diff options
Diffstat (limited to 'examples')
| -rwxr-xr-x | examples/dump-dataset-metadata.scm | 220 | ||||
| -rwxr-xr-x | examples/dump-generif.scm | 159 | ||||
| -rwxr-xr-x | examples/dump-phenotype.scm | 131 | ||||
| -rwxr-xr-x | examples/dump-probeset.scm | 213 | ||||
| -rwxr-xr-x | examples/dump-publication.scm | 90 | ||||
| -rwxr-xr-x | examples/dump-species-metadata.scm | 141 | ||||
| -rwxr-xr-x | examples/dump-tissue.scm | 66 |
7 files changed, 1020 insertions, 0 deletions
diff --git a/examples/dump-dataset-metadata.scm b/examples/dump-dataset-metadata.scm new file mode 100755 index 0000000..aa7a5f2 --- /dev/null +++ b/examples/dump-dataset-metadata.scm @@ -0,0 +1,220 @@ +#! /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 %dump-directory + (list-ref (command-line) 2)) + + + +;; One email ID in the Investigators table has spaces in it. This +;; function fixes that. +(define (fix-email-id email) + (string-delete #\space email)) + +(define (investigator-attributes->id first-name last-name email) + ;; There is just one record corresponding to "Evan Williams" which + ;; does not have an email ID. To accommodate that record, we + ;; construct the investigator ID from not just the email ID, but + ;; also the first and the last names. It would be preferable to just + ;; find Evan Williams' email ID and insert it into the database. + (string->identifier "investigator" + (string-join + ;; Add special case for Yohan Bossé whose name + ;; has unprintable characters. + ;; TODO: Fix Yohan Bossé's name in the database. + (let ((last-name (if (string=? first-name "Yohan") + "Bosse" + last-name))) + (list first-name last-name (fix-email-id email))) + "_"))) + +(define-dump dump-investigators + ;; There are a few duplicate entries. We group by email to + ;; deduplicate. + (tables (Investigators) + "GROUP BY Email") + (schema-triples + ;; TODO: Are ranges required for FOAF predicates? Can they not be + ;; obtained from the FOAF spec? + (foaf:name rdfs:range rdfs:Literal) + (foaf:givenName rdfs:range rdfs:Literal) + (foaf:familyName rdfs:range rdfs:Literal) + (foaf:phone rdfs:range rdfs:Literal) + (foaf:mbox rdfs:range rdfs:Literal) + (foaf:homepage rdfs:range rdfs:Literal) + (gn:address rdfs:range rdfs:Literal) + (gn:city rdfs:range rdfs:Literal) + (gn:state rdfs:range rdfs:Literal) + (gn:zipCode rdfs:range rdfs:Literal) + (gn:country rdfs:range rdfs:Literal)) + (triples (investigator-attributes->id (field Investigators FirstName) + (field Investigators LastName) + (field Investigators Email)) + (set rdf:type 'foaf:Person) + ;; Special case Yohan Bossé's name since the last name has + ;; unprintable characters. + (set foaf:name (string-append (field Investigators FirstName) " " + (if (string=? (field Investigators FirstName) "Yohan") + "Bossé" + (field Investigators LastName)))) + (set foaf:givenName (field Investigators FirstName)) + ;; Special case Yohan Bossé's name since the last name has + ;; unprintable characters. + (set foaf:familyName (if (string=? (field Investigators FirstName) "Yohan") + "Bossé" + (field Investigators LastName))) + (set foaf:phone (field Investigators Phone)) + (set foaf:mbox (fix-email-id (field Investigators Email))) + (set foaf:homepage (field Investigators Url)) + (set gn:address (field Investigators Address)) + (set gn:city (field Investigators City)) + (set gn:state (field Investigators State)) + (set gn:zipCode (field Investigators ZipCode)) + (set gn:country (field Investigators Country)))) + +(define-dump dump-info-files + (tables (InfoFiles + (left-join PublishFreeze "ON InfoFiles.InfoPageName = PublishFreeze.Name") + (left-join GenoFreeze "ON InfoFiles.InfoPageName = GenoFreeze.Name") + (left-join ProbeSetFreeze "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name") + (left-join Datasets "USING (DatasetId)") + (left-join DatasetStatus "USING (DatasetStatusId)") + (left-join Species "USING (SpeciesId)") + (left-join Tissue "USING (TissueId)") + (left-join Investigators "USING (InvestigatorId)") + (left-join AvgMethod "USING (AvgMethodId)") + (left-join GeneChip "USING (GeneChipId)")) + "WHERE GN_AccesionId IS NOT NULL") + (schema-triples + (gn:datasetOfInvestigator rdfs:domain gn:dataset) + (gn:datasetOfInvestigator rdfs:range foaf:Person) + (gn:datasetOfSpecies rdfs:domain gn:dataset) + (gn:datasetOfSpecies rdfs:range gn:species) + (gn:datasetOfInbredSet rdfs:domain gn:dataset) + (gn:datasetOfInbredSet rdfs:range gn:inbredSet) + (gn:datasetOfTissue rdfs:domain gn:dataset) + (gn:datasetOfTissue rdfs:range gn:tissue) + (gn:normalization rdfs:domain gn:dataset) + (gn:normalization rdfs:range