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-rw-r--r--rdf-documentation/dump-phenotype.md114
1 files changed, 58 insertions, 56 deletions
diff --git a/rdf-documentation/dump-phenotype.md b/rdf-documentation/dump-phenotype.md
index c36861b..dc9b6dd 100644
--- a/rdf-documentation/dump-phenotype.md
+++ b/rdf-documentation/dump-phenotype.md
@@ -1,40 +1,42 @@
# Phenotypes Metadata
## 'dump-publishfreeze'
-
## Generated Triples:
The following SQL query was executed:
```sql
-SELECT PublishFreeze.Name, PublishFreeze.Name, PublishFreeze.FullName, PublishFreeze.ShortName, PublishFreeze.CreateTime, InbredSet.Name AS InbredSetName FROM PublishFreeze LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = PublishFreeze.Name LEFT JOIN InbredSet ON PublishFreeze.InbredSetId = InbredSet.InbredSetId WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL
+SELECT PublishFreeze.Name, PublishFreeze.Name, PublishFreeze.FullName, PublishFreeze.ShortName, PublishFreeze.CreateTime, InbredSet.Name FROM PublishFreeze LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = PublishFreeze.Name LEFT JOIN InbredSet ON PublishFreeze.InbredSetId = InbredSet.InbredSetId WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND InfoFiles.InfoFileId IS NULL
```
The above query results to triples that have the form:
```text
-gn:Publishfreeze_name_ -> rdf:type -> gn:phenotypeDataset
-gn:Publishfreeze_name_ -> gn-term:name -> PublishFreeze(Name)
-gn:Publishfreeze_name_ -> gn-term:fullName -> PublishFreeze(FullName)
-gn:Publishfreeze_name_ -> gn-term:shortName -> PublishFreeze(ShortName)
+gn:Publishfreeze_name_ -> rdf:type -> gnc:phenotypeDataset
+gn:Publishfreeze_name_ -> rdfs:label -> PublishFreeze(Name)
+gn:Publishfreeze_name_ -> skos:prefLabel -> PublishFreeze(FullName)
+gn:Publishfreeze_name_ -> skos:altLabel -> PublishFreeze(ShortName)
gn:Publishfreeze_name_ -> dct:created -> "PublishFreeze(CreateTime)"^^xsd:date
-gn:Publishfreeze_name_ -> gn-term:datasetOfInbredSet -> gn:inbredSet_inbredset_inbredsetname
+gn:Publishfreeze_name_ -> gnt:belongsToInbredSet -> gn:Inbredset_name
```
Here's an example query:
```sparql
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gn-term: <http://genenetwork.org/terms/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX gnt: <http://genenetwork.org/terms/>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
-SELECT ?s ?p ?o WHERE {
- ?s rdf:type gn:phenotypeDataset .
- ?s gn-term:name "B6D2F2-PSUPublish" .
- ?s gn-term:fullName "B6D2F2 PSU Phenotypes" .
+SELECT * WHERE {
+ ?s rdf:type gnc:phenotypeDataset .
+ ?s rdfs:label "B6D2F2-PSUPublish" .
+ ?s skos:prefLabel "B6D2F2 PSU Phenotypes" .
?s ?p ?o .
}
```
@@ -42,63 +44,64 @@ SELECT ?s ?p ?o WHERE {
Expected Result:
```rdf
-gn:B6d2f2_psupublish rdf:type gn:phenotypeDataset .
-gn:B6d2f2_psupublish gn-term:name "B6D2F2-PSUPublish" .
-gn:B6d2f2_psupublish gn-term:fullName "B6D2F2 PSU Phenotypes" .
-gn:B6d2f2_psupublish gn-term:shortName "B6D2F2 PSU Publish" .
+gn:B6d2f2_psupublish rdf:type gnc:phenotypeDataset .
+gn:B6d2f2_psupublish rdfs:label "B6D2F2-PSUPublish" .
+gn:B6d2f2_psupublish skos:prefLabel "B6D2F2 PSU Phenotypes" .
+gn:B6d2f2_psupublish skos:altLabel "B6D2F2 PSU Publish" .
gn:B6d2f2_psupublish dct:created "2015-03-18"^^xsd:date .
-gn:B6d2f2_psupublish gn-term:datasetOfInbredSet gn:inbredSet_b6d2f2-psu .
