diff options
| -rwxr-xr-x | examples/dump-probeset.scm | 138 |
1 files changed, 115 insertions, 23 deletions
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm index 6b1b7a8..0a6e07b 100755 --- a/examples/dump-probeset.scm +++ b/examples/dump-probeset.scm @@ -20,51 +20,143 @@ (list-ref (command-line) 2)) -(define-dump dump-probeset +(define-dump dump-probeset-0 (tables (ProbeSet - (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId"))) + (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")) + "LIMIT 2000000 OFFSET 0") (schema-triples (gn:name rdfs:range rdfs:Literal) (gn:probeset rdfs:range rdfs:Literal)) (triples (ontology 'probeset: - (regexp-substitute/global - #f "[^A-Za-z0-9:]" - (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)" - name)) - 'pre "_" 'post)) + (string-trim-both + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (field ("IFNULL(NULLIF(TRIM(ProbeSet.Name), ''), ProbeSet.Id)" + name)) + 'pre "_" 'post))) (set rdf:type 'gn:probeset) (set gn:chipOf (string->identifier "platform" (field GeneChip Name))) (set gn:name (field ProbeSet Name)) - (set gn:symbol (field ProbeSet Symbol)) + (set gn:symbol (delete-substrings (field ProbeSet Symbol) "\"")) (set gn:description (sanitize-rdf-string (field ProbeSet description))) (set gn:chr (field ProbeSet Chr)) (set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double)) - (multiset gn:tissue (map string-trim-both - (string-split - (field ("IFNULL(ProbeSet.Tissue, '')" Tissue)) - #\,))) - (multiset gn:alias (map string-trim-both - (string-split (sanitize-rdf-string (field ProbeSet alias)) - #\;))) - (set gn:unigene (field ProbeSet UniGeneId)) - (set gn:generif (ontology 'generif: (field ProbeSet GeneId))) - (set gn:genbank (field ProbeSet GenbankId)) + ;; For now have the tissue, and alias as one line without + ;; splitting to make the dump faster + ;; (set gn:tissue (field ("IFNULL(ProbeSet.Tissue, '')" Tissue))) + ;; (set gn:alias (field ProbeSet alias)) + ;; (set gn:generif (ontology 'generif: (field ProbeSet GeneId))) (set gn:blatSeq (sanitize-rdf-string (string-trim-both (field ProbeSet BlatSeq)))) (set gn:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq))) - (set gn:omim (sanitize-rdf-string (string-trim-both (field ProbeSet OMIM)))) - (set gn:RefSeq_TranscriptId (field ProbeSet RefSeq_TranscriptId)) + ;; (set gn:unigene (field ProbeSet UniGeneId)) + ;; (set gn:genbank (field ProbeSet GenbankId)) + ;; (set gn:omim (sanitize-rdf-string (string-trim-both (field ProbeSet OMIM)))) + ;; (set gn:RefSeq_TranscriptId (field ProbeSet RefSeq_TranscriptId)) (set gn:uniProtReference (ontology 'uniprot: - (field ProbeSet UniProtID))))) + (field ProbeSet UniProtID))))) + +(define-dump dump-probeset-1 + (tables (ProbeSet + (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")) + "LIMIT 2000000 OFFSET 2000000") + (schema-triples + (gn:name rdfs:range rdfs:Literal) + (gn:probeset rdfs:range rdfs:Literal)) + (triples (ontology + 'probeset: + (string-trim-both + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (field ("IFNULL(NULLIF(TRIM(ProbeSet.Name), ''), ProbeSet.Id)" + name)) + 'pre "_" 'post))) + (set rdf:type 'gn:probeset) + (set gn:chipOf (string->identifier "platform" (field GeneChip Name))) + (set gn:name (field ProbeSet Name)) + (set gn:symbol (delete-substrings (field ProbeSet Symbol) "\"")) + (set gn:description (sanitize-rdf-string + (field ProbeSet description))) + (set gn:chr (field ProbeSet Chr)) + (set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double)) + (set gn:blatSeq (sanitize-rdf-string + (string-trim-both (field ProbeSet BlatSeq)))) + (set gn:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq))) + (set gn:uniProtReference (ontology 'uniprot: + (field ProbeSet UniProtID))))) +(define-dump dump-probeset-2 + (tables (ProbeSet + (left-join GeneChip "ON GeneChip.Id = ProbeSet.ChipId")) + "WHERE ProbeSet.Name IS NOT NULL LIMIT 2000000 OFFSET 4000000") + (schema-triples + (gn:name rdfs:range rdfs:Literal) + (gn:probeset rdfs:range rdfs:Literal)) + (triples (ontology + 'probeset: + (string-trim-both + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)" + name)) + 'pre "_" 'post))) + (set rdf:type 'gn:probeset) + (set gn:chipOf (string->identifier "platform" (field GeneChip Name))) + (set gn:name (field ProbeSet Name)) + (set gn:symbol (delete-substrings (field ProbeSet Symbol) "\"")) + (set gn:description (sanitize-rdf-string + (field ProbeSet description))) + (set gn:chr (field ProbeSet Chr)) + (set gn:mb (annotate-field (field ("IFNULL(ProbeSet.Mb, '')" Mb)) '^^xsd:double)) + (set gn:blatSeq (sanitize-rdf-string + (string-trim-both (field ProbeSet BlatSeq)))) + (set gn:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq))) + (set gn:uniProtReference (ontology 'uniprot: + (field ProbeSet UniProtID))))) (call-with-target-database %connection-settings (lambda (db) - (with-output-to-file (string-append %dump-directory "dump-probeset.ttl") + (with-output-to-file (string-append %dump-directory "dump-probeset-0.ttl") + (lambda () + (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 "owl:" "<http://www.w3.org/2002/07/owl#>") + (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") + (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 "uniprot:" "<http://purl.uniprot.org/uniprot/>") + (prefix "up:" "<http://purl.uniprot.org/core/>") + (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (prefix "probeset:" "<http://genenetwork.org/probeset/>") + (newline) + (dump-probeset-0 db)) + #:encoding "utf8") + (with-output-to-file (string-append %dump-directory "dump-probeset-1.ttl") + (lambda () + (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 "owl:" "<http://www.w3.org/2002/07/owl#>") + (prefix "phenotype:" "<http://genenetwork.org/phenotype/>") + (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 "uniprot:" "<http://purl.uniprot.org/uniprot/>") + (prefix "up:" "<http://purl.uniprot.org/core/>") + (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") + (prefix "probeset:" "<http://genenetwork.org/probeset/>") + (newline) + (dump-probeset-1 db)) + #:encoding "utf8") + (with-output-to-file (string-append %dump-directory "dump-probeset-2.ttl") (lambda () (prefix "dct:" "<http://purl.org/dc/terms/>") (prefix "foaf:" "<http://xmlns.com/foaf/0.1/>") @@ -80,5 +172,5 @@ (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") (prefix "probeset:" "<http://genenetwork.org/probeset/>") (newline) - (dump-probeset db)) + (dump-probeset-2 db)) #:encoding "utf8"))) |