gn:avgMethod) + (gn:datasetOfPlatform rdfs:domain gn:dataset) + (gn:datasetOfPlatform rdfs:range gn:geneChip) + (gn:accessionId rdfs:range rdfs:Literal) + (gn:datasetStatusName rdfs:range rdfs:Literal) + (gn:summary rdfs:range rdfs:Literal) + (gn:aboutTissue rdfs:range rdfs:Literal) + (gn:geoSeries rdfs:range rdfs:Literal) + (gn:name rdfs:range rdfs:Literal) + (gn:title rdfs:range rdfs:Literal) + (gn:specifics rdfs:range rdfs:Literal) + (gn:datasetGroup rdfs:range rdfs:Literal) + (gn:aboutCases rdfs:range rdfs:Literal) + (gn:aboutPlatform rdfs:range rdfs:Literal) + (gn:aboutDataProcessing rdfs:range rdfs:Literal) + (gn:notes rdfs:range rdfs:Literal) + (gn:experimentDesign rdfs:range rdfs:Literal) + (gn:contributors rdfs:range rdfs:Literal) + (gn:citation rdfs:range rdfs:Literal) + (gn:acknowledgment rdfs:range rdfs:Literal)) + (triples (string->identifier "dataset" + (field InfoFiles InfoPageName)) + ;; Add GeneChipName and GeoPlatform: + ;; GeneChip.GeneChipName AS gene_chip_name + ;; GeneChip.GeoPlatform AS geo_platform + (set rdf:type (string->symbol + (field ("IF(GenoFreeze.Id IS NOT NULL, 'gn:genotypeDataset', IF(PublishFreeze.Id IS NOT NULL, 'gn:phenotypeDataset', 'gn:dataset'))" + rdfType)))) + (set gn:name (field InfoFiles InfoPageName)) + (set dct:created + (field ("IFNULL(GenoFreeze.CreateTime, IFNULL(PublishFreeze.CreateTime, IFNULL(ProbeSetFreeze.CreateTime, '')))" + createTimeGenoFreeze))) + (set gn:datasetOfInvestigator + (investigator-attributes->id (field Investigators FirstName) + (field Investigators LastName) + (field Investigators Email))) + (set gn:accessionId (string-append "GN" (number->string + (field InfoFiles GN_AccesionId)))) + (set gn:datasetStatusName (string-downcase + (field DatasetStatus DatasetStatusName))) + (set gn:datasetOfSpecies (string->identifier "species" + (field Species FullName BinomialName))) + (set gn:datasetOfTissue (string->identifier "tissue" + (field Tissue Short_Name))) + (set gn:normalization + (string->identifier "avgmethod" + ;; If AvgMethodName is NULL, assume N/A. + (if (string-blank? (field AvgMethod Name AvgMethodName)) + "N/A" (field AvgMethod Name AvgMethodName)))) + (set gn:datasetOfPlatform + (string->identifier "platform" + (field GeneChip Name GeneChip))) + (set gn:summary + (sanitize-rdf-string (field Datasets Summary))) + (set gn:aboutTissue + (sanitize-rdf-string (field Datasets AboutTissue))) + (set gn:geoSeries + (and (not (string-prefix-ci? "no geo series" + (field Datasets GeoSeries))) + (field Datasets GeoSeries))) + (set gn:title (field InfoFiles Title)) + (set gn:specifics (sanitize-rdf-string (field InfoFiles Specifics))) + (set gn:datasetGroup (field Datasets DatasetName DatasetGroup)) + (set gn:aboutCases (sanitize-rdf-string (field Datasets AboutCases))) + (set gn:aboutPlatform (sanitize-rdf-string (field Datasets AboutPlatform))) + (set gn:aboutDataProcessing (sanitize-rdf-string + (field Datasets AboutDataProcessing))) + (set gn:notes (sanitize-rdf-string (field Datasets Notes))) + (set gn:experimentDesign (sanitize-rdf-string + (field Datasets ExperimentDesign))) + (set gn:contributors (sanitize-rdf-string (field Datasets Contributors))) + (set gn:citation (sanitize-rdf-string (field Datasets Citation))) + (set gn:acknowledgment (sanitize-rdf-string + (field Datasets Acknowledgment))))) + + + + +(call-with-target-database + %connection-settings + (lambda (db) + (with-output-to-file (string-append %dump-directory "dump-info-pages.ttl") + (lambda () + (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>") + (prefix "dct:" "<http://purl.org/dc/terms/>") + (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") + (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + (prefix "gn:" "<http://genenetwork.org/>") + (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>") + (prefix "homologene:" "<https://bio2rdf.org/homologene:>") + (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>") + (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>") + (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>") + (prefix "omim:" "<https://www.omim.org/entry/>") + (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") + (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") + (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>") + (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>") + (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") + (prefix "up:" "<http://purl.uniprot.org/core/>") + (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (newline) + (dump-info-files db) + (dump-investigators db)) + #:encoding "utf8"))) diff --git a/examples/dump-generif.scm