+gn:B6d2f2_psupublish gnt:belongsToInbredSet gn:B6d2f2-psupublish .
```
## 'dump-phenotypes'
-
## Generated Triples:
The following SQL query was executed:
```sql
-SELECT CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '_')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation)) AS abbrev, CAST(CONVERT(BINARY CONVERT(IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation) USING latin1) USING utf8) AS VARCHAR(100)) AS PhenotypeName, CAST(CONVERT(BINARY CONVERT(Phenotype.Post_publication_description USING latin1) USING utf8) AS CHAR(10000)) AS postPubDescr, Phenotype.Original_description, CAST(CONVERT(BINARY CONVERT(Phenotype.Pre_publication_description USING latin1) USING utf8) AS VARCHAR(15000)) AS prePubDesc, Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, IFNULL(PublishXRef.mean, '') AS mean, PublishXRef.Locus, IFNULL(PublishXRef.LRS, '') AS lrs, IFNULL(PublishXRef.additive, '') AS additive, PublishXRef.Sequence, IFNULL(InfoFiles.InfoPageName, IFNULL(PublishFreeze.Name, '')) AS DatasetName, IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT)) AS pmid, Publication.Id FROM Phenotype LEFT JOIN PublishXRef ON Phenotype.Id = PublishXRef.PhenotypeId LEFT JOIN Publication ON Publication.Id = PublishXRef.PublicationId LEFT JOIN PublishFreeze ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = PublishFreeze.Name
+SELECT CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '_')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation)) AS abbrev, IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation) AS PhenotypeName, CONCAT(InbredSet.Name, '_', PublishXRef.Id) AS phenotypeAltName, Phenotype.Post_publication_description, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Owner, IFNULL(PublishXRef.mean, '') AS mean, PublishXRef.Locus, IFNULL(PublishXRef.LRS, '') AS lrs, IFNULL(PublishXRef.additive, '') AS additive, PublishXRef.Sequence, InfoFiles.InfoPageName, IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT)) AS pmid, Publication.Id FROM Phenotype LEFT JOIN PublishXRef ON Phenotype.Id = PublishXRef.PhenotypeId LEFT JOIN Publication ON Publication.Id = PublishXRef.PublicationId LEFT JOIN InbredSet ON InbredSet.InbredSetId = PublishXRef.InbredSetId LEFT JOIN PublishFreeze ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = PublishFreeze.Name WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND PublishFreeze.Id IS NOT NULL
```
The above query results to triples that have the form:
```text
-gn:Abbrev -> rdf:type -> gn:phenotype
-gn:Abbrev -> gn-term:name -> PhenotypeName
-gn:Abbrev -> gn-term:publicationDescription -> postPubDescr
-gn:Abbrev -> gn-term:originalDescription -> PhenotypeOriginal_description
-gn:Abbrev -> gn-term:prePublicationDescription -> prePubDesc
-gn:Abbrev -> gn-term:prePublicationAbbreviation -> PhenotypePre_publication_abbreviation
-gn:Abbrev -> gn-term:postPublicationAbbreviation -> PhenotypePost_publication_abbreviation
-gn:Abbrev -> gn-term:labCode -> Phenotype(Lab_code)
-gn:Abbrev -> gn-term:submitter -> PhenotypeSubmitter
-gn:Abbrev -> gn-term:owner -> PhenotypeOwner
-gn:Abbrev -> gn-term:mean -> "mean"^^xsd:double
-gn:Abbrev -> gn-term:locus -> PublishXRef(Locus)
-gn:Abbrev -> gn-term:LRS -> "lrs"^^xsd:float
-gn:Abbrev -> gn-term:additive -> "additive"^^xsd:decimal
-gn:Abbrev -> gn-term:sequence -> "PublishXRef(Sequence)"^^xsd:int
-gn:Abbrev -> gn-term:phenotypeOfDataset -> gn:Datasetname
-gn:Abbrev -> gn-term:phenotypeOfPublication -> pubmed:pmid
+gn:Abbrev -> rdf:type -> gnc:phenotype
+gn:Abbrev -> skos:prefLabel -> PhenotypeName
+gn:Abbrev -> skos:altLabel -> phenotypeAltName
+gn:Abbrev -> dct:description -> PhenotypePost_publication_description
+gn:Abbrev -> gnt:abbreviation -> Phenotype(Post_publication_abbreviation)
+gn:Abbrev -> gnt:labCode -> Phenotype(Lab_code)
+gn:Abbrev -> gnt:submitter -> PhenotypeSubmitter
+gn:Abbrev -> dct:contributor -> PhenotypeOwner
+gn:Abbrev -> gnt:mean -> "mean"^^xsd:double
+gn:Abbrev -> gnt:locus -> PublishXRef(Locus)
+gn:Abbrev -> gnt:LRS -> "lrs"^^xsd:double
+gn:Abbrev -> gnt:additive -> "additive"^^xsd:double
+gn:Abbrev -> gnt:sequence -> "PublishXRef(Sequence)"^^xsd:integer
+gn:Abbrev -> gnt:belongsToDataset -> gn:Infofiles_infopagename_
+gn:Abbrev -> dct:isReferencedBy -> pubmed:pmid
+gn:Abbrev -> dct:contributor -> PhenotypeOwner
```
Here's an example query:
```sparql
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gn-term: <http://genenetwork.org/terms/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX gnt: <http://genenetwork.org/terms/>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
-SELECT ?s ?p ?o WHERE {
- ?s rdf:type gn:phenotype .
