ISWC2022 Challenge

/International Semantic Web Challenge (ISWC) 2022
Two tasks are proposed :

Using federated SPARQL query that will consume Bio2RDF’s endpoints.
Using any programming approach that will consume Kibio’s Elasticsearch indexes.

Will REST JSON-LD APIs do better over SPARQL endpoints ? We will see.

How can we run the Wikidata FAIR paper SPARQL query without using Wikidata SPARQL endpoint ?

Two tasks are proposed :

Using federated SPARQL query that will consume Bio2RDF’s endpoints.
Using any programming approach that will consume Kibio’s Elasticsearch indexes.

Will REST JSON-LD APIs do better over SPARQL endpoints ? We will see.

SELECT DISTINCT ?compound ?compoundLabel where {

  # gene has genetic association with a respiratory disease  
  ?gene       wdt:P31    wd:Q7187 .
  ?gene       wdt:P2293  ?diseaseGA .
  ?diseaseGA  wdt:P279*  wd:Q3286546 .

  # gene product is localized to the membrane
  ?gene     wdt:P688             ?protein .
  ?protein  wdt:P681             ?cc .
  ?cc       wdt:P279*|wdt:P361*  wd:Q14349455 .

  # gene is involved in a pathway with another gene (gene2)
  ?pathway  wdt:P31   wd:Q4915012 ;
            wdt:P527  ?gene ;
            wdt:P527  ?gene2 .
  ?gene2    wdt:P31   wd:Q7187 . 

  # gene2 product has a Ser/Thr protein kinase domain AND known enzyme inhibitor  
  ?gene2     wdt:P688  ?protein2 .
  ?protein2  wdt:P129  ?compound ;
             wdt:P527  wd:Q24787419 ;
             p:P129    ?s2 .
  ?s2        ps:P129   ?cp2 .
  ?compound  wdt:P31   wd:Q11173 .
  FILTER EXISTS {?s2 pq:P366 wd:Q427492 .}

  SERVICE wikibase:label { bd:serviceParam wikibase:language "en". }
}

The query can be run using this link https://tinyurl.com/53ra32bp

Specifically, this query (depicted schematically at right) retrieves genes that are (i) associated with a respiratory system disease, (ii) that encode a membrane-bound protein, and (iii) that sit within the same biochemical pathway as (iv) a second gene encoding a protein with a serine-threonine kinase domain and (v) a known inhibitor, and reports a list of those inhibitors.

Two tasks are proposed :

Using federated SPARQL query that will consume Bio2RDF’s endpoints.
Using any programming approach that will consume Kibio’s Elasticsearch indexes.

How to participate

Challenge Wikidata datasets

Challenge datasources to be used

Challenge rules