b/examples/dump-generif.scm new file mode 100755 index 0000000..415cb67 --- /dev/null +++ b/examples/dump-generif.scm @@ -0,0 +1,159 @@ +#! /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 %dump-directory + (list-ref (command-line) 2)) + + + +(define-dump dump-genewiki-symbols + (tables (GeneRIF_BASIC + (left-join Species "USING (SpeciesId)")) + "GROUP BY GeneId ORDER BY BINARY symbol") + (schema-triples + (gn:symbol rdfs:domain gn:geneWikiEntry) + (gn:wikiEntryOfSpecies rdfs:range gn:species) + (gn:taxid rdfs:domain gn:geneWikiEntry)) + (triples (ontology 'generif: (field GeneRIF_BASIC GeneId)) + (multiset gn:symbol (string-split (field ("GROUP_CONCAT(DISTINCT symbol)" symbol)) + #\,)) + (multiset gn:wikiEntryOfSpecies + (string-split + (field ("GROUP_CONCAT(DISTINCT Species.SpeciesName)" species)) + #\,)) + (multiset gn:taxId (map (cut ontology 'taxon: <>) + (string-split (field ("GROUP_CONCAT(DISTINCT TaxID)" taxId)) + #\,))))) + +(define-dump dump-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 + (gn:geneWikiEntry a rdfs:Class) + (gn:geneWikiEntry a owl:Class) + (gn:geneWikiEntry rdfs:comment "Represents GeneRIF Entries") + (gn:geneCategory rdfs:domain gn:geneWikiEntry) + (gn:geneWikiEntryOfGn rdfs:domain gn:geneWikiEntry) + (gn:geneWikiEntry rdfs:domain gn:geneWikiEntry)) + (triples + (let ([geneid (field GeneRIF_BASIC GeneId)]) + (if (eq? geneid 0) + (ontology 'gn:anonSymbol_ + (field GeneRIF symbol)) + (ontology 'generif: + geneid))) + (set rdf:type + (if (string-null? (field ("IFNULL(GeneRIF_BASIC.GeneId, '')" geneWikiEntryP))) + "" + 'gn:geneWikiEntry)) + (set gn:wikiEntryOfSpecies + (field Species SpeciesName)) + ;; This only dumps symbols not present in the GeneRIF_BASIC table + (set gn:symbol (let ([geneid (field GeneRIF_BASIC GeneId)]) + (if (eq? geneid 0) + (field GeneRIF symbol) + ""))) + (multiset gn:geneWikiEntryOfGn + (let* ([entries + (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 gn: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 gn: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-dump dump-ncbi-genewiki-entries + (tables (GeneRIF_BASIC) + "GROUP BY GeneId, comment, createtime") + (schema-triples + (gn:geneWikiEntryofNCBI rdfs:domain gn:geneWikiEntry)) + (triples (ontology 'generif: + (field GeneRIF_BASIC GeneId)) + (set gn:geneWikiEntryOfNCBI + (blank-node + (set gn: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)))))) + + + +(call-with-target-database + %connection-settings + (lambda (db) + (with-output-to-file (string-append %dump-directory "dump-generif.ttl") + (lambda () + (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") + (prefix "gn:" "<http://genenetwork.org/>") + (prefix "dct:" "<http://purl.org/dc/terms/>") + (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + (prefix "up:" "<http://purl.uniprot.org/core/>") + (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>") + (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") + (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") + (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>") + (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>") + (prefix "omim:" "<https://www.omim.org/entry/>") + (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>") + (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") + (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>") + (prefix "homologene:" "<https://bio2rdf.org/homologene:>") + (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>") + (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>") + (newline) + (dump-genewiki-symbols db) + (dump-gn-genewiki-entries db) + (dump-ncbi-genewiki-entries db)) + #:encoding "utf8"))) diff --git a/examples/dump-phenotype.scm b/examples/dump-phenotype.scm new file mode 100755 index 0000000..842e7e8 --- /dev/null +++ b/examples/dump-phenotype.scm @@ -0,0 +1,131 @@ +#! /usr/bin/env guile +!# + +(use-modules (rnrs programs) + (rnrs io ports) + (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 %dump-directory + (list-ref (command-line) 2)) + + + +;; Only dump publish freeze entries that were not dumped from the InfoFiles page +(define-dump dump-publishfreeze + (tables (PublishFreeze + (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name") + (left-join InbredSet "ON PublishFreeze.InbredSetId = InbredSet.InbredSetId")) + "WHERE PublishFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL") + (schema-triples + (gn:datasetOfInbredSet rdfs:range gn:inbredSet) + (gn:name rdfs:range rdfs:Literal) + (gn:fullName rdfs:range rdfs:Literal) + (gn:shortName rdfs:range rdfs:Literal) + (gn:createTime rdfs:range rdfs:Literal)) + (triples (string->identifier "dataset" (field PublishFreeze Name)) + (set rdf:type 'gn:phenotypeDataset) + (set gn:name (field PublishFreeze Name)) + (set gn:fullName (field PublishFreeze FullName)) + (set gn:shortName (field PublishFreeze ShortName)) + (set gn:createTime (field PublishFreeze CreateTime)) + (set gn:datasetOfInbredSet + (string->identifier "inbredSet" (field InbredSet Name InbredSetName))))) + +(define-dump dump-phenotypes + (tables (Phenotype + (left-join PublishXRef "ON Phenotype.Id = PublishXRef.PhenotypeId") + (left-join Publication "ON Publication.Id = PublishXRef.PublicationId") + (left-join PublishFreeze "ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId") + (left-join InfoFiles "ON InfoFiles.InfoPageName = PublishFreeze.Name"))) + (schema-triples + (gn:phenotypeDataset rdfs:subPropertyOf gn:dataset)) + (triples (ontology 'phenotype: + (regexp-substitute/global #f "[^A-Za-z0-9:]" + (field ("CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, ':')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation))" abbrev)) + 'pre "_" 'post)) + (set rdf:type 'gn:phenotype) + (set gn:name (sanitize-rdf-string + (field + ("CAST(CONVERT(BINARY CONVERT(CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '-')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation)) USING latin1) USING utf8) AS VARCHAR(10000))" + abbrev)))) + ;; There is no row with an empty post-publication description so + ;; use this field as the main publication description + (set gn:publicationDescription + (sanitize-rdf-string + (field ("CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000))" + postPubDescr)))) + (set gn:originalDescription (sanitize-rdf-string + (delete-substrings + (field Phenotype Original_description) + "Original post publication description: "))) + (set gn:prePublicationDescription + (sanitize-rdf-string + (field + ("CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000))" + prePubDesc)))) + (set gn:prePublicationAbbreviation (sanitize-rdf-string (field Phenotype Pre_publication_abbreviation))) + (set gn:postPublicationAbbreviation (sanitize-rdf-string (field Phenotype Post_publication_abbreviation))) + (set gn:labCode (field Phenotype Lab_code)) + (set gn:submitter (sanitize-rdf-string (field Phenotype Submitter))) + (set gn:owner (sanitize-rdf-string (field Phenotype Owner))) + (set gn:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean)) + '^^xsd:double)) + (set gn:locus (field PublishXRef Locus)) + (set gn:LRS (annotate-field (field ("IFNULL(PublishXRef.LRS, '')" lrs)) '^^xsd:float)) + (set gn:additive (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:decimal)) + (set gn:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:int)) + (set gn:phenotypeOfDataset (string->identifier "dataset" (field PublishFreeze Name))) + (set gn:phenotypeOfPublication + (let ((pmid (field + ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))" + pmid))) + (publication-id (field Publication Id))) + (if (string-null? pmid) + (string->identifier "publication" + (number->string publication-id)) + (ontology 'pubmed: pmid)))))) + + +(call-with-target-database + %connection-settings + (lambda (db) + (with-output-to-file (string-append %dump-directory "dump-phenotype.ttl") + (lambda () + (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>") + (prefix "dct:" "<http://purl.org/dc/terms/>") + (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") + (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + (prefix "gn:" "<http://genenetwork.org/>") + (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>") + (prefix "homologene:" "<https://bio2rdf.org/homologene:>") + (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>") + (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>") + (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>") + (prefix "omim:" "<https://www.omim.org/entry/>") + (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") + (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") + (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>") + (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>") + (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") + (prefix "up:" "<http://purl.uniprot.org/core/>") + (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (newline) + (dump-publishfreeze db) + (dump-phenotypes db)) + #:encoding "utf8"))) diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm new file mode 100755 index 0000000..d1ea2ae --- /dev/null +++ b/examples/dump-probeset.scm @@ -0,0 +1,213 @@ +#! /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 %dump-directory + (list-ref (command-line) 