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author | Munyoki Kilyungi | 2023-08-21 14:54:21 +0300 |
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committer | Munyoki Kilyungi | 2023-08-21 14:56:57 +0300 |
commit | 51b3c0548c98e0bc05e11a89cbf6b75d31b9f8d5 (patch) | |
tree | ab3d7c6f589ed8480f0a9d451566681bcfd8eaaf /examples/generif.scm | |
parent | 849874fdfe11003f05abe5f82efde974a8c8a388 (diff) | |
download | gn-transform-databases-51b3c0548c98e0bc05e11a89cbf6b75d31b9f8d5.tar.gz |
Remove "dump-" prefix
Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>
Diffstat (limited to 'examples/generif.scm')
-rwxr-xr-x | examples/generif.scm | 150 |
1 files changed, 150 insertions, 0 deletions
diff --git a/examples/generif.scm b/examples/generif.scm new file mode 100755 index 0000000..0b3c8e4 --- /dev/null +++ b/examples/generif.scm @@ -0,0 +1,150 @@ +#! /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 genewiki-symbols + (tables (GeneRIF_BASIC + (left-join Species "USING (SpeciesId)")) + "GROUP BY GeneId ORDER BY BINARY symbol") + (schema-triples + (gnt:symbol rdfs:domain gn-term:geneWikiEntry) + (gnt:wikiEntryOfSpecies rdfs:range gn:species) + (gnt:taxid rdfs:domain gn-term:geneWikiEntry)) + (triples (ontology 'generif: (field GeneRIF_BASIC GeneId)) + (multiset gnt:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol)) + #\,)) + (multiset gnt:wikiEntryOfSpecies + (string-split + (field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species)) + #\,)) + (multiset gnt:taxId (map (cut ontology 'ncbiTaxon: <>) + (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId)) + #\,))))) + +(define-transformer gn-genewiki-entries + (tables (GeneRIF + (left-join GeneRIF_BASIC "USING (symbol)") + (left-join Species "ON Species.SpeciesId = GeneRIF.SpeciesId") + (left-join GeneRIFXRef "ON GeneRIFXRef.GeneRIFId = GeneRIF.Id") + (left-join GeneCategory "ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id")) + "WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 GROUP BY GeneRIF.symbol") + (schema-triples + (gnt:geneWikiEntry a rdfs:Class) + (gnt:geneWikiEntry a owl:Class) + (gnt:geneWikiEntry rdfs:comment "Represents GeneRIF Entries") + (gnt:geneCategory rdfs:domain gn:geneWikiEntry) + (gnt:geneWikiEntryOfGn rdfs:domain gn:geneWikiEntry) + (gnt:geneWikiEntry rdfs:domain gn:geneWikiEntry)) + (triples + (let ([geneid (field GeneRIF_BASIC GeneId)]) + (if (eq? geneid 0) + (ontology 'gnt:anonSymbol_ + (field GeneRIF symbol)) + (ontology 'generif: + geneid))) + (set rdf:type + (if (string-null? (field ("IFNULL(GeneRIF_BASIC.GeneId, '')" geneWikiEntryP))) + "" + 'gn:geneWikiEntry)) + (set gnt:wikiEntryOfSpecies + (string->binomial-name (field Species FullName))) + ;; This only dumps symbols not present in the GeneRIF_BASIC table + (set gnt:symbol (let ([geneid (field GeneRIF_BASIC GeneId)]) + (if (eq? geneid 0) + (field GeneRIF symbol) + ""))) + (multiset gnt:geneWikiEntryOfGn + (let* ([entries + (sanitize-rdf-string + (field + ("GROUP_CONCAT(DISTINCT CONCAT_WS('::::', IFNULL(GeneCategory.Name, ''), IFNULL(GeneRIF.PubMed_ID, ''), GeneRIF.email, CAST(CONVERT(BINARY CONVERT(GeneRIF.comment USING latin1) USING utf8) AS VARCHAR(15000)), GeneRIF.createtime, IFNULL(weburl, '')) SEPARATOR';;;;;')" + wikientry)))] + [comments (string-split-substring entries ";;;;;")]) + (map + (match-lambda + ((genecategory pmid email text createtime weburl) + (blank-node + (set gnt:geneCategory genecategory) + (multiset dct:source + (map (lambda (el) (if (string-null? el) + "" + (ontology 'pubmed: el))) + (string-split pmid #\space))) + (set dct:creator (regexp-substitute/global #f "@.*$" + email + 'pre + "" + 'post)) + (set gnt:geneWikiEntry + (annotate-field text '^^xsd:string)) + (set dct:created (annotate-field + createtime + '^^xsd:datetime)) + (set foaf:homepage weburl)))) + (map + (cut string-split-substring <> "::::") + comments)))))) + +(define-transformer ncbi-genewiki-entries + (tables (GeneRIF_BASIC) + "GROUP BY GeneId, comment, createtime") + (schema-triples + (gnt:geneWikiEntryofNCBI rdfs:domain gn:geneWikiEntry)) + (triples (ontology 'generif: + (field GeneRIF_BASIC GeneId)) + (set gnt:geneWikiEntryOfNCBI + (blank-node + (set gnt:geneWikiEntry + (annotate-field (field GeneRIF_BASIC comment) + '^^xsd:string)) + (multiset dct:source (map (lambda (el) (if (string-null? el) + "" + (ontology 'pubmed: el))) + (string-split (field ("GROUP_CONCAT(PubMed_ID)" pmids)) + #\,))) + (set dct:created (annotate-field (time-unix->string + (field GeneRIF_BASIC createtime) "~5") + '^^xsd:datetime)))))) + + + +(with-documentation + (name "GeneRIF Metadata") + (connection %connection-settings) + (table-metadata? #f) + (prefixes + '(("rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + ("rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + ("gn:" "<http://genenetwork.org/id/>") + ("gnc:" "<http://genenetwork.org/category/>") + ("gnt:" "<http://genenetwork.org/term/>") + ("dct:" "<http://purl.org/dc/terms/>") + ("pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + ("ncbiTaxon:" "<https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>") + ("generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + ("xsd:" "<http://www.w3.org/2001/XMLSchema#>") + ("owl:" "<http://www.w3.org/2002/07/owl#>"))) + (inputs + (list ;; genewiki-symbols + gn-genewiki-entries + ;; ncbi-genewiki-entries + )) + (outputs + '(#:documentation "./docs/generif.md" + #:rdf "./verified-data/generif.ttl"))) |