diff options
Diffstat (limited to 'examples/dump-probeset.scm')
| -rwxr-xr-x | examples/dump-probeset.scm | 39 |
1 files changed, 0 insertions, 39 deletions
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm index a71f708..8e809a5 100755 --- a/examples/dump-probeset.scm +++ b/examples/dump-probeset.scm @@ -20,14 +20,6 @@ (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") @@ -144,35 +136,6 @@ (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 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 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id") - (schema-triples - (gn:avgMethod rdfs:range rdfs:Literal) - (gn:dataScale rdfs:range rdfs:Literal)) - (triples - (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)) - (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 @@ -203,7 +166,5 @@ (prefix "xsd:" "<http://www.w3.org/2001/XMLSchema#>") (prefix "probeset:" "<http://genenetwork.org/probeset/>") (newline) - (dump-gene-chip db) - (dump-probesetfreeze db) (dump-probeset db)) #:encoding "utf8"))) |