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Wikidata and the Semantic Web of Food


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

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Wikidata and the Semantic Web of Food

  1. 1. Benjamin Good, TSRI IC-Foods, UC Davis, 2016 @bgood and the Semantic Web of Food
  2. 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. 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. 4. It’s a knowledge base! • Anyone can edit (human or robot) • Anyone can use (CC0)
  5. 5. Deeply integrated
  6. 6. Elements of the kb are called ‘items’
  7. 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. 8. Item: Q84
  9. 9. Inter-item links form a giant knowledge graph Everything is connected Reelin, Heart disease, Barack Obama, everything.. SPARQL endpoint for Wikidata
  10. 10. Example question: repurposing Metformin Metformin ?disease interacts with protein geneencoded by genetic association Might treat ? Solute carrier family 22 member 3 SLC22A3 prostate cancer
  11. 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. 12. Application #1 Wikipedia enhancement Burgstaller et al (2016)
  13. 13. Application #2 Wikigenomes
  14. 14. 1 requirement for any Semantic Web • Unambiguous, accessible way of naming and defining things
  15. 15. You say Tomato, I say: 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. 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. 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 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).