added chemical affects gene query

Author: webyrd

contrib/medikanren2/neo/Will/chemical-affects-gene.rkt

@@ -0,0 +1,29 @@
+#lang racket/base
+
+(require
+ "../../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt"
+ "../../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt"
+ "../../../../medikanren2/neo/neo-server/neo-server-utils.rkt"
+ "../utils.rkt"
+ json
+ racket/format
+ racket/list
+ racket/match
+ racket/set
+ racket/pretty
+ racket/string)
+
+;; finds a list of compounds that affect a provided set of genes
+(define (chem-affects-gene gene-list)
+  (time (remove-duplicates
+         (query:X->Known
+          (set->list
+           (get-non-deprecated/mixin/abstract-ins-and-descendent-classes*-in-db
+            '("biolink:ChemicalEntity")))
+          (set->list
+           (get-non-deprecated/mixin/absreact-ins-and-descendent-predicates*-in-db
+            '("biolink:affects")))
+          (set->list (curie-synonyms-and-descendents gene-list))))))
+
+;; test with BRCA2 gene
+(define chem-affects-BRCA2 (chem-affects-gene (list "HGNC:1101")))

contrib/medikanren2/neo/utils.rkt

@@ -5,6 +5,8 @@
 
          get-props
 
+         curie-synonyms-and-descendents
+
          write-answers-to-tsv
 
          get-source
@@ -24,9 +26,14 @@
          racket/match
          "../../../medikanren2/neo/neo-server/neo-server-utils.rkt"
          "../../../medikanren2/neo/neo-low-level/query-low-level-multi-db.rkt"
+         "../../../medikanren2/neo/neo-utils/neo-helpers-multi-db.rkt"         
          "../../../medikanren2/neo/neo-utils/neo-helpers-without-db.rkt"
          )
 
+(define (curie-synonyms-and-descendents curie-list)
+  (get-descendent-curies*-in-db
+   (curies->synonyms-in-db curie-list)))
+
 (define (concept->name curie)
   (let ((id-name-val
          (remove-duplicates (filter (lambda (cl)