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| -rwxr-xr-x | examples/probesets.scm | 123 |
1 files changed, 0 insertions, 123 deletions
diff --git a/examples/probesets.scm b/examples/probesets.scm deleted file mode 100755 index 1bbfec8..0000000 --- a/examples/probesets.scm +++ /dev/null @@ -1,123 +0,0 @@ -#! /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 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)) - (set skos:altLabel (sanitize-rdf-string (field ProbeSet alias))) - (set gnt:uses_genechip (string->identifier "platform" (field GeneChip Name) #:separator "_")) - (set gnt:has_target_id - (field ("NULLIF(TRIM(ProbeSet.TargetId), '')" - TargetId))) - (set gnt:symbol (field ProbeSet Symbol)) - (set dct:description (sanitize-rdf-string (field ProbeSet description))) - (set gnt:targets_region - (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: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: - (field ("IFNULL(ProbeSet.HomoloGeneID, '')" - HomoloGeneID)))) - (set gnt:has_uniprot_id (ontology 'uniprot: - (field ("IFNULL(ProbeSet.UniProtID, '')" - UniProtID)))) - (set gnt:has_pub_chem_id (ontology - 'pubchem: - (field ("IFNULL(ProbeSet.PubChem_ID, '')" - PubChem_ID)))) - (set gnt:has_kegg_id (ontology - 'kegg: - (field ("IFNULL(ProbeSet.KEGG_ID, '')" - KEGG_ID)))) - (set gnt:has_omim_id (ontology - 'omim: - (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: - (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))) - (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#>") - ("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)))) |