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
191
|
#! /usr/bin/env guile
!#
(use-modules (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))
(define-dump dump-probeset
(tables (ProbeSet
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")))
(schema-triples
(gnc:probeset a skos:Concept)
(gnc:probeset
skos:description
"This is a set of controlled terms that are used to describe a given probeset")
(gnt:hasChip a owl:ObjectProperty)
(gnt:hasChip rdfs:domain gnc:probeset)
(gnt:hasTargetId a owl:ObjectProperty)
(gnt:hasTargetId rdfs:domain gnc:probeset)
(gnt:symbol rdfs:domain gnc:probeset)
(gnt:targetsRegion a owl:ObjectProperty)
(gnt:targetsRegion rdfs:domain gnc:probeset)
(gnt:chr rdfs:domain gnc:probeset)
(gnt:mb rdfs:domain gnc:probeset)
(gnt:mbMm8 rdfs:domain gnc:probeset)
(gnt:mb2016 rdfs:domain gnc:probeset)
(gnt:hasSpecificity a owl:ObjectProperty)
(gnt:hasSpecificity rdfs:domain gnc:probeset)
(gnt:hasBlatScore a owl:ObjectProperty)
(gnt:hasBlatScore rdfs:domain gnc:probeset)
(gnt:hasBlatMbStart a owl:ObjectProperty)
(gnt:hasBlatMbStart rdfs:domain gnc:probeset)
(gnt:hasBlatMbStart2016 a owl:ObjectProperty)
(gnt:hasBlatMbStart2016 rdfs:domain gnc:probeset)
(gnt:hasBlatMbEnd a owl:ObjectProperty)
(gnt:hasBlatMbEnd rdfs:domain gnc:probeset)
(gnt:hasBlatMbEnd2016 a owl:ObjectProperty)
(gnt:hasBlatMbEnd2016 rdfs:domain gnc:probeset)
(gnt:hasBlatSeq a owl:ObjectProperty)
(gnt:hasBlatSeq rdfs:domain gnc:probeset)
(gnt:hasTargetSeq a owl:ObjectProperty)
(gnt:hasTargetSeq rdfs:domain gnc:probeset)
(gnt:hasHomologeneId a owl:ObjectProperty)
(gnt:hasHomologeneId rdfs:domain gnc:probeset)
(gnt:hasPubChemId a owl:ObjectProperty)
(gnt:hasPubChemId rdfs:domain gnc:probeset)
(gnt:hasKeggId a owl:ObjectProperty)
(gnt:hasKeggId rdfs:domain gnc:probeset)
(gnt:hasOmimId a owl:ObjectProperty)
(gnt:hasOmimId rdfs:domain gnc:probeset)
(gnt:hasChebiId a owl:ObjectProperty)
(gnt:hasChebiId rdfs:domain gnc:probeset))
(triples
(let ((id (field ("IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name))"
ProbeSetIdName)))
(probeset-id (field ProbeSet Id)))
(if (string-null? id)
(string->identifier
"probeset"
(number->string
probeset-id))
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
id
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)))
(set rdf:type 'gnc:probeset)
(set rdfs:label (field ProbeSet Name))
(set skos:altLabel
(replace-substrings
(field ProbeSet alias)
'(("\r\n" . "; "))))
(set gnt:hasChip
(string->identifier
"platform"
(field ("IFNULL(GeneChip.Name, '')" GeneChipName))))
(set gnt:hasTargetId
(field ("NULLIF(TRIM(ProbeSet.TargetId), '')"
TargetId)))
(set gnt:symbol (field ProbeSet Symbol))
(set dct:description (sanitize-rdf-string (field ProbeSet description)))
(set gnt:targetsRegion
(sanitize-rdf-string
(field ("NULLIF(TRIM(ProbeSet.Probe_set_target_region), '')"
Probe_set_target_region))))
(set gnt:chr (field ProbeSet Chr))
(set gnt:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
(set gnt:mbMm8 (annotate-field (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8))
'^^xsd:double))
(set gnt:mb2016
(annotate-field (field ("IFNULL(ProbeSet.Mb_2016, '')" Mb_2016))
'^^xsd:double))
(set gnt:hasSpecificity
(annotate-field (field ("IFNULL(ProbeSet.Probe_set_specificity, '')"
Probe_set_specificity))
'^^xsd:double))
(set gnt:hasBlatScore
(annotate-field (field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')"
Probe_set_BLAT_score))
'^^xsd:double))
(set gnt:hasBlatMbStart
(annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')"
Probe_set_Blat_Mb_start))
'^^xsd:double))
(set gnt:hasBlatMbStart2016
(annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '')"
Probe_set_Blat_Mb_start_2016))
'^^xsd:double))
(set gnt:hasBlatMbEnd
(annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')"
Probe_set_Blat_Mb_end))
'^^xsd:double))
(set gnt:hasBlatMbEnd2016
(annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '')"
Probe_set_Blat_Mb_start_2016))
'^^xsd:double))
(set gnt:hasBlatSeq (sanitize-rdf-string (field ProbeSet BlatSeq)))
(set gnt:hasTargetSeq (sanitize-rdf-string (field ProbeSet TargetSeq)))
(set gnt:hasHomologeneId (ontology 'homologene:
(field ("IFNULL(ProbeSet.HomoloGeneID, '')"
HomoloGeneID))))
(set gnt:hasUniprotId (ontology 'uniprot:
(field ("IFNULL(ProbeSet.UniProtID, '')"
UniProtID))))
(set gnt:hasPubChemId (ontology
'pubchem:
(field ("IFNULL(ProbeSet.PubChem_ID, '')"
PubChem_ID))))
(set gnt:hasKeggId (ontology
'kegg:
(field ("IFNULL(ProbeSet.KEGG_ID, '')"
KEGG_ID))))
(set gnt:hasOmimId (ontology
'omim:
(let ((omim (field ("IFNULL(ProbeSet.OMIM, '')"
OMIM))))
(if (number? omim)
omim
(regexp-substitute/global
#f "[^0-9]"
omim
'pre "" 'post)))))
(set gnt:hasChebiId (ontology
'chebi:
(field ("IFNULL(ProbeSet.ChEBI_ID, '')"
ChEBI_ID))))))
(dump-with-documentation
(name "ProbeSet Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("gn:" "<http://genenetwork.org/id/>")
("probeset:" "<http://genenetwork.org/probeset/>")
("gnc:" "<http://genenetwork.org/category/>")
("gnt:" "<http://genenetwork.org/term/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("kegg:" "<http://bio2rdf.org/ns/kegg#>")
("pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>")
("omim:" "<https://www.omim.org/entry/>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("uniprot:" "<http://purl.uniprot.org/uniprot/>")
("chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>")
("dct:" "<http://purl.org/dc/terms/>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("homologene:" "<https://bio2rdf.org/homologene:>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
(inputs
(list dump-probeset))
(outputs
'(#:documentation "./docs/dump-probeset.md"
#:rdf "./verified-data/dump-probeset.ttl")))
|