2)) + + +(define-dump dump-gene-chip + (tables (GeneChip)) + (schema-triples + (gn:name rdfs:range rdfs:Literal)) + (triples (string->identifier "platform" (field GeneChip Name)) + (set rdf:type 'gn:platform) + (set gn:name (field GeneChip GeneChipName)))) + +(define-dump dump-probeset + (tables (ProbeSet + (left-join ProbeSetXRef "ON ProbeSetXRef.ProbeSetId = ProbeSet.Id") + (left-join ProbeSetFreeze "ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id") + (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId"))) + (schema-triples + (gn:name rdfs:range rdfs:Literal)) + (triples (ontology 'gn:probeset_ (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)" + name))) + (set gn:probesetOfDataset + (string->identifier + "dataset" + (field ProbeSetFreeze Name))) + (set gn:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean)) + '^^xsd:double)) + (set gn:se (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se)) + '^^xsd:double)) + (set gn:LRS (annotate-field (field ("IFNULL(ProbeSetXRef.LRS, '')" LRS)) + '^^xsd:double)) + (set gn:pValue (annotate-field (field ("IFNULL(ProbeSetXRef.pValue, '')" pValue)) + '^^xsd:double)) + (set gn:additive (annotate-field (field ("IFNULL(ProbeSetXRef.additive, '')" additive)) + '^^xsd:double)) + (set gn:h2 (annotate-field (field ("IFNULL(ProbeSetXRef.h2, '')" h2)) + '^^xsd:float)) + (set gn:locus (field ProbeSetXRef Locus)) + (set gn:chipOf (string->identifier "platform" (field GeneChip Name))) + (set gn:name (field ProbeSet Name)) + (set gn:symbol (field ProbeSet Symbol)) + (set gn:description (field ProbeSet description)) + (set gn:chr (field ProbeSet Chr)) + (set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double)) + (set gn:chr_2016 (field ProbeSet Chr_2016)) + (set gn:mb_2016 (annotate-field (field ("IFNULL(ProbeSet.Mb_2016, '')" Mb_2016)) '^^xsd:double)) + (set gn:alias (string-trim-both (field ProbeSet alias))) + (set gn:generif (ontology 'generif: (field ProbeSet GeneId))) + (set gn:genbank (ontology 'nuccore: (field ProbeSet GenbankId))) + (set gn:snp (field ("IFNULL(ProbeSet.SNP, '')" SNP))) + (set gn:blatSeq (string-trim-both (field ProbeSet BlatSeq))) + (set gn:targetSeq (field ProbeSet TargetSeq)) + (set gn:unigene (field ProbeSet UniGeneId)) + (set gn:strandProbe (field ProbeSet Strand_Probe)) + (set gn:strandGene (field ProbeSet Strand_Gene)) + (set gn:omim (ontology 'omim: (field ProbeSet OMIM))) + (set gn:comments (sanitize-rdf-string (field ProbeSet comments))) + (set gn:targetRegion (field ProbeSet Probe_set_target_region)) + (set gn:specificity (annotate-field + (field ("IFNULL(ProbeSet.Probe_set_specificity, '')" Probe_set_specificity)) + '^^xsd:double)) + (set gn:blatScore (annotate-field + (field ("IFNULL(ProbeSet.Probe_set_BLAT_score, '')" Probe_set_BLAT_score)) + '^^xsd:double)) + (set gn:blatMbStart (annotate-field + (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '')" Probe_set_Blat_Mb_start)) + '^^xsd:double)) + (set gn:blatMbend (annotate-field + (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '')" Probe_set_Blat_Mb_end)) + '^^xsd:double)) + (set gn:blatMbStart2016 + (annotate-field + (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '')" Probe_set_Blat_Mb_start_2016)) '^^xsd:double)) + (set gn:blatMbend2016 + (annotate-field + (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end_2016, '')" Probe_set_Blat_Mb_end_2016)) '^^xsd:double)) + (set gn:strand (field ProbeSet Probe_set_strand)) + (set gn:noteByRW (field ProbeSet Probe_set_Note_by_RW)) + (set gn:flag (field ProbeSet flag)) + (set gn:symbolH (field ProbeSet Symbol_H)) + (set gn:descriptionH (field ProbeSet Description_H)) + (set gn:chromosomeH (field ProbeSet chromosome_H)) + (set gn:mbH (annotate-field (field ProbeSet MB_H) '^^xsd:double)) + (set gn:aliasH (field ProbeSet alias_H)) + (set gn:geneIdH (field ProbeSet GeneId_H)) + (set gn:chrNum (field ("IFNULL(ProbeSet.chr_num, '')" chr_num))) + (set gn:nameNum (field ("IFNULL(ProbeSet.name_num, '')" name_num))) + (set gn:probeTargetDescription (field ProbeSet Probe_Target_Description)) + (set gn:RefSeq_TranscriptId (ontology 'nuccore: (field ProbeSet RefSeq_TranscriptId))) + (set gn:ENSEMBLGeneId (string-trim-both + (field ProbeSet ENSEMBLGeneId))) + (set gn:Chr_mm8 (field ("IFNULL(ProbeSet.Chr_mm8, '')" Chr_mm8))) + (set gn:Mb_mm8 (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8))) + (set gn:probeSetBlatMbStart_mm8 + (annotate-field + (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_start_mm8, '')" Probe_set_Blat_Mb_start_mm8)) + '^^xsd:double)) + (set gn:probeSetBlatMbEnd_mm8 + (annotate-field + (field ("IFNULL(ProbeSet.Probe_set_Blat_Mb_end_mm8, '')" Probe_set_Blat_Mb_end_mm8)) + '^^xsd:double)) + (set gn:homoloGeneID (ontology + 'homologene: + (field ProbeSet HomoloGeneID))) + (set gn:biotype_ENS (field ProbeSet Biotype_ENS)) + (set gn:proteinName (field ProbeSet ProteinName)) + (set gn:uniProtReference (ontology 'uniprot: + (field ProbeSet UniProtID))) + (set gn:flybase_Id (field ProbeSet Flybase_Id)) + (set gn:RGD_ID (field ("IFNULL(ProbeSet.RGD_ID, '')" RGD_ID))) + (set gn:hgnc (ontology + 'hgnc: (field ProbeSet HGNC_ID))) + (set gn:HMDB_ID (field ProbeSet HMDB_ID)) + (set gn:confidence (field ("IFNULL(ProbeSet.Confidence, '')" Confidence))) + (set gn:chebi_ID (ontology + 'chebi: + (field + ("IFNULL(ProbeSet.ChEBI_ID, '')" + ChEBI_ID)))) + (set gn:CASNumber (field ProbeSet CAS_number)) + (set gn:PubChemID (ontology + 'pubchem: + (field + ("IFNULL(ProbeSet.PubChem_ID, '')" + PubChem_ID)))) + (set gn:chemSpiderID (field ("IFNULL(ProbeSet.ChemSpider_ID, '')" ChemSpider_ID))) + (set gn:uniiID (field ProbeSet UNII_ID)) + (set gn:ECNumber (field ProbeSet EC_number)) + (set gn:keggID (ontology 'kegg: + (field ProbeSet KEGG_ID))) + (set gn:molecularWeight (annotate-field (field ProbeSet Molecular_Weight) '^^xsd:double)) + (set gn:nugowikiID (field ("IFNULL(ProbeSet.Nugowiki_ID, '')" Nugowiki_ID))) + (set gn:type (field ProbeSet Type)) + (set gn:tissue (field ProbeSet Tissue)) + (set gn:primaryName (field ProbeSet PrimaryName)) + (set gn:secondaryNames (field ProbeSet SecondaryNames)) + (set gn:peptideSequence (field ProbeSet PeptideSequence)))) + +;; Molecular Traits are also referred to as ProbeSets +(define-dump dump-probesetfreeze + (tables (ProbeSetFreeze + (left-join ProbeFreeze "USING (ProbeFreezeId)") + (left-join AvgMethod "ON AvgMethod.AvgMethodId = ProbeSetFreeze.AvgID") + (left-join InbredSet "ON ProbeFreeze.InbredSetId=InbredSet.Id") + (left-join Tissue "USING (TissueId)")) + "WHERE ProbeSetFreeze.public > 0 GROUP BY ProbeFreeze.Id") + (schema-triples + (gn:molecularTrait rdfs:range rdfs:Literal)) + (triples + (string->identifier "dataset" (field ProbeSetFreeze Name)) + (set rdf:type 'gn:dataset) + (set gn:avgMethod (string->identifier "avgmethod" (field AvgMethod Name))) + (set gn:fullName (field ProbeSetFreeze FullName)) + (set gn:shortName (field ProbeSetFreeze ShortName)) + (set dct:created (annotate-field + (field ProbeSetFreeze CreateTime) + '^^xsd:datetime)) + (set gn:dataScale (field ProbeSetFreeze DataScale)) + (set gn:tissueName (string->identifier "tissue" (field Tissue Short_Name))) + (set gn:datasetOfInbredSet + (string->identifier "inbredSet" (field InbredSet Name InbredSetName))))) + + + +(call-with-target-database + %connection-settings + (lambda (db) + (with-output-to-file (string-append %dump-directory "dump-probeset.ttl") + (lambda () + (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>") + (prefix "dct:" "<http://purl.org/dc/terms/>") + (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") + (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + (prefix "gn:" "<http://genenetwork.org/>") + (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>") + (prefix "homologene:" "<https://bio2rdf.org/homologene:>") + (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>") + (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>") + (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>") + (prefix "omim:" "<https://www.omim.org/entry/>") + (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") + (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") + (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>") + (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>") + (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") + (prefix "up:" "<http://purl.uniprot.org/core/>") + (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (newline) + (dump-gene-chip db) + (dump-probeset db) + (dump-probesetfreeze db)) + #:encoding "utf8"))) diff --git a/examples/dump-publication.scm b/examples/dump-publication.scm new file mode 100755 index 0000000..bed957a --- /dev/null +++ b/examples/dump-publication.scm @@ -0,0 +1,90 @@ +#! /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 %dump-directory + (list-ref (command-line) 2)) + + + +(define-dump dump-publication + (tables (Publication)) + (schema-triples + (gn:pubMedId rdfs:range rdfs:Literal) + (gn:title rdfs:range rdfs:Literal) + (gn:journal rdfs:range rdfs:Literal) + (gn:volume rdfs:range rdfs:Literal) + (gn:pages rdfs:range rdfs:Literal) + (gn:month rdfs:range rdfs:Literal) + (gn:year rdfs:range rdfs:Literal) + (gn:author rdfs:range rdfs:Literal) + (gn:abstract rdfs:range