blob: a45fd0af7da0fbfa3a5a3f54b98baf286aecdabc (
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
|
#! /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-gene-chip
(tables (GeneChip))
(schema-triples
(gn-term:name rdfs:range rdfs:Literal))
(triples (string->identifier "platform" (field GeneChip Name))
(set rdf:type 'gn:platform)
(set gn-term:name (field GeneChip GeneChipName))
(set gn-term:geoPlatform
(ontology 'geoSeries:
(string-trim-both (field GeneChip GeoPlatform))))))
;; Molecular Traits are also referred to as ProbeSets
(define-dump dump-probesetfreeze
(tables (ProbeSetFreeze
(left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name")
(left-join ProbeFreeze "USING (ProbeFreezeId)")
(left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID")
(left-join InbredSet "ON ProbeFreeze.InbredSetId = InbredSet.Id")
(left-join Tissue "ON ProbeFreeze.TissueId = Tissue.TissueId"))
"WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id")
(schema-triples
(gn-term:avgMethod rdfs:range rdfs:Literal)
(gn-term:dataScale rdfs:range rdfs:Literal)
(gn:probesetDataset rdf:subClassOf gn:dataset))
(triples
(string->identifier
""
(regexp-substitute/global
#f "[^A-Za-z0-9:]"
(field ProbeSetFreeze Name)
'pre "_" 'post)
#:separator ""
#:proc string-capitalize-first)
(set rdf:type 'gn:probesetDataset)
(set gn-term:avgMethod (string->identifier "avgmethod" (field AvgMethod Name)))
(set gn-term:fullName (field ProbeSetFreeze FullName))
(set gn-term:shortName (field ProbeSetFreeze ShortName))
(set dct:created (annotate-field
(field ProbeSetFreeze CreateTime)
'^^xsd:datetime))
(set gn-term:dataScale (field ProbeSetFreeze DataScale))
(set gn-term:tissueName (string->identifier "tissue" (field Tissue Short_Name)))
(set gn-term:datasetOfInbredSet
(string->identifier "inbredSet" (field InbredSet Name InbredSetName)))))
(dump-with-documentation
(name "Probeset freeze metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
("gn:" "<http://genenetwork.org/id/>")
("gn-term:" "<http://genenetwork.org/term/>")
("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#>")))
(inputs
(list dump-gene-chip
dump-probesetfreeze))
(outputs
'(#:documentation "./docs/dump-gene-chip.md"
#:rdf "./verified-data/dump-probesetfreeze.ttl")))
|
