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-rw-r--r--rdf-documentation/dataset-metadata.md (renamed from rdf-documentation/dump-info-pages.md)248
-rw-r--r--rdf-documentation/dump-gene-chip.md118
-rw-r--r--rdf-documentation/dump-phenotype.md121
-rw-r--r--rdf-documentation/dump-probeset-metadata.md58
-rw-r--r--rdf-documentation/dump-probeset-summary-stats.md60
-rw-r--r--rdf-documentation/dump-species-metadata.md373
-rw-r--r--rdf-documentation/generif-metadata.md170
-rw-r--r--rdf-documentation/genotype-metadata.md (renamed from rdf-documentation/dump-genotype.md)55
-rw-r--r--rdf-documentation/phenotype-metadata.md71
-rw-r--r--rdf-documentation/probeset-metadata.md (renamed from rdf-documentation/dump-probeset.md)2
-rw-r--r--rdf-documentation/publication-metadata.md (renamed from rdf-documentation/dump-publication.md)2
-rw-r--r--rdf-documentation/species-metadata.md375
-rw-r--r--rdf-documentation/tissue-metadata.md (renamed from rdf-documentation/dump-tissue.md)2
13 files changed, 863 insertions, 792 deletions
diff --git a/rdf-documentation/dump-info-pages.md b/rdf-documentation/dataset-metadata.md
index e7b42bf..20f3e29 100644
--- a/rdf-documentation/dump-info-pages.md
+++ b/rdf-documentation/dataset-metadata.md
@@ -1,12 +1,12 @@
# Info files / Investigators Metadata
-## 'dump-info-files'
+## 'info-files'
## Generated Triples:
The following SQL query was executed:
```sql
-SELECT InfoFiles.InfoPageName, IF(GenoFreeze.Id IS NOT NULL, 'gnc:genotypeDataset', IF(PublishFreeze.Id IS NOT NULL, 'gnc:phenotypeDataset', IF(ProbeSetFreeze.Name IS NOT NULL, 'gnc:probesetDataset', 'gnc:dataset'))) AS rdfType, InfoFiles.InfoPageName, IFNULL(GenoFreeze.FullName, IFNULL(PublishFreeze.FullName, '')) AS DatasetFullName, Datasets.DatasetName AS DatasetGroup, InfoFiles.InfoFileTitle, Datasets.PublicationTitle, IFNULL(GenoFreeze.CreateTime, IFNULL(PublishFreeze.CreateTime, IFNULL(ProbeSetFreeze.CreateTime, ''))) AS createTimeGenoFreeze, Investigators.FirstName, Investigators.LastName, Investigators.Email, Organizations.OrganizationName, InfoFiles.GN_AccesionId, DatasetStatus.DatasetStatusName, InbredSet.Name AS InbredSetName, Tissue.Short_Name, AvgMethod.Name AS AvgMethodName, AvgMethod.Name AS AvgMethodName, GeneChip.Name AS GeneChip, Datasets.Summary, IFNULL(Datasets.GeoSeries, '') AS GeoSeries, Datasets.AboutTissue, InfoFiles.Specifics, Datasets.AboutCases, Datasets.AboutPlatform, Datasets.AboutDataProcessing, Datasets.Notes, Datasets.ExperimentDesign, Datasets.Contributors, Datasets.Citation, InfoFiles.Data_Source_Acknowledge, Datasets.Acknowledgment FROM InfoFiles LEFT JOIN PublishFreeze ON InfoFiles.InfoPageName = PublishFreeze.Name LEFT JOIN GenoFreeze ON InfoFiles.InfoPageName = GenoFreeze.Name LEFT JOIN ProbeSetFreeze ON InfoFiles.InfoPageName = ProbeSetFreeze.Name LEFT JOIN InbredSet ON InfoFiles.InbredSetId = InbredSet.InbredSetId LEFT JOIN Species ON InfoFiles.SpeciesId = Species.SpeciesId LEFT JOIN Datasets USING (DatasetId) LEFT JOIN DatasetStatus USING (DatasetStatusId) LEFT JOIN Tissue USING (TissueId) LEFT JOIN Investigators USING (InvestigatorId) LEFT JOIN AvgMethod USING (AvgMethodId) LEFT JOIN Organizations USING (OrganizationId) LEFT JOIN GeneChip USING (GeneChipId) WHERE GN_AccesionId IS NOT NULL
