diff options
Diffstat (limited to 'examples/dump-probeset.scm')
-rwxr-xr-x | examples/dump-probeset.scm | 55 |
1 files changed, 11 insertions, 44 deletions
diff --git a/examples/dump-probeset.scm b/examples/dump-probeset.scm index bbf5d8d..c28f7dd 100755 --- a/examples/dump-probeset.scm +++ b/examples/dump-probeset.scm @@ -48,44 +48,19 @@ (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 (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:omim (ontology 'omim: (field ProbeSet OMIM))) - (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:strand (field ProbeSet Probe_set_strand)) - (set gn:chrNum (field ("IFNULL(ProbeSet.chr_num, '')" chr_num))) - (set gn:nameNum (field ("IFNULL(ProbeSet.name_num, '')" name_num))) - (set gn:RefSeq_TranscriptId (ontology 'nuccore: (field ProbeSet RefSeq_TranscriptId))) - (set gn:Chr_mm8 (field ("IFNULL(ProbeSet.Chr_mm8, '')" Chr_mm8))) - (set gn:Mb_mm8 (field ("IFNULL(ProbeSet.Mb_mm8, '')" Mb_mm8))) + (set gn:genbank (field ProbeSet GenbankId)) + (set gn:blatSeq (sanitize-rdf-string + (string-trim-both (field ProbeSet BlatSeq)))) + (set gn:targetSeq (sanitize-rdf-string (field ProbeSet TargetSeq))) + (set gn:omim + (ontology + 'omim: + (field ("IF(ProbeSet.OMIM REGEXP '^-?[0-9]+$' > 0, ProbeSet.OMIM, '')" OMIM)))) + (set gn:RefSeq_TranscriptId (field ProbeSet RefSeq_TranscriptId)) (set gn:uniProtReference (ontology 'uniprot: - (field ProbeSet UniProtID))) - (set gn:PubChemID (ontology - 'pubchem: - (field - ("IFNULL(ProbeSet.PubChem_ID, '')" - PubChem_ID)))) - (multiset gn:tissue (map string-trim-both - (string-split - (field ("IFNULL(ProbeSet.Tissue, '')" Tissue)) - #\,))) - (set gn:primaryName (field ProbeSet PrimaryName)) - (set gn:secondaryNames (field ProbeSet SecondaryNames)) - (set gn:peptideSequence (field ProbeSet PeptideSequence)))) + (field ProbeSet UniProtID))))) @@ -94,20 +69,12 @@ (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#>") |