rdfs:Literal)) + (triples + (let ((pmid (field + ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))" + pmid))) + (publication-id (field Publication Id))) + (if (string-null? pmid) + (string->identifier "publication" + (number->string publication-id)) + (ontology 'pubmed: pmid))) + (set rdf:type 'gn:publication) + (set gn:pubMedId (field ("IFNULL(PubMed_ID, '')" pubmedId))) + (set gn:title (field Publication Title)) + (set gn:journal (field Publication Journal)) + (set gn:volume (field Publication Volume)) + (set gn:pages (field Publication Pages)) + (set gn:month (field Publication Month)) + (set gn:year (field Publication Year)) + (multiset gn:author + ;; The authors field is a comma + ;; separated list. Split it. + (map string-trim (string-split (sanitize-rdf-string (field Publication Authors)) #\,))) + (set gn:abstract + (sanitize-rdf-string (field Publication Abstract))))) + + + +(call-with-target-database + %connection-settings + (lambda (db) + (with-output-to-file (string-append %dump-directory "dump-publication.ttl") + (lambda () + (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>") + (prefix "dct:" "<http://purl.org/dc/terms/>") + (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") + (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + (prefix "gn:" "<http://genenetwork.org/>") + (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>") + (prefix "homologene:" "<https://bio2rdf.org/homologene:>") + (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>") + (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>") + (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>") + (prefix "omim:" "<https://www.omim.org/entry/>") + (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") + (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") + (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>") + (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>") + (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") + (prefix "up:" "<http://purl.uniprot.org/core/>") + (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (newline) + (dump-publication db)) + #:encoding "utf8"))) diff --git a/examples/dump-species-metadata.scm b/examples/dump-species-metadata.scm new file mode 100755 index 0000000..ed4113c --- /dev/null +++ b/examples/dump-species-metadata.scm @@ -0,0 +1,141 @@ +#! /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 %dump-directory + (list-ref (command-line) 2)) + + + +(define-dump dump-species + (tables (Species)) + (schema-triples + (gn:name rdfs:range rdfs:Literal) + (gn:displayName rdfs:range rdfs:Literal) + (gn:binomialName rdfs:range rdfs:Literal) + (gn:family rdfs:range rdfs:Literal)) + (triples (string->identifier "species" (field Species FullName)) + (set rdf:type 'gn:species) + (set gn:name (field Species SpeciesName)) + (set gn:displayName (field Species MenuName)) + (set gn:binomialName (field Species FullName)) + (set gn:family (field Species Family)) + (set up:organism (ontology 'taxon: (field Species TaxonomyId))))) + +(define-dump dump-strain + (tables (Strain + (join Species "ON Strain.SpeciesId = Species.SpeciesId"))) + (schema-triples + (gn:strainOfSpecies rdfs:domain gn:strain) + (gn:strainOfSpecies rdfs:range gn:species) + (gn:name rdfs:range rdfs:Literal) + (gn:alias rdfs:range rdfs:Literal) + (gn:symbol rdfs:range rdfs:Literal)) + (triples (string->identifier + "strain" + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (field ("CAST(CONVERT(BINARY CONVERT(Strain.Name USING latin1) USING utf8) AS VARCHAR(15000))" StrainName)) + 'pre "_" 'post)) + (set rdf:type 'gn:strain) + (set gn:strainOfSpecies + (string->identifier "species" (field Species FullName))) + ;; Name, and maybe a second name + (set gn:name (sanitize-rdf-string (field Strain Name))) + (set gn:name (sanitize-rdf-string (field Strain Name2))) + (set gn:alias (sanitize-rdf-string (field Strain Alias))) + (set gn:symbol (field Strain Symbol)))) + +(define-dump dump-mapping-method + (tables (MappingMethod)) + (triples (string->identifier "mappingMethod" (field MappingMethod Name)) + (set rdf:type 'gn:mappingMethod))) + +(define-dump dump-inbred-set + (tables (InbredSet + (left-join Species "ON InbredSet.SpeciesId=Species.Id") + (left-join MappingMethod + "ON InbredSet.MappingMethodId=MappingMethod.Id"))) + (schema-triples + (gn:fullName rdfs:range rdfs:Literal) + (gn:geneticType rdfs:range rdfs:Literal) + (gn:inbredSetCode rdfs:range rdfs:Literal) + (gn:inbredFamily rdfs:range rdfs:Literal) + (gn:inbredSetOfSpecies rdfs:range gn:species) + (gn:inbredSetType rdfs:range rdfs:Literal) + (gn:phenotype rdfs:range