Remove "dump-" prefix

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

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")))