+SELECT InfoFiles.InfoPageName, IF(GenoFreeze.Id IS NOT NULL, 'gnc:genotypeDataset', IF(PublishFreeze.Id IS NOT NULL, 'gnc:phenotypeDataset', IF(ProbeSetFreeze.Name IS NOT NULL, 'gnc:probesetDataset', 'gnc:dataset'))) AS rdfType, InfoFiles.InfoPageName, IFNULL(GenoFreeze.FullName, IFNULL(PublishFreeze.FullName, '')) AS DatasetFullName, Datasets.DatasetName AS DatasetGroup, InfoFiles.InfoFileTitle, Datasets.PublicationTitle, IFNULL(GenoFreeze.CreateTime, IFNULL(PublishFreeze.CreateTime, IFNULL(ProbeSetFreeze.CreateTime, ''))) AS createTimeGenoFreeze, Investigators.FirstName, Investigators.LastName, Investigators.Email, Organizations.OrganizationName, InfoFiles.GN_AccesionId, DatasetStatus.DatasetStatusName, InbredSet.Name, Tissue.Short_Name, AvgMethod.Name AS AvgMethodName, AvgMethod.Name AS AvgMethodName, GeneChip.Name AS GeneChip, Datasets.Summary, IFNULL(Datasets.GeoSeries, '') AS GeoSeries, Datasets.AboutTissue, InfoFiles.Specifics, Datasets.AboutCases, Datasets.AboutPlatform, Datasets.AboutDataProcessing, Datasets.Notes, Datasets.ExperimentDesign, Datasets.Contributors, Datasets.Citation, InfoFiles.Data_Source_Acknowledge, Datasets.Acknowledgment FROM InfoFiles LEFT JOIN PublishFreeze ON InfoFiles.InfoPageName = PublishFreeze.Name LEFT JOIN GenoFreeze ON InfoFiles.InfoPageName = GenoFreeze.Name LEFT JOIN ProbeSetFreeze ON InfoFiles.InfoPageName = ProbeSetFreeze.Name LEFT JOIN InbredSet ON InfoFiles.InbredSetId = InbredSet.InbredSetId LEFT JOIN Species ON InfoFiles.SpeciesId = Species.SpeciesId LEFT JOIN Datasets USING (DatasetId) LEFT JOIN DatasetStatus USING (DatasetStatusId) LEFT JOIN Tissue USING (TissueId) LEFT JOIN Investigators USING (InvestigatorId) LEFT JOIN AvgMethod USING (AvgMethodId) LEFT JOIN Organizations USING (OrganizationId) LEFT JOIN GeneChip USING (GeneChipId) WHERE GN_AccesionId IS NOT NULL
```
The above query results to triples that have the form:
@@ -23,7 +23,7 @@ gn:Infofiles_infopagename_ -> gdmt:hasCreatorInfo -> gn:investigator_investigato
gn:Infofiles_infopagename_ -> gdmt:hasCreatorAffiliation -> Organizations(OrganizationName)
gn:Infofiles_infopagename_ -> gdmt:hasDatasetIdentifierSubType -> GNInfoFiles(GN_AccesionId)
gn:Infofiles_infopagename_ -> gdmt:hasRightsInfo -> datasetstatus(datasetstatusname)
-gn:Infofiles_infopagename_ -> gnt:belongsToInbredSet -> gn:inbredSet_inbredset_inbredsetname
+gn:Infofiles_infopagename_ -> gnt:belongsToSet -> gn:setInbredset_name
gn:Infofiles_infopagename_ -> gnt:hasTissue -> gn:tissue_tissue_short_name
gn:Infofiles_infopagename_ -> gnt:usesNormalization -> gn:avgmethod_avgmethod_avgmethodname
gn:Infofiles_infopagename_ -> gnt:usesPlatform -> gn:platform_genechip_genechip
@@ -78,7 +78,7 @@ gn:Br_u_0803_m gdmt:hasCreatorInfo gn:investigator_robert_williams_rwilliams_uth
gn:Br_u_0803_m gdmt:hasCreatorAffiliation "University of Tennessee Health Science Center" .
gn:Br_u_0803_m gdmt:hasDatasetIdentifierSubType "GN1" .
gn:Br_u_0803_m gdmt:hasRightsInfo "public" .
-gn:Br_u_0803_m gnt:belongsToInbredSet gn:inbredSet_bxd .
+gn:Br_u_0803_m gnt:belongsToSet gn:setBxd .
gn:Br_u_0803_m gnt:hasTissue gn:tissue_brn .
gn:Br_u_0803_m gnt:usesNormalization gn:avgmethod_mas5 .
gn:Br_u_0803_m gnt:usesPlatform gn:platform_mg_u74av2 .
@@ -93,7 +93,187 @@ gn:Br_u_0803_m gnt:hasAcknowledgement "<p>Data were generated with funds to RWW
```
-## 'dump-investigators'
+## 'publishfreeze'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+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 -> 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_ -> gnt:belongsToSet -> gn:setInbredset_name
+```
+Here's an example query:
+
+```sparql
+PREFIX v: <http://www.w3.org/2006/vcard/ns#>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX gdmt: <http://vocab.fairdatacollective.org/gdmt/>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+PREFIX geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>
+PREFIX gnt: <http://genenetwork.org/term/>
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+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 * WHERE {
+ ?s rdf:type gnc:phenotypeDataset .
