blob: a0de6b807cfb0b7ddba1664f55cb9e5b80280384 (
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
|
#! /usr/bin/env guile
!#
(use-modules (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 gene-chip
(tables (GeneChip
(left-join Species "USING (SpeciesId)")))
(schema-triples
(gnc:gene_chip a skos:Concept)
(gnc:gene_chip
skos:description
"This is a set of controlled terms that are used to describe a given gene chip/platform")
(gnt:has_geo_series_id rdfs:domain gnc:platform)
(gnt:has_geo_series_id rdfs:domain gnc:gene_chip)
(gnt:has_go_tree_value a owl:ObjectProperty)
(gnt:has_go_tree_value skos:definition "This resource the following GO tree value")
(gnt:has_go_tree_value rdfs:domain gnc:gene_chip))
(triples (string->identifier "platform" (field GeneChip Name) #:separator "_")
(set rdf:type 'gnc:gene_chip)
(set rdfs:label (field GeneChip GeneChipName))
(set skos:prefLabel (field GeneChip Name))
(set skos:altLabel (field ("IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL)"
Title)))
(set gnt:has_go_tree_value (field GeneChip Go_tree_value))
(set xkos:classifiedUnder
(string->identifier "" (remap-species-identifiers (field Species Fullname)) #:separator ""))
(set gnt:has_geo_series_id
(ontology 'geoSeries:
(string-trim-both (field GeneChip GeoPlatform))))))
(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 "Info files / Investigators Metadata")
(connection %connection-settings)
(table-metadata? #f)
(prefixes
'(("v:" "<http://www.w3.org/2006/vcard/ns#>")
("foaf:" "<http://xmlns.com/foaf/0.1/#term_>")
("xsd:" "<http://www.w3.org/2001/XMLSchema#>")
("dcat:" "<http://www.w3.org/ns/dcat#>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")
("xkos:" "<http://rdf-vocabulary.ddialliance.org/xkos#>")
("geoSeries:" "<http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>")
("gnt:" "<http://rdf.genenetwork.org/v1/term/>")
("gn:" "<http://rdf.genenetwork.org/v1/id/>")
("gnc:" "<http://rdf.genenetwork.org/v1/category/>")
("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>")
("owl:" "<http://www.w3.org/2002/07/owl#>")
("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>")
("taxon:" "<http://purl.uniprot.org/taxonomy/>")
("dct:" "<http://purl.org/dc/terms/>")))
(inputs
(list gene-chip))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))
|
