furanoneHDMF4-hydroxy-2,5-dimethylfuran-3-one

CAS registry numberPubChem ID (CID)InChIInChIKeyChemSpider IDUNIIChEMBL IDChEBI IDECHA InfoCard IDBeilstein Registry NumberHMDB ID

Database ids..

Labels, definitions, article links

I say Q250455

Acknowledgements

Gene Wikidata TeamAndra 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)

Contactbgood@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).