- ?s gn-term:name "CBLWT2" .
- ?s gn-term:publicationDescription "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" .
- ?s gn-term:originalDescription "Cerebellum weight [mg]" .
+SELECT * WHERE {
+ ?s rdf:type gnc:phenotype .
+ ?s skos:prefLabel "CBLWT2" .
+ ?s skos:altLabel "BXD_10001" .
+ ?s dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" .
?s ?p ?o .
}
```
@@ -106,19 +109,18 @@ SELECT ?s ?p ?o WHERE {
Expected Result:
```rdf
-gn:Bxdpublish_cblwt2 rdf:type gn:phenotype .
-gn:Bxdpublish_cblwt2 gn-term:name "CBLWT2" .
-gn:Bxdpublish_cblwt2 gn-term:publicationDescription "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" .
-gn:Bxdpublish_cblwt2 gn-term:originalDescription "Cerebellum weight [mg]" .
-gn:Bxdpublish_cblwt2 gn-term:prePublicationDescription "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" .
-gn:Bxdpublish_cblwt2 gn-term:postPublicationAbbreviation "CBLWT2" .
-gn:Bxdpublish_cblwt2 gn-term:submitter "robwilliams" .
-gn:Bxdpublish_cblwt2 gn-term:mean "52.13529418496525"^^xsd:double .
-gn:Bxdpublish_cblwt2 gn-term:locus "rs48756159" .
-gn:Bxdpublish_cblwt2 gn-term:LRS "13.4974911471087"^^xsd:float .
-gn:Bxdpublish_cblwt2 gn-term:additive "2.39444435069444"^^xsd:decimal .
-gn:Bxdpublish_cblwt2 gn-term:sequence "1"^^xsd:int .
-gn:Bxdpublish_cblwt2 gn-term:phenotypeOfDataset gn:Bxdpublish .
-gn:Bxdpublish_cblwt2 gn-term:phenotypeOfPublication pubmed:11438585 .
+gn:Bxdpublish_cblwt2 rdf:type gnc:phenotype .
+gn:Bxdpublish_cblwt2 skos:prefLabel "CBLWT2" .
+gn:Bxdpublish_cblwt2 skos:altLabel "BXD_10001" .
+gn:Bxdpublish_cblwt2 dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" .
+gn:Bxdpublish_cblwt2 gnt:abbreviation "CBLWT2" .
+gn:Bxdpublish_cblwt2 gnt:submitter "robwilliams" .
+gn:Bxdpublish_cblwt2 gnt:mean "52.13529418496525"^^xsd:double .
+gn:Bxdpublish_cblwt2 gnt:locus "rs48756159" .
+gn:Bxdpublish_cblwt2 gnt:LRS "13.4974911471087"^^xsd:double .
+gn:Bxdpublish_cblwt2 gnt:additive "2.39444435069444"^^xsd:double .
+gn:Bxdpublish_cblwt2 gnt:sequence "1"^^xsd:integer .
+gn:Bxdpublish_cblwt2 gnt:belongsToDataset gn:Bxdpublish .
+gn:Bxdpublish_cblwt2 dct:isReferencedBy pubmed:11438585 .
```
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-10 00:26:44 +0000