aboutsummaryrefslogtreecommitdiff
path: root/examples/phenotype.scm
blob: 2a6b192d9a44cc28a5d8e4611584a17cc0cdc180 (plain)
1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
102
103
104
105
106
107
108
109
110
111
112
113
114
115
116
117
118
119
120
121
122
123
124
125
126
127
128
129
130
131
132
133
134
135
136
137
138
139
#! /usr/bin/env guile
!#

(use-modules (rnrs programs)
             (rnrs io ports)
             (srfi srfi-1)
             (srfi srfi-26)
             (ice-9 getopt-long)
             (ice-9 match)
             (ice-9 regex)
             (transform strings)
             (transform sql)
             (transform triples)
             (transform special-forms))


(define-transformer phenotypes
  (tables (PublishXRef
           (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
           (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
           (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))
          "WHERE PublishXRef.InbredSetId IN (SELECT PublishFreeze.InbredSetId FROM PublishFreeze)")
  (schema-triples
   (gnt:abbreviation a owl:ObjectProperty)
   (gnt:abbreviation rdfs:domain gnc:Phenotype)
   (gnt:abbreviation skos:definition "The abbreviation used for this resource")
   (gnt:labCode a owl:ObjectProperty)
   (gnt:labCode rdfs:domain gnc:Phenotype)
   (gnt:submitter a owl:ObjectProperty)
   (gnt:submitter rdfs:domain gnc:Phenotype)
   (gnt:submitter skos:definition "A person who submitted this resource to GN")
   (gnt:mean a rdf:Property)
   (gnt:mean a qb:MeasureProperty)
   (gnt:mean rdfs:subPropertyOf sdmx-measure:obsValue)
   (gnt:mean rdfs:domain gnc:Phenotype)
   (gnt:mean rdfs:range xsd:double)
   (gnt:LRS a rdf:Property)
   (gnt:LRS a qb:MeasureProperty)
   (gnt:LRS rdfs:subPropertyOf sdmx-measure:obsValue)
   (gnt:LRS rdfs:domain gnc:Phenotype)
   (gnt:LRS rdfs:range xsd:double)
   (gnt:locus a rdf:Property)
   (gnt:locus a qb:MeasureProperty)
   (gnt:locus rdfs:subPropertyOf sdmx-measure:obsValue)
   (gnt:locus rdfs:domain gnc:Phenotype)
   (gnt:locus rdfs:range rdfs:Literal)
   (gnt:additive rdfs:domain gnc:Phenotype)
   (gnt:additive rdfs:range xsd:double)
   (gnt:sequence rdfs:domain gnc:Phenotype)
   (gnt:sequence rdfs:range xsd:integer))
  (triples (string->identifier
            "trait"
            (field ("CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
                    Phenotype)))
    (set rdf:type 'gnc:Phenotype)
    (set xkos:classifiedUnder
         (string->identifier
          "set" (field InbredSet Name InbredSetName)
          #:separator ""
          #:proc string-capitalize-first))
    ;; This is the trait's name
    (set rdfs:label
         (let ((trait-id (field PublishXRef Id)))
           (if (number? trait-id)
               (number->string trait-id)
               trait-id)))
    (set skos:altLabel
         (field ("CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
                 Phenotype)))
    ;; All phenotypes have a post-publication description
    (set dct:description
         (sanitize-rdf-string
          (field Phenotype Post_publication_description)))
    ;; All phenotypes have a post-publication abbreviation
    (set gnt:abbreviation (field Phenotype Post_publication_abbreviation))
    (set gnt:labCode (field Phenotype Lab_code))
    (set gnt:submitter
         (sanitize-rdf-string (field Phenotype Submitter)))
    (multiset dct:contributor
              (string-split
               (sanitize-rdf-string (field Phenotype Owner))
               #\,))
    (set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
                                  '^^xsd:double))
    (set gnt:locus (field PublishXRef Locus))
    (set gnt:LRS (annotate-field
                  (field ("IFNULL(PublishXRef.LRS, '')" lrs))
                  '^^xsd:double))
    (set gnt:additive
         (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive))
                         '^^xsd:double))
    (set gnt:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:integer))
    (set dct:isReferencedBy
         (let ((pmid (field
                      ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))"
                       pmid)))
               (publication-id (field Publication Id)))
           (if (string-null? pmid)
               (string->identifier "unpublished"
                                   (number->string publication-id))
               (ontology 'pubmed: pmid))))))



(let* ((option-spec
        '((settings (single-char #\s) (value #t))
          (output (single-char #\o) (value #t))
          (documentation (single-char #\d) (value #t))))
       (options (getopt-long (command-line) option-spec))
       (settings (option-ref options 'settings #f))
       (output (option-ref options 'output #f))
       (documentation (option-ref options 'documentation #f))
       (%connection-settings
        (call-with-input-file settings
          read)))
  (with-documentation
   (name "Phenotypes Metadata")
   (connection %connection-settings)
   (table-metadata? #f)
   (prefixes
    '(("dct:" "<http://purl.org/dc/terms/>")
      ("gn:" "<http://genenetwork.org/id/>")
      ("owl:" "<http://www.w3.org/2002/07/owl#>")
      ("gnc:" "<http://genenetwork.org/category/>")
      ("gnt:" "<http://genenetwork.org/terms/>")
      ("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
      ("skos:" "<http://www.w3.org/2004/02/skos/core#>")
      ("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
      ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
      ("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
      ("qb:" "<http://purl.org/linked-data/cube#>")
      ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
   (inputs
    (list
     phenotypes))
   (outputs
    `(#:documentation ,documentation
      #:rdf ,output))))