diff options
| -rwxr-xr-x | examples/dataset-metadata.scm | 30 | ||||
| -rwxr-xr-x | examples/gene-chip.scm | 78 |
2 files changed, 79 insertions, 29 deletions
diff --git a/examples/dataset-metadata.scm b/examples/dataset-metadata.scm index 38dac9c..23dd48e 100755 --- a/examples/dataset-metadata.scm +++ b/examples/dataset-metadata.scm @@ -12,33 +12,6 @@ (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)))))) - (define-transformer info-files (tables (InfoFiles (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name") @@ -455,8 +428,7 @@ (list info-files publishfreeze genofreeze - probesetfreeze - gene-chip)) + probesetfreeze)) (outputs `(#:documentation ,documentation #:rdf ,output)))) diff --git a/examples/gene-chip.scm b/examples/gene-chip.scm new file mode 100755 index 0000000..a0de6b8 --- /dev/null +++ b/examples/gene-chip.scm @@ -0,0 +1,78 @@ +#! /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)))) |