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
149
150
151
152
153
154
155
156
157
158
159
160
161
162
163
164
165
166
167
168
169
170
171
172
173
174
175
176
177
178
179
180
181
182
183
184
185
186
187
188
189
190
|
#! /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 (blank-p str)
(if (string-blank? str) #f str))
(define-transformer gn:set->gn:dataset
(tables (Species
(inner-join InbredSet "ON InbredSet.SpeciesId = Species.Id")
(inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id"))
"WHERE PublishFreeze.public > 0 AND Species.Name != 'monkey' GROUP BY Species.Name, PublishFreeze.ShortName")
(triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")
(multiset gnt:has_phenotype_data
(map (cut string->identifier "dataset" <> #:separator "_")
(string-split
(field ("GROUP_CONCAT(PublishFreeze.Name SEPARATOR ',')"
dataset_name))
#\,)))))
(define-transformer gn:dataset->gn:trait
(tables (PublishXRef
(left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId")
(inner-join PublishFreeze "ON PublishFreeze.InbredSetId = InbredSet.Id")
(left-join Publication "ON Publication.Id = PublishXRef.PublicationId")
(left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))
"WHERE InbredSet.public > 0")
(triples (string->identifier "dataset" (field PublishFreeze Name) #:separator "_")
(set gnt:has_phenotype_trait
(let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation)))
(pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation)))
(post-desc (blank-p (field Phenotype Post_publication_description)))
(pre-desc (blank-p (field Phenotype Post_publication_description))))
(string->identifier
"trait"
(format #f "~a_~a" (field PublishFreeze Name)
(or post-abbrev pre-abbrev post-desc pre-desc))
#:separator "_")))))
(define-transformer gnc:phenotype->gn:phenotype
(tables (Phenotype))
(triples "gnc:phenotype"
(set skos:member
(let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation)))
(pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation)))
(post-desc (blank-p (field Phenotype Post_publication_description)))
(pre-desc (blank-p (field Phenotype Post_publication_description))))
(string->identifier
"phenotype"
(or post-abbrev pre-abbrev post-desc pre-desc)
#:separator "_")))))
(define-transformer gn:phenotype->metadata
(tables (Phenotype))
(triples (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation)))
(pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation)))
(post-desc (blank-p (field Phenotype Post_publication_description)))
(pre-desc (blank-p (field Phenotype Post_publication_description))))
(string->identifier
"phenotype"
(or post-abbrev pre-abbrev post-desc pre-desc)
#:separator "_"))
(set rdf:type 'gnc: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 (sanitize-rdf-string (field Phenotype Post_publication_abbreviation)))
(set gnt:has_lab_code (field Phenotype Lab_code))
(set gnt:submitter
(sanitize-rdf-string (field Phenotype Submitter)))
(set dct:contributor (sanitize-rdf-string (field Phenotype Owner)))
(set skos:member
(let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation)))
(pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation)))
(post-desc (blank-p (field Phenotype Post_publication_description)))
(pre-desc (blank-p (field Phenotype Post_publication_description))))
(string->identifier
"phenotype"
(or post-abbrev pre-abbrev post-desc pre-desc)
#:separator "_")))))
(define-transformer gn:trait->gn:phenotype
(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 InbredSet.public > 0")
(triples (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation)))
(pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation)))
(post-desc (blank-p (field Phenotype Post_publication_description)))
(pre-desc (blank-p (field Phenotype Post_publication_description))))
(string->identifier
"trait"
(format #f "~a_~a" (field PublishFreeze Name)
(or post-abbrev pre-abbrev post-desc pre-desc))
#:separator "_"))
(set rdf:type 'gnc:phenotype_trait)
(set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_"))
(set owl:equivalentClass
(field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)"
Phenotype)))
(set dct:references
(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))))
(set gnt:has_phenotype
(let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation)))
(pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation)))
(post-desc (blank-p (field Phenotype Post_publication_description)))
(pre-desc (blank-p (field Phenotype Post_publication_description))))
(string->identifier
"phenotype"
(or post-abbrev pre-abbrev post-desc pre-desc)
#:separator "_")))
(set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean))
'^^xsd:double))
(set gnt:locus
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(sanitize-rdf-string (field PublishXRef Locus))
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first))
(set gnt:lod_score (annotate-field
(field ("IFNULL((PublishXRef.LRS/4.604), '')" 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 rdfs:comment (sanitize-rdf-string (field PublishXRef comments)))))
(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://rdf.genenetwork.org/v1/id/>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
("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#>")
("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>")))
(inputs
(list gn:set->gn:dataset gn:dataset->gn:trait gnc:phenotype->gn:phenotype gn:phenotype->metadata gn:trait->gn:phenotype))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
|
