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#! /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)
(web uri))
(define-transformer probeset->metadata
(tables (ProbeSet
(left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId"))
"WHERE ProbeSet.Name IS NOT NULL AND TRIM(ProbeSet.Name) != ''")
(triples
(string->identifier "probeset" (field ProbeSet Name))
(set rdf:type 'gnc:probeset)
(set skos:prefLabel (field ProbeSet Name))
(multiset skos:altLabel
(map string-trim-both
(string-split (sanitize-rdf-string (field ProbeSet alias)) #\;)))
(set gnt:uses_genechip (string->identifier "platform" (field GeneChip Name) #:separator "_"))
(set gnt:has_target_id (string-trim-both (sanitize-rdf-string (field ProbeSet TargetId))))
(set gnt:symbol (string-trim-both (field ProbeSet Symbol)))
(set dct:description (sanitize-rdf-string (field ProbeSet description)))
(set gnt:targets_region (string-trim-both (sanitize-rdf-string (field ProbeSet Probe_set_target_region))))
(set gnt:chr (field ProbeSet Chr))
(set gnt:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double))
(set gnt:mb_mm8 (annotate-field (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8))
'^^xsd:double))
(set gnt:has_specificity
(field ("IFNULL(ProbeSet.Probe_set_specificity, '')"
Probe_set_specificity)))
(set gnt:has_blat_score
(field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')"
Probe_set_BLAT_score)))
(set gnt:has_blat_mb_start
(annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')"
Probe_set_Blat_Mb_start))
'^^xsd:double))
(set gnt:has_blat_mb_end
(annotate-field (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')"
Probe_set_Blat_Mb_end))
'^^xsd:double))
(set gnt:has_blat_seq (sanitize-rdf-string (field ProbeSet BlatSeq)))
(set gnt:has_target_seq (sanitize-rdf-string (field ProbeSet TargetSeq)))
(set gnt:has_homologene_id (ontology 'homologene:
(uri-encode
(field ("IFNULL(ProbeSet.HomoloGeneID, '')"
HomoloGeneID)))))
(set gnt:has_uniprot_id (ontology 'uniprot:
(uri-encode
(field ("IFNULL(ProbeSet.UniProtID, '')"
UniProtID)))))
(set gnt:has_pub_chem_id (ontology
'pubchem:
(uri-encode
(field ("IFNULL(ProbeSet.PubChem_ID, '')"
PubChem_ID)))))
(set gnt:has_kegg_id (ontology
'kegg:
(uri-encode
(field ("IFNULL(ProbeSet.KEGG_ID, '')"
KEGG_ID)))))
(set gnt:has_omim_id (ontology
'omim:
(uri-encode
(let ((omim (field ("IFNULL(ProbeSet.OMIM, '')"
OMIM))))
(if (number? omim)
omim
(regexp-substitute/global
#f "[^0-9]"
omim
'pre "" 'post))))))
(set gnt:has_chebi_id (ontology
'chebi:
(uri-encode
(field ("IFNULL(ProbeSet.ChEBI_ID, '')"
ChEBI_ID)))))))
(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)))
(call-with-target-database
%connection-settings
(lambda (db)
(with-documentation
(name "ProbeSet Metadata")
(connection %connection-settings)
(table-metadata? #f)
(total-rows (assoc-ref
(sql-find db "SELECT count(*) AS count from ProbeSet")
"count"))
(rows-per-chunk 1000000)
(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#>")
("qb:" "<http://purl.org/linked-data/cube#>")
("sdmx-measure:" "<http://purl.org/linked-data/sdmx/2009/measure#>")
("skos:" "<http://www.w3.org/2004/02/skos/core#>")))
(inputs
(list probeset->metadata))
(outputs
`(#:documentation ,documentation
#:rdf ,output))))))
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