aboutsummaryrefslogtreecommitdiff
path: root/examples/dump-phenotype.scm
blob: 983756b9cb5247f32bc423bbe7e077802453315f (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
140
141
142
143
144
145
146
147
148
#! /usr/bin/env guile
!#

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



(define %connection-settings
  (call-with-input-file (list-ref (command-line) 1)
    read))



;; Only dump publish freeze entries that were not dumped from the InfoFiles page
(define-dump dump-publishfreeze
  (tables (PublishFreeze
           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")
           (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId"))
          "WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL")
  (schema-triples
   (gnt:datasetOfInbredSet rdfs:range gn:inbredSet)
   (gnt:name rdfs:range rdfs:Literal)
   (gnt:fullName rdfs:range rdfs:Literal)
   (gnt:shortName rdfs:range rdfs:Literal)
   (gn:phenotypeDataset rdf:subClassOf gn:dataset))
  (triples
      (string->identifier
       ""
       (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                 (field PublishFreeze Name)
                                 'pre "_" 'post)
       #:separator ""
       #:proc string-capitalize-first)
    (set rdf:type 'gnc:phenotypeDataset)
    (set gnt:name (field PublishFreeze Name))
    (set gnt:fullName (field PublishFreeze FullName))
    (set gnt:shortName (field PublishFreeze ShortName))
    (set dct:created (annotate-field
                      (field PublishFreeze CreateTime)
                      '^^xsd:date))
    (set gnt:datasetOfInbredSet
         (string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))

(define-dump dump-phenotypes
  (tables (Phenotype
           (left-join PublishXRef "ON Phenotype.Id = PublishXRef.PhenotypeId")
           (left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
           (left-join PublishFreeze "ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId")
           (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name")))
  (schema-triples
   (gn:phenotypeDataset rdfs:subPropertyOf gn:dataset)
   (gnt:publicationDescription rdfs:range rdfs:Literal)
   (gnt:originalDescription rdfs:range rdfs:Literal)
   (gnt:prePublicationDescription rdfs:range rdfs:Literal)
   (gnt:postPublicationAbbreviation rdfs:range rdfs:Literal)
   (gnt:labCode rdfs:range rdfs:Literal)
   (gnt:submitter rdfs:range rdfs:Literal)
   (gnt:owner rdfs:range rdfs:Literal)
   (gnt:mean rdfs:range xsd:double)
   (gnt:LRS rdfs:range xsd:float)
   (gnt:locus rdfs:range rdfs:Literal)
   (gnt:additive rdfs:range xsd:decimal)
   (gnt:sequence rdfs:range rdfs:Literal)
   (gnt:phenotypeOfPublication rdfs:range gn-term:pubMedId))
  (triples (string->identifier
            ""
            (regexp-substitute/global #f "[^A-Za-z0-9:]"
                                        (field ("CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '_')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation))" abbrev))
                                        'pre "_" 'post)
            #:separator ""
            #:proc string-capitalize-first)
    (set rdf:type 'gnc:phenotype)
    (set gnt:name (sanitize-rdf-string
                  (field
                   ("CAST(CONVERT(BINARY CONVERT(IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation) USING latin1) USING utf8) AS VARCHAR(100))"
                    PhenotypeName))))
    ;; There is no row with an empty post-publication description so
    ;; use this field as the main publication description
    (set gnt:publicationDescription
         (sanitize-rdf-string
          (field ("CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000))"
                  postPubDescr))))
    (set gnt:originalDescription (sanitize-rdf-string
                                 (delete-substrings
                                  (field Phenotype Original_description)
                                  "Original post publication description: ")))
    (set gnt:prePublicationDescription
         (sanitize-rdf-string
          (field
           ("CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000))"
            prePubDesc))))
    (set gnt:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation)))
    (set gnt:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
    (set gnt:labCode (field Phenotype Lab_code))
    (set gnt:submitter (sanitize-rdf-string (field Phenotype Submitter)))
    (set gnt:owner (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:float))
    (set gnt:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal))
    (set gnt:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int))
    (set gnt:phenotypeOfDataset
         (string->identifier
          ""
          (field
           ("IFNULL(InfoFiles.InfoPageName, IFNULL(PublishFreeze.Name, ''))" DatasetName))
          #:separator ""
          #:proc string-capitalize-first))
    (set gnt:phenotypeOfPublication
         (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))))))


(dump-with-documentation
 (name "Phenotypes Metadata")
 (connection %connection-settings)
 (table-metadata? #f)
 (prefixes
  '(("dct:" "<http://purl.org/dc/terms/>")
    ("gn:" "<http://genenetwork.org/id/>")
    ("gnc:" "<http://genenetwork.org/category/>")
    ("gnt:" "<http://genenetwork.org/terms/>")
    ("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#>")
    ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
 (inputs
  (list dump-publishfreeze
        dump-phenotypes))
 (outputs
  '(#:documentation "./docs/dump-phenotype.md"
    #:rdf "./verified-data/dump-phenotype.ttl")))