Combining with other linked databases Andra Waagmeester, Dragan Espenschied Known variants in the CIViC database for genes reported in a WikiPathways pathway on Bladder Cancer

Primary Sources: ● Wikipathways (Q7999828) ● NCBI Gene (Q20641742) ● CIViCdb (Q27612411) ● Disease Ontology (Q5282129) Example 1: Wikidata contains public data

“All structured data from the main and property namespace is available under the CC0 License; text in the other namespaces is available under the Creative Commons Attribution-ShareAlike License; additional terms may apply. By using this site, you agree to the Terms of Use and Privacy Policy.” Wikidata requirement for Notability

An item is acceptable if and only if it fulfills at least one of these two goals, that is if it meets at least one of the criteria below:

● It contains at least one valid sitelink to a page on , , , , , , Wikidata, , , or . ● It refers to an instance of a clearly identifiable conceptual or material entity.it can be described using serious and publicly available references. ● It fulfills some structural need, https://www.wikidata.org/wiki/Wikidata:Notability Wikidata property proposals

“Before a new property is created, it has to be discussed here. When after some time there are some supporters, but no or very few opponents, the property is created by a property creator or an administrator.

You can propose a property here or on one of the subject-specific pages listed below.”

https://www.wikidata.org/wiki/Wikidata:Property_proposal Structure of a Federated Query Wikidata supports federation on a limited set of endpoints

● On 27 endpoints (https://www.mediawiki.org/wiki/Wikidata_query_service/User_Manual#Feder ation) ● Europeana, Biblioteca Virtual Miguel de Cervantes, Biblioteca Nacional de España, Smithsonian American Art Museum, Bibliothèque nationale de France, DBPedia, Getty Vocabularies, INSEE, Istituto per i beni artistici, culturali e naturali, Italian Chamber of Deputies, Nomisma.org, Smart Points of Interest, UK Department for Communities and Local Government, UK Office for National Statistics, UK ordnance survey, URI Burnder, WikiPathways, MW2SPARQL, Yale Center for British Art, Linked Geodata, Linked Open Street Map, Framester, AGROVOC Example 2: Integrating with more detailed data

Example 3: Integrating Wikidata from a remote SPARQL endpoint

“all human UniProt entries with a sequence variants that leads to a loss of function, and also physically interacts with a drug used as an enzyme inhibitor.”

Making sense of Zika in the americas

1. Install a SPARQL endpoint locally 2. Model data with Wikidata properties 3. Convert data into RDF 4. Load 5. Query 6. Live: Demo Live demo