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Get rid of a GroundedSchemeNode #167

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merged 3 commits into from
Mar 18, 2020
Merged

Get rid of a GroundedSchemeNode #167

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8dde206
Get rid of a GroundedSchemeNode
linas Mar 17, 2020
3b7346d
Move code closer to it's caller
linas Mar 18, 2020
2654b6c
Bug-fix unit test
linas Mar 18, 2020
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101 changes: 57 additions & 44 deletions annotation/functions.scm
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Original file line number Diff line number Diff line change
Expand Up @@ -481,31 +481,63 @@ in the specified namespaces."

;; ------------------------------------------------------

;; Gene interactors for genes in the pathway
(define do-pathway-gene-interactors
(lambda (pw)
(run-query (BindLink
(VariableList
(TypedVariable (VariableNode "$g1") (Type 'GeneNode))
(TypedVariable (VariableNode "$g2") (Type 'GeneNode))
(TypedVariable (VariableNode "$p1") (Type 'MoleculeNode))
(TypedVariable (VariableNode "$p2") (Type 'MoleculeNode)))
(AndLink
(MemberLink (VariableNode "$p1") pw)
(MemberLink (VariableNode "$p2") pw)
(EvaluationLink (PredicateNode "expresses") (ListLink (VariableNode "$g1") (VariableNode "$p1")))
(EvaluationLink (PredicateNode "expresses") (ListLink (VariableNode "$g2") (VariableNode "$p2")))
(EvaluationLink (PredicateNode "interacts_with") (ListLink (VariableNode "$g1") (VariableNode "$g2")))
)
(ExecutionOutputLink
(GroundedSchemaNode "scm: generate-interactors")
(ListLink
pw
(VariableNode "$g1")
(VariableNode "$g2")
))
))
))
(define (generate-interactors path var1 var2)
; (biogrid-reported-pathways) is a cache of the interactions that have
; already been handled. Defined in util.scm and cleared in main.scm.
(if (or (equal? var1 var2)
((biogrid-reported-pathways) (Set var1 var2))) #f
(let ([output (find-pubmed-id var1 var2)])
(if (null? output)
(EvaluationLink
(PredicateNode "interacts_with")
(ListLink var1 var2))
(EvaluationLink
(PredicateNode "has_pubmedID")
(ListLink
(EvaluationLink
(PredicateNode "interacts_with")
(ListLink var1 var2))
output)))))
)

(define (do-pathway-gene-interactors pw)
"
Gene interactors for genes in the pathway.

This finds all pentagons, where two proteins appear on the same
pathway, the genes expressing those proteins are known, and the
two genes are interacting. That is,

pathway <--is-in-- protein-1 <--expresses-- gene-1
pathway <--is-in-- protein-2 <--expresses-- gene-2
gene-1 <--interacts--> gene-2
"
; Find all interaction
(define gene-pentagons
(run-query (Get
(VariableList
(TypedVariable (Variable "$g1") (Type 'GeneNode))
(TypedVariable (Variable "$g2") (Type 'GeneNode))
(TypedVariable (Variable "$p1") (Type 'MoleculeNode))
(TypedVariable (Variable "$p2") (Type 'MoleculeNode)))
(And
(Member (Variable "$p1") pw)
(Member (Variable "$p2") pw)
(Evaluation (Predicate "expresses")
(List (Variable "$g1") (Variable "$p1")))
(Evaluation (Predicate "expresses")
(List (Variable "$g2") (Variable "$p2")))
(Evaluation (Predicate "interacts_with")
(List (Variable "$g1") (Variable "$g2")))))))

(filter-map
(lambda (gene-path)
(define g1 (gar gene-path))
(define g2 (gdr gene-path))
(cog-delete gene-path) ; get rid of unused ListLink
(generate-interactors pw g1 g2))
gene-pentagons)
)

;; Cache previous results, so that they are not recomputed again,
;; if the results are already known. Note that this function accounts
Expand Down Expand Up @@ -696,25 +728,6 @@ in the specified namespaces."
)
)

(define-public (generate-interactors path var1 var2)
; (biogrid-reported-pathways) is a cache of the interactions that have
; already been handled. Defined in util.scm and cleared in main.scm.
(if (or (equal? var1 var2)
((biogrid-reported-pathways) (Set var1 var2))) '()
(let ([output (find-pubmed-id var1 var2)])
(if (null? output)
(EvaluationLink
(PredicateNode "interacts_with")
(ListLink var1 var2))
(EvaluationLink
(PredicateNode "has_pubmedID")
(ListLink
(EvaluationLink
(PredicateNode "interacts_with")
(ListLink var1 var2))
output)))))
)

;; ------------------------------------------------------
(define (do-find-pubmed-id gene-set)
"
Expand Down