diff options
| -rw-r--r-- | rdf-documentation/dump-gene-chip.md | 26 | ||||
| -rw-r--r-- | rdf-documentation/dump-genotype.md | 22 | ||||
| -rw-r--r-- | rdf-documentation/dump-info-pages.md | 32 | ||||
| -rw-r--r-- | rdf-documentation/dump-phenotype.md | 30 | ||||
| -rw-r--r-- | rdf-documentation/dump-probeset-metadata.md | 58 | ||||
| -rw-r--r-- | rdf-documentation/dump-probeset.md | 62 | ||||
| -rw-r--r-- | rdf-documentation/dump-publication.md | 10 | ||||
| -rw-r--r-- | rdf-documentation/dump-species-metadata.md | 40 | ||||
| -rw-r--r-- | rdf-documentation/dump-tissue.md | 8 |
9 files changed, 87 insertions, 201 deletions
diff --git a/rdf-documentation/dump-gene-chip.md b/rdf-documentation/dump-gene-chip.md index e25573a..80217d8 100644 --- a/rdf-documentation/dump-gene-chip.md +++ b/rdf-documentation/dump-gene-chip.md @@ -20,12 +20,13 @@ gn:platform_genechip_name -> gn-term:geoPlatform -> geoSeries:GeneChip(GeoPlatfo Here's an example query: ```sparql -@prefix geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> . -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/term/> . -@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 geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> +PREFIX gn: <http://genenetwork.org/id/> +PREFIX dct: <> +PREFIX gn-term: <http://genenetwork.org/term/> +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#> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:platform . @@ -70,12 +71,13 @@ gn:Probesetfreeze_name_ -> gn-term:datasetOfInbredSet -> gn:inbredSet_inbredset_ Here's an example query: ```sparql -@prefix geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> . -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/term/> . -@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 geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> +PREFIX gn: <http://genenetwork.org/id/> +PREFIX dct: <> +PREFIX gn-term: <http://genenetwork.org/term/> +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#> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:probesetDataset . diff --git a/rdf-documentation/dump-genotype.md b/rdf-documentation/dump-genotype.md index cc35bc4..a27c230 100644 --- a/rdf-documentation/dump-genotype.md +++ b/rdf-documentation/dump-genotype.md @@ -23,11 +23,12 @@ gn:Genofreeze_name_ -> gn-term:datasetOfInbredSet -> gn:_inbredset_inbredsetname Here's an example query: ```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/term/> . -@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 dct: <http://purl.org/dc/terms/> +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gn-term: <http://genenetwork.org/term/> +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#> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:genotypeDataset . @@ -79,11 +80,12 @@ gn:Abbrev -> gn-term:cM -> "Chr_mm8"^^xsd:int Here's an example query: ```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/term/> . -@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 dct: <http://purl.org/dc/terms/> +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gn-term: <http://genenetwork.org/term/> +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#> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:genotype . diff --git a/rdf-documentation/dump-info-pages.md b/rdf-documentation/dump-info-pages.md index 7cd2ecd..9cf7401 100644 --- a/rdf-documentation/dump-info-pages.md +++ b/rdf-documentation/dump-info-pages.md @@ -45,14 +45,14 @@ gn:Infofiles_infopagename_ -> gn-term:acknowledgment -> DatasetsAcknowledgment Here's an example query: ```sparql -@prefix foaf: <http://xmlns.com/foaf/0.1/> . -@prefix geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> . -@prefix gn-term: <http://genenetwork.org/term/> . -@prefix gn: <http://genenetwork.org/id/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix taxon: <http://purl.uniprot.org/taxonomy/> . -@prefix dct: <http://purl.org/dc/terms/> . +PREFIX foaf: <http://xmlns.com/foaf/0.1/> +PREFIX geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> +PREFIX gn-term: <http://genenetwork.org/term/> +PREFIX gn: <http://genenetwork.org/id/> +PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX taxon: <http://purl.uniprot.org/taxonomy/> +PREFIX dct: <http://purl.org/dc/terms/> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:dataset . @@ -117,14 +117,14 @@ gn:investigator_investigators_firstname_investigators_lastname_investigators_ema Here's an example query: ```sparql -@prefix foaf: <http://xmlns.com/foaf/0.1/> . -@prefix geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> . -@prefix gn-term: <http://genenetwork.org/term/> . -@prefix gn: <http://genenetwork.org/id/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix taxon: <http://purl.uniprot.org/taxonomy/> . -@prefix dct: <http://purl.org/dc/terms/> . +PREFIX foaf: <http://xmlns.com/foaf/0.1/> +PREFIX geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=> +PREFIX gn-term: <http://genenetwork.org/term/> +PREFIX gn: <http://genenetwork.org/id/> +PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX taxon: <http://purl.uniprot.org/taxonomy/> +PREFIX dct: <http://purl.org/dc/terms/> SELECT ?s ?p ?o WHERE { ?s rdf:type foaf:Person . diff --git a/rdf-documentation/dump-phenotype.md b/rdf-documentation/dump-phenotype.md index 62e5488..c36861b 100644 --- a/rdf-documentation/dump-phenotype.md +++ b/rdf-documentation/dump-phenotype.md @@ -17,18 +17,19 @@ 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_ -> dc-termt:created -> "PublishFreeze(CreateTime)"^^xsd:date +gn:Publishfreeze_name_ -> dct:created -> "PublishFreeze(CreateTime)"^^xsd:date gn:Publishfreeze_name_ -> gn-term:datasetOfInbredSet -> gn:inbredSet_inbredset_inbredsetname ``` Here's an example query: ```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/terms/> . -@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/> . +PREFIX dct: <http://purl.org/dc/terms/> +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gn-term: <http://genenetwork.org/terms/> +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 . @@ -45,7 +46,7 @@ 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 dc-termt:created "2015-03-18"^^xsd:date . +gn:B6d2f2_psupublish dct:created "2015-03-18"^^xsd:date . gn:B6d2f2_psupublish gn-term:datasetOfInbredSet gn:inbredSet_b6d2f2-psu . ``` @@ -85,12 +86,13 @@ gn:Abbrev -> gn-term:phenotypeOfPublication -> pubmed:pmid Here's an example query: ```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/terms/> . -@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/> . +PREFIX dct: <http://purl.org/dc/terms/> +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gn-term: <http://genenetwork.org/terms/> +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 . diff --git a/rdf-documentation/dump-probeset-metadata.md b/rdf-documentation/dump-probeset-metadata.md deleted file mode 100644 index b47ce20..0000000 --- a/rdf-documentation/dump-probeset-metadata.md +++ /dev/null @@ -1,58 +0,0 @@ -# Probeset Metadata -## 'dump-probeset-metadata' - - -## Generated Triples: - -The following SQL query was executed: - -```sql -SELECT CONCAT(ProbeSetFreeze.Name,':',IFNULL(ProbeSet.Name, ProbeSet.Id)) AS ProbeSetName, IFNULL(ProbeSet.Name, ProbeSet.Id) AS name, ProbeSetFreeze.Name, IFNULL(ProbeSetXRef.mean, '') AS mean, IFNULL(ProbeSetXRef.se, '') AS se, ProbeSetXRef.Locus, IFNULL(ProbeSetXRef.LRS, '') AS LRS, IFNULL(ProbeSetXRef.pValue, '') AS pValue, IFNULL(ProbeSetXRef.additive, '') AS additive, IFNULL(ProbeSetXRef.h2, '') AS h2 FROM ProbeSetXRef LEFT JOIN ProbeSet ON ProbeSetXRef.ProbeSetId = ProbeSet.Id LEFT JOIN ProbeSetFreeze ON ProbeSetXRef.ProbeSetFreezeId = ProbeSetFreeze.Id WHERE ProbeSetFreeze.public > 0 AND ProbeSetFreeze.confidentiality < 1 -``` - -The above query results to triples that have the form: - -```text -gn:probesetData_probesetname -> rdf:type -> gn:probesetData -gn:probesetData_probesetname -> gn-term:hasProbeset -> probeset:name -gn:probesetData_probesetname -> gn-term:probesetOfDataset -> probeset:ProbeSetFreeze_Name_ -gn:probesetData_probesetname -> gn-term:mean -> "mean"^^xsd:double -gn:probesetData_probesetname -> gn-term:se -> "se"^^xsd:double -gn:probesetData_probesetname -> gn-term:locus -> ProbeSetXRef(Locus) -gn:probesetData_probesetname -> gn:LRS -> "LRS"^^xsd:double -gn:probesetData_probesetname -> gn-term:pValue -> "pValue"^^xsd:double -gn:probesetData_probesetname -> gn-term:additive -> "additive"^^xsd:double -gn:probesetData_probesetname -> gn-term:h2 -> "h2"^^xsd:float -``` -Here's an example query: - -```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/id/> . -@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#> . - -SELECT ?s ?p ?o WHERE { - ?s rdf:type gn:probesetData . - ?s gn-term:hasProbeset probeset:100001_at . - ?s gn-term:probesetOfDataset probeset:HC_U_0304_R . - ?s gn-term:mean #{"8.14033666666667"^^xsd:double}# . - ?s ?p ?o . -} -``` - -Expected Result: - -```rdf -gn:probesetData_hc_u_0304_r:100001_at rdf:type gn:probesetData . -gn:probesetData_hc_u_0304_r:100001_at gn-term:hasProbeset probeset:100001_at . -gn:probesetData_hc_u_0304_r:100001_at gn-term:probesetOfDataset probeset:HC_U_0304_R . -gn:probesetData_hc_u_0304_r:100001_at gn-term:mean "8.14033666666667"^^xsd:double . -gn:probesetData_hc_u_0304_r:100001_at gn-term:se "0.023595817125580502"^^xsd:double . -gn:probesetData_hc_u_0304_r:100001_at gn-term:locus "rsm10000021399" . -gn:probesetData_hc_u_0304_r:100001_at gn:LRS "12.2805314427567"^^xsd:double . -gn:probesetData_hc_u_0304_r:100001_at gn-term:pValue "0.118"^^xsd:double . -gn:probesetData_hc_u_0304_r:100001_at gn-term:additive "0.0803547619047631"^^xsd:double . -``` - diff --git a/rdf-documentation/dump-probeset.md b/rdf-documentation/dump-probeset.md deleted file mode 100644 index 5b4de63..0000000 --- a/rdf-documentation/dump-probeset.md +++ /dev/null @@ -1,62 +0,0 @@ -# ProbeSet Metadata -## 'dump-probeset' - -## Schema Triples: - -```text -gn-term:name -> rdfs:range -> rdfs:Literal -gn-term:probeset -> rdfs:range -> rdfs:Literal -``` -## Generated Triples: - -The following SQL query was executed: - -```sql -SELECT IFNULL(NULLIF(TRIM(ProbeSet.Name), ''), ProbeSet.Id) AS name, GeneChip.Name, ProbeSet.Name, ProbeSet.Symbol, ProbeSet.description, ProbeSet.Chr, IFNULL(ProbeSet.Mb, '') AS Mb, ProbeSet.BlatSeq, ProbeSet.TargetSeq, ProbeSet.UniProtID FROM ProbeSet LEFT JOIN GeneChip ON GeneChip.Id = ProbeSet.ChipId -``` - -The above query results to triples that have the form: - -```text -probeset:name -> rdf:type -> gn-id:probeset -probeset:name -> gn-term:chipOf -> gn-id:platform_genechip_name -probeset:name -> gn-term:name -> ProbeSet(Name) -probeset:name -> gn-term:symbol -> ProbeSet(Symbol) -probeset:name -> gn-term:description -> ProbeSetdescription -probeset:name -> gn-term:chr -> ProbeSet(Chr) -probeset:name -> gn-term:mb -> "Mb"^^xsd:double -probeset:name -> gn-term:blatSeq -> ProbeSetBlatSeq -probeset:name -> gn-term:targetSeq -> ProbeSetTargetSeq -probeset:name -> gn-term:uniProtReference -> uniprot:ProbeSet(UniProtID) -``` -Here's an example query: - -```sparql -@prefix probeset: <http://genenetwork.org/probeset/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-r . -@prefix uniprot: <http://purl.uniprot.org/uniprot/> . - -SELECT ?s ?p ?o WHERE { - ?s rdf:type gn-id:probeset . - ?s gn-term:chipOf gn-id:platform_mg_u74av2 . - ?s gn-term:name "MG_U74AV2" . - ?s gn-term:symbol "Cd3g" . - ?s ?p ?o . -} -``` - -Expected Result: - -```rdf -probeset:100001_at rdf:type gn-id:probeset . -probeset:100001_at gn-term:chipOf gn-id:platform_mg_u74av2 . -probeset:100001_at gn-term:name "MG_U74AV2" . -probeset:100001_at gn-term:symbol "Cd3g" . -probeset:100001_at gn-term:description "CD3d antigen, gamma polypeptide" . -probeset:100001_at gn-term:chr "9" . -probeset:100001_at gn-term:mb "44.970689"^^xsd:double . -probeset:100001_at gn-term:blatSeq "CTCTGTTGCAAAATGAACAGCTGTACAGCCCCTCAAGGACCGGGAATATGACCAGTACAGCCATCTCCAAGGAAACCAACTGAGGAAGAAGTGAACTCAGCAGGACTCAGGGTGTCCCCACAATGCATTTTGGAGAGAGCCCAGACTGCAAGCAGAGAGGAAGAACTGAGGAAAACAAGCACAGCGTGGTGTT" . -probeset:100001_at gn-term:targetSeq "ctctgttgcaaaatgaacagctgtaccagcccctcaaggaccgggaatatgaccagtacagccatctccaaggaaaccaactgaggaagaagtgaactcagcaggactcagggtgtccccccttntatccagcacccagaatcaaaacaatgcattttggagagagcccagtagagagattttcaaccctacaggtagactgcaagcagagaggaagaactgtcaaagaaattttggtcttttttttttttttnncaaaataaaataaaagcttggaggagccagtggtatgantnnnnnntgnancanttgtcaaccttgtttggggttnncagcaccccacccccagaccccccaaaaaaattcagtgaaggaaaacaagcacagcgtggtgtt" . -``` - diff --git a/rdf-documentation/dump-publication.md b/rdf-documentation/dump-publication.md index a40b597..90a366c 100644 --- a/rdf-documentation/dump-publication.md +++ b/rdf-documentation/dump-publication.md @@ -27,11 +27,11 @@ pubmed:pmid -> gn:author -> PublicationAuthors Here's an example query: ```sparql -@prefix gn-term: <http://genenetwork.org/terms/> . -@prefix gn: <http://genenetwork.org/id/> . -@prefix pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . +PREFIX gn-term: <http://genenetwork.org/terms/> +PREFIX gn: <http://genenetwork.org/id/> +PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:publication . diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md index f64232f..31ad4e2 100644 --- a/rdf-documentation/dump-species-metadata.md +++ b/rdf-documentation/dump-species-metadata.md @@ -23,11 +23,11 @@ gn:Species_fullname -> gn-term:organism -> taxon:Species(TaxonomyId) Here's an example query: ```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/term/> . -@prefix rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix taxon: <http://purl.uniprot.org/taxonomy/> . +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gn-term: <http://genenetwork.org/term/> +PREFIX rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX taxon: <http://purl.uniprot.org/taxonomy/> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:species . @@ -73,11 +73,11 @@ gn:Strainname -> gn-term:symbol -> Strain(Symbol) Here's an example query: ```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/term/> . -@prefix rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix taxon: <http://purl.uniprot.org/taxonomy/> . +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gn-term: <http://genenetwork.org/term/> +PREFIX rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX taxon: <http://purl.uniprot.org/taxonomy/> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:strain . @@ -116,11 +116,11 @@ gn:mappingMethod_mappingmethod_name -> rdf:type -> gn:mappingMethod Here's an example query: ```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/term/> . -@prefix rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix taxon: <http://purl.uniprot.org/taxonomy/> . +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gn-term: <http://genenetwork.org/term/> +PREFIX rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX taxon: <http://purl.uniprot.org/taxonomy/> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:mappingMethod . @@ -155,11 +155,11 @@ gn:avgmethod_avgmethod_name -> gn-term:normalization -> AvgMethod(Normalization) Here's an example query: ```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/term/> . -@prefix rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . -@prefix taxon: <http://purl.uniprot.org/taxonomy/> . +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gn-term: <http://genenetwork.org/term/> +PREFIX rdf: <https://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> +PREFIX taxon: <http://purl.uniprot.org/taxonomy/> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:avgMethod . diff --git a/rdf-documentation/dump-tissue.md b/rdf-documentation/dump-tissue.md index 12271e8..6306399 100644 --- a/rdf-documentation/dump-tissue.md +++ b/rdf-documentation/dump-tissue.md @@ -19,10 +19,10 @@ gn:tissue_tissue_short_name -> gn-term:name -> Tissue(Name) Here's an example query: ```sparql -@prefix gn: <http://genenetwork.org/id/> . -@prefix gn-term: <http://genenetwork.org/terms/> . -@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> . -@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> . +PREFIX gn: <http://genenetwork.org/id/> +PREFIX gn-term: <http://genenetwork.org/terms/> +PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> +PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> SELECT ?s ?p ?o WHERE { ?s rdf:type gn:tissue . |