The best explanation I can offer is that the optimizer does weird things sometimes, especially with subqueries: in my experience, subqueries rarely bring the optimization I expect. However, *named* subqueries often perform a lot better (they run exactly once). This version of your query runs in less than a second: PREFIX wp: <http://vocabularies.wikipathways.org/wp#> <http://vocabularies.wikipathways.org/wp#> PREFIX dcterms: <http://purl.org/dc/terms/> <http://purl.org/dc/terms/> PREFIX dc: <http://purl.org/dc/elements/1.1/> <http://purl.org/dc/elements/1.1/> SELECT DISTINCT ?metabolite1Label ?metabolite2Label ?mass1 ?mass2 WITH { SELECT ?metabolite1 ?metabolite2 WHERE { ?pathwayItem wdt:P2410 "WP706"; wdt:P2888 ?pwIri. SERVICE <http://sparql.wikipathways.org/> <http://sparql.wikipathways.org/> { ?pathway dc:identifier ?pwIri. ?interaction rdf:type wp:Interaction; wp:participants ?wpmb1, ?wpmb2; dcterms:isPartOf ?pathway. FILTER (?wpmb1 != ?wpmb2) ?wpmb1 wp:bdbWikidata ?metabolite1. ?wpmb2 wp:bdbWikidata ?metabolite2. } } } AS %metabolites WHERE { INCLUDE %metabolites. ?metabolite1 wdt:P2067 ?mass1. ?metabolite2 wdt:P2067 ?mass2. SERVICE wikibase:label { bd:serviceParam wikibase:language "[AUTO_LANGUAGE],en". } } Cheers, Lucas On 26.06.2017 21:58, Andra Waagmeester wrote: I am puzzled by a pattern I am seeing in submitting nested SELECT statements to the WDQS. In cases where a federated query to the WDQS time out, it helps to include redundant SELECT statements for the same query to resolve. The following query does not resolve: [image: Inline image 1] source: https://gist.github.com/andrawaag/ba1b7d1b9adf06e9d45afa98c1d1e239 results: http://tinyurl.com/ybl55tk4 When the lines 7 and 9 in the above example are duplicated, suddenly the query does resolve [image: Inline image 2] source: https://gist.github.com/andrawaag/7e2e793342011f66bb6a3ea7bb5a1326 results: http://tinyurl.com/y9mjkejo What is the added value of a double SELECT (line 7,8 and line 10,11). Also the lines 5 and 9 had to be separated by a SELECT statement to be successful. Is this an implementation issue, or am I doing something wrong? kind regards, Andra Waagmeester _______________________________________________ Wikidata mailing listWikidata@lists.wikimedia.orghttps://lists.wikimedia.org/mailman/listinfo/wikidata _______________________________________________ Wikidata mailing list Wikidata(a)lists.wikimedia.org https://lists.wikimedia.org/mailman/listinfo/wikidata