+ ?s rdfs:label "B6D2F2-PSUPublish" .
+ ?s skos:prefLabel "B6D2F2 PSU Phenotypes" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+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 gnt:belongsToSet gn:setB6d2f2-psupublish .
+```
+
+
+## 'genofreeze'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT GenoFreeze.Name, GenoFreeze.Name, GenoFreeze.FullName, GenoFreeze.ShortName, GenoFreeze.CreateTime, InbredSet.Name FROM GenoFreeze LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = GenoFreeze.Name LEFT JOIN InbredSet ON GenoFreeze.InbredSetId = InbredSet.InbredSetId WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:Genofreeze_name_ -> rdf:type -> gnc:genotypeDataset
+gn:Genofreeze_name_ -> rdfs:label -> GenoFreeze(Name)
+gn:Genofreeze_name_ -> skos:prefLabel -> GenoFreeze(FullName)
+gn:Genofreeze_name_ -> skos:altLabel -> GenoFreeze(ShortName)
+gn:Genofreeze_name_ -> dct:created -> "GenoFreeze(CreateTime)"^^xsd:date
+gn:Genofreeze_name_ -> gnt:belongsToSet -> gn:setInbredset_name
+```
+Here's an example query:
+
+```sparql
+PREFIX v: <http://www.w3.org/2006/vcard/ns#>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX gdmt: <http://vocab.fairdatacollective.org/gdmt/>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+PREFIX geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>
+PREFIX gnt: <http://genenetwork.org/term/>
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+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 * WHERE {
+ ?s rdf:type gnc:genotypeDataset .
+ ?s rdfs:label "B6D2RIGeno" .
+ ?s skos:prefLabel "B6D2RI Genotypes" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:B6d2rigeno rdf:type gnc:genotypeDataset .
+gn:B6d2rigeno rdfs:label "B6D2RIGeno" .
+gn:B6d2rigeno skos:prefLabel "B6D2RI Genotypes" .
+gn:B6d2rigeno skos:altLabel "B6D2RIGeno" .
+gn:B6d2rigeno dct:created "2022-10-24"^^xsd:date .
+gn:B6d2rigeno gnt:belongsToSet gn:setB6d2rigeno .
+```
+
+
+## 'probesetfreeze'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT ProbeSetFreeze.Name, AvgMethod.Name AS AvgMethodName, AvgMethod.Name AS AvgMethodName, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.Name, ProbeSetFreeze.Name2, ProbeSetFreeze.CreateTime, ProbeSetFreeze.DataScale, Tissue.Short_Name, InbredSet.Name FROM 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 ON ProbeFreeze.TissueId = Tissue.TissueId WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:Probesetfreeze_name_ -> rdf:type -> gnc:probesetDataset
+gn:Probesetfreeze_name_ -> gnt:usesNormalization -> gn:avgmethod_avgmethod_avgmethodname
+gn:Probesetfreeze_name_ -> dct:title -> ProbeSetFreeze(FullName)
+gn:Probesetfreeze_name_ -> rdfs:label -> ProbeSetFreeze(ShortName)
+gn:Probesetfreeze_name_ -> skos:prefLabel -> ProbeSetFreeze(Name)
+gn:Probesetfreeze_name_ -> skos:altLabel -> ProbeSetFreeze(Name2)
+gn:Probesetfreeze_name_ -> dct:created -> "ProbeSetFreeze(CreateTime)"^^xsd:datetime
+gn:Probesetfreeze_name_ -> gnt:usesDataScale -> ProbeSetFreeze(DataScale)
+gn:Probesetfreeze_name_ -> gnt:hasTissue -> gn:tissue_tissue_short_name
+gn:Probesetfreeze_name_ -> gnt:belongsToSet -> gn:setInbredset_name
+```
+Here's an example query:
+
+```sparql
+PREFIX v: <http://www.w3.org/2006/vcard/ns#>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX gdmt: <http://vocab.fairdatacollective.org/gdmt/>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+PREFIX geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>
+PREFIX gnt: <http://genenetwork.org/term/>
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+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 * WHERE {
+ ?s rdf:type gnc:probesetDataset .
+ ?s gnt:usesNormalization gn:avgmethod_rankinv .
+ ?s dct:title "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
+ ?s rdfs:label "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:Cmmtubcbxdp00cerilm0513 rdf:type gnc:probesetDataset .
+gn:Cmmtubcbxdp00cerilm0513 gnt:usesNormalization gn:avgmethod_rankinv .
+gn:Cmmtubcbxdp00cerilm0513 dct:title "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
+gn:Cmmtubcbxdp00cerilm0513 rdfs:label "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
+gn:Cmmtubcbxdp00cerilm0513 skos:prefLabel "CMMTUBCBXDP00CerILM0513" .
