diff options
| -rwxr-xr-x | examples/dump-probeset.scm | 48 |
1 files changed, 22 insertions, 26 deletions
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm index d1ea2ae..0b37514 100755 --- a/examples/dump-probeset.scm +++ b/examples/dump-probeset.scm @@ -35,12 +35,17 @@ (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))) + (triples (ontology + 'probeset: + (field ("IFNULL(ProbeSet.Name, ProbeSet.Id)" + name))) (set gn:probesetOfDataset - (string->identifier - "dataset" - (field ProbeSetFreeze Name))) + (ontology + 'probeset: + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (field ProbeSetFreeze Name) + 'pre "_" 'post))) (set gn:mean (annotate-field (field ("IFNULL(ProbeSetXRef.mean, '')" mean)) '^^xsd:double)) (set gn:se (annotate-field (field ("IFNULL(ProbeSetXRef.se, '')" se)) @@ -60,8 +65,6 @@ (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))) @@ -86,21 +89,8 @@ (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)) @@ -157,16 +147,21 @@ ;; Molecular Traits are also referred to as ProbeSets (define-dump dump-probesetfreeze (tables (ProbeSetFreeze + (left-join InfoFiles "ON InfoFiles.InfoPageName = ProbeSetFreeze.Name") (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") + "WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id") (schema-triples - (gn:molecularTrait rdfs:range rdfs:Literal)) + (gn:avgMethod rdfs:range rdfs:Literal) + (gn:dataScale rdfs:range rdfs:Literal)) (triples - (string->identifier "dataset" (field ProbeSetFreeze Name)) - (set rdf:type 'gn:dataset) + (ontology 'probeset: + (regexp-substitute/global #f "[^A-Za-z0-9:]" + (field ProbeSetFreeze Name) + 'pre "_" 'post)) + (set rdf:type 'gn:probesetDataset) (set gn:avgMethod (string->identifier "avgmethod" (field AvgMethod Name))) (set gn:fullName (field ProbeSetFreeze FullName)) (set gn:shortName (field ProbeSetFreeze ShortName)) @@ -206,8 +201,9 @@ (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-gene-chip db) - (dump-probeset db) - (dump-probesetfreeze db)) + (dump-probesetfreeze db) + (dump-probeset db)) #:encoding "utf8"))) |