gn:inbredSetType) + (gn:genotype rdfs:range gn:inbredSetType) + (gn:inbredSetOfMappingMethod rdfs:range gn:mappingMethod)) + (triples (string->identifier "inbredSet" (field InbredSet Name)) + (set rdf:type 'gn:inbredSet) + (set gn:binomialName (field InbredSet FullName)) + (set gn:geneticType (field InbredSet GeneticType)) + (set gn:inbredFamily (field InbredSet Family)) + (set gn:inbredSetOfMappingMethod (field MappingMethod Name)) + (set gn:inbredSetCode (field InbredSet InbredSetCode)) + (set gn:inbredSetOfSpecies + (string->identifier "species" (field Species FullName BinomialName))) + (set gn:genotype + (field ("IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '')" genotypeP))) + (set gn:phenotype + (field ("IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '')" phenotypeP))))) + +(define-dump dump-avg-method + ;; The Name and Normalization fields seem to be the same. Dump only + ;; the Name field. + (tables (AvgMethod)) + (schema-triples + (gn:name rdfs:range rdfs:Literal)) + (triples (string->identifier "avgmethod" (field AvgMethod Name)) + (set rdf:type 'gn:avgMethod) + (set gn:name (field AvgMethod Name)))) + + + +(call-with-target-database + %connection-settings + (lambda (db) + (with-output-to-file (string-append %dump-directory "dump-species-metadata.ttl") + (lambda () + (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>") + (prefix "dct:" "<http://purl.org/dc/terms/>") + (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") + (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + (prefix "gn:" "<http://genenetwork.org/>") + (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>") + (prefix "homologene:" "<https://bio2rdf.org/homologene:>") + (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>") + (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>") + (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>") + (prefix "omim:" "<https://www.omim.org/entry/>") + (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") + (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") + (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>") + (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>") + (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") + (prefix "up:" "<http://purl.uniprot.org/core/>") + (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (newline) + (dump-species db) + (dump-strain db) + (dump-mapping-method db) + (dump-inbred-set db) + (dump-avg-method db)) + #:encoding "utf8"))) diff --git a/examples/dump-tissue.scm b/examples/dump-tissue.scm new file mode 100755 index 0000000..3d55383 --- /dev/null +++ b/examples/dump-tissue.scm @@ -0,0 +1,66 @@ +#! /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 %dump-directory + (list-ref (command-line) 2)) + + + +(define-dump dump-tissue + ;; The Name and TissueName fields seem to be identical. BIRN_lex_ID + ;; and BIRN_lex_Name are mostly NULL. + (tables (Tissue)) + (schema-triples + (gn:name rdfs:range rdfs:Literal)) + ;; Hopefully the Short_Name field is distinct and can be used as an + ;; identifier. + (triples (string->identifier "tissue" (field Tissue Short_Name)) + (set rdf:type 'gn:tissue) + (set gn:name (field Tissue Name)))) + + + +(call-with-target-database + %connection-settings + (lambda (db) + (with-output-to-file (string-append %dump-directory "dump-tissue.ttl") + (lambda () + (prefix "chebi:" "<http://purl.obolibrary.org/obo/CHEBI_>") + (prefix "dct:" "<http://purl.org/dc/terms/>") + (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") + (prefix "generif:" "<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>") + (prefix "gn:" "<http://genenetwork.org/>") + (prefix "hgnc:" "<http://bio2rdf.org/hgnc:>") + (prefix "homologene:" "<https://bio2rdf.org/homologene:>") + (prefix "kegg:" "<http://bio2rdf.org/ns/kegg#>") + (prefix "molecularTrait:" "<http://genenetwork.org/molecular-trait/>") + (prefix "nuccore:" "<https://www.ncbi.nlm.nih.gov/nuccore/>") + (prefix "omim:" "<https://www.omim.org/entry/>") + (prefix "owl:" "<http://www.w3.org/2002/07/owl#>") + (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") + (prefix "pubchem:" "<https://pubchem.ncbi.nlm.nih.gov/>") + (prefix "pubmed:" "<http://rdf.ncbi.nlm.nih.gov/pubmed/>") + (prefix "rdf:" "<http://www.w3.org/1999/02/22-rdf-syntax-ns#>") + (prefix "rdfs:" "<http://www.w3.org/2000/01/rdf-schema#>") + (prefix "taxon:" "<http://purl.uniprot.org/taxonomy/>") + (prefix "uniprot:" "<http://purl.uniprot.org/uniprot/>") + (prefix "up:" "<http://purl.uniprot.org/core/>") + (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (newline) + (dump-tissue db)) + #:encoding "utf8"))) |