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-rwxr-xr-xexamples/dump-probeset.scm184
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diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm
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@@ -1,184 +0,0 @@
-#! /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-transformer 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)))
- (string->identifier
- "probeset"
- (if (string-null? id)
- (number->string probeset-id)
- (regexp-substitute/global
- #f "[^A-Za-z0-9:]"
- id
- 'pre "_" 'post))))
- (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
- (field ("IFNULL(ProbeSet.Probe_set_specificity, '')"
- Probe_set_specificity)))
- (set gnt:hasBlatScore
- (field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')"
- Probe_set_BLAT_score)))
- (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")))