diff options
Diffstat (limited to 'examples/phenotype.scm')
| -rwxr-xr-x | examples/phenotype.scm | 105 |
1 files changed, 66 insertions, 39 deletions
diff --git a/examples/phenotype.scm b/examples/phenotype.scm index af47b51..3e69607 100755 --- a/examples/phenotype.scm +++ b/examples/phenotype.scm @@ -61,43 +61,76 @@ (or post-abbrev pre-abbrev post-desc pre-desc) #:separator "_"))))) -(define-transformer phenotypes +(define-transformer gnc:set->gn:trait (tables (PublishXRef (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") (left-join Publication "ON Publication.Id = PublishXRef.PublicationId") - (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId"))) - (triples (string->identifier + (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")) + "WHERE InbredSet.public > 0") + (triples (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_") + (set gnt:has_phenotype_trait + (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation))) + (pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation))) + (post-desc (blank-p (field Phenotype Post_publication_description))) + (pre-desc (blank-p (field Phenotype Post_publication_description)))) + (string->identifier "trait" - (field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)" - Phenotype)) - #:separator "_") - (set rdf:type 'gnc:phenotype) - (set gnt:has_strain + (format #f "~a_~a" (field InbredSet Name InbredSetName) + (or post-abbrev pre-abbrev post-desc pre-desc)) + #:separator "_"))))) + +(define-transformer gn:trait->gn:phenotype + (tables (PublishXRef + (left-join InbredSet "ON InbredSet.InbredSetId = PublishXRef.InbredSetId") + (left-join Publication "ON Publication.Id = PublishXRef.PublicationId") + (left-join Phenotype "ON Phenotype.Id = PublishXRef.PhenotypeId")) + "WHERE InbredSet.public > 0") + (triples (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation))) + (pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation))) + (post-desc (blank-p (field Phenotype Post_publication_description))) + (pre-desc (blank-p (field Phenotype Post_publication_description)))) + (string->identifier + "trait" + (format #f "~a_~a" (field InbredSet Name InbredSetName) + (or post-abbrev pre-abbrev post-desc pre-desc)) + #:separator "_")) + (set rdf:type 'gnc:phenotype_trait) + (set gnt:has_strain (string->identifier "set" (field InbredSet Name InbredSetName) #:separator "_")) + (set owl:equivalentClass (string->identifier - "set" (field InbredSet Name InbredSetName) + "trait" + (field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)" + Phenotype)) #:separator "_")) - ;; This is the trait's name - (set gnt:trait_id - (let ((trait-id (field PublishXRef Id))) - (if (number? trait-id) - (number->string trait-id) - trait-id))) - (set skos:altLabel - (field ("CONCAT(IFNULL(InbredSet.InbredSetCode, PublishXRef.InbredSetId), '_', PublishXRef.Id)" - Phenotype))) - ;; All phenotypes have a post-publication description - (set dct:description - (sanitize-rdf-string - (field Phenotype Post_publication_description))) - ;; All phenotypes have a post-publication abbreviation - (set gnt:abbreviation (field Phenotype Post_publication_abbreviation)) - (set gnt:labCode (field Phenotype Lab_code)) - (set gnt:submitter - (sanitize-rdf-string (field Phenotype Submitter))) - (set dct:contributor (sanitize-rdf-string (field Phenotype Owner))) + (set dct:references + (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 "unpublished" + (number->string publication-id)) + (ontology 'pubmed: pmid)))) + (set gnt:has_phenotype + (let ((post-abbrev (blank-p (field Phenotype Post_publication_abbreviation))) + (pre-abbrev (blank-p (field Phenotype Pre_publication_abbreviation))) + (post-desc (blank-p (field Phenotype Post_publication_description))) + (pre-desc (blank-p (field Phenotype Post_publication_description)))) + (string->identifier + "phenotype" + (or post-abbrev pre-abbrev post-desc pre-desc) + #:separator "_"))) (set gnt:mean (annotate-field (field ("IFNULL(PublishXRef.mean, '')" mean)) '^^xsd:double)) - (set gnt:locus (sanitize-rdf-string (field PublishXRef Locus))) + (set gnt:locus + (string->identifier + "" + (regexp-substitute/global + #f "[^A-Za-z0-9:]" + (sanitize-rdf-string (field PublishXRef Locus)) + 'pre "_" 'post) + #:separator "" + #:proc string-capitalize-first)) (set gnt:lod_score (annotate-field (field ("IFNULL((PublishXRef.LRS/4.604), '')" lrs)) '^^xsd:double)) @@ -105,15 +138,7 @@ (annotate-field (field ("IFNULL(PublishXRef.additive, '')" additive)) '^^xsd:double)) (set gnt:sequence (annotate-field (field PublishXRef Sequence) '^^xsd:integer)) - (set dct:isReferencedBy - (let ((pmid (field - ("IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT))" - pmid))) - (publication-id (field Publication Id PublicationId))) - (if (string-null? pmid) - (string->identifier "unpublished" - (number->string publication-id)) - (ontology 'pubmed: pmid)))))) + (set rdfs:comment (sanitize-rdf-string (field PublishXRef comments))))) @@ -149,7 +174,9 @@ (inputs (list gnc:phenotype->gn:phenotype - gn:phenotype->metadata)) + gn:phenotype->metadata + gnc:set->gn:trait + gn:trait->gn:phenotype)) (outputs `(#:documentation ,documentation #:rdf ,output)))) |