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Diffstat (limited to 'examples/dump-probeset.scm')
| -rwxr-xr-x | examples/dump-probeset.scm | 184 |
1 files changed, 0 insertions, 184 deletions
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm deleted file mode 100755 index 3a55506..0000000 --- a/examples/dump-probeset.scm +++ /dev/null @@ -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"))) |