+gn:Cmmtubcbxdp00cerilm0513 skos:altLabel "CMMTUBCBXDP00CerILMMay13" .
+gn:Cmmtubcbxdp00cerilm0513 dct:created "2013-04-22"^^xsd:datetime .
+gn:Cmmtubcbxdp00cerilm0513 gnt:usesDataScale "log2" .
+gn:Cmmtubcbxdp00cerilm0513 gnt:hasTissue gn:tissue_cb .
+gn:Cmmtubcbxdp00cerilm0513 gnt:belongsToSet gn:setCmmtubcbxdp00cerilm0513 .
+```
+
+
+## 'investigators'
## Generated Triples:
@@ -153,3 +333,61 @@ gn:investigator_evan_williams_ foaf:familyName "Williams" .
gn:investigator_evan_williams_ v:country-name "Switzerland" .
```
+
+## 'gene-chip'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT GeneChip.Name, GeneChip.GeneChipName, GeneChip.Name, IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL) AS Title, GeneChip.Go_tree_value, Species.Fullname, GeneChip.GeoPlatform FROM GeneChip LEFT JOIN Species USING (SpeciesId)
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:platform_genechip_name -> rdf:type -> gnc:geneChip
+gn:platform_genechip_name -> rdfs:label -> GeneChip(GeneChipName)
+gn:platform_genechip_name -> skos:prefLabel -> GeneChip(Name)
+gn:platform_genechip_name -> skos:altLabel -> Title
+gn:platform_genechip_name -> gnt:hasGOTreeValue -> GeneChip(Go_tree_value)
+gn:platform_genechip_name -> gnt:belongsToSpecies -> gn:Species_fullname
+gn:platform_genechip_name -> gnt:hasGeoSeriesId -> geoSeries:GeneChip(GeoPlatform)
+```
+Here's an example query:
+
+```sparql
+PREFIX v: <http://www.w3.org/2006/vcard/ns#>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX gdmt: <http://vocab.fairdatacollective.org/gdmt/>
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
+PREFIX geoSeries: <http://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=>
+PREFIX gnt: <http://genenetwork.org/term/>
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+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 * WHERE {
+ ?s rdf:type gnc:geneChip .
+ ?s rdfs:label "Affy Mouse Genome U74Av2 (GPL81)" .
+ ?s skos:prefLabel "MG_U74AV2" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:platform_mg_u74av2 rdf:type gnc:geneChip .
+gn:platform_mg_u74av2 rdfs:label "Affy Mouse Genome U74Av2 (GPL81)" .
+gn:platform_mg_u74av2 skos:prefLabel "MG_U74AV2" .
+gn:platform_mg_u74av2 gnt:hasGOTreeValue "affy_mg_u74av2" .
+gn:platform_mg_u74av2 gnt:belongsToSpecies gn:Mus_musculus .
+gn:platform_mg_u74av2 gnt:hasGeoSeriesId geoSeries:GPL81 .
+```
+
diff --git a/rdf-documentation/dump-gene-chip.md b/rdf-documentation/dump-gene-chip.md
deleted file mode 100644
index abd68d8..0000000
--- a/rdf-documentation/dump-gene-chip.md
+++ /dev/null
@@ -1,118 +0,0 @@
-# Probeset freeze metadata
-## 'dump-gene-chip'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT GeneChip.Name, GeneChip.GeneChipName, GeneChip.Name, IF(GeneChip.GeneChipName != GeneChip.Title, Title, NULL) AS Title, GeneChip.Go_tree_value, Species.Fullname, GeneChip.GeoPlatform FROM GeneChip LEFT JOIN Species USING (SpeciesId)
-```
-
-The above query results to triples that have the form:
-
-```text
-gn:platform_genechip_name -> rdf:type -> gnc:geneChip
-gn:platform_genechip_name -> rdfs:label -> GeneChip(GeneChipName)
-gn:platform_genechip_name -> skos:prefLabel -> GeneChip(Name)
-gn:platform_genechip_name -> skos:altLabel -> Title
-gn:platform_genechip_name -> gnt:hasGOTreeValue -> GeneChip(Go_tree_value)
-gn:platform_genechip_name -> gnt:belongsToSpecies -> gn:Species_fullname
-gn:platform_genechip_name -> gnt:hasGeoSeriesId -> geoSeries:GeneChip(GeoPlatform)
-```
-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 gnc: <http://genenetwork.org/category/>
-PREFIX dct: <http://purl.org/dc/terms/>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
-PREFIX gnt: <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 * WHERE {
- ?s rdf:type gnc:geneChip .
- ?s rdfs:label "Affy Mouse Genome U74Av2 (GPL81)" .
- ?s skos:prefLabel "MG_U74AV2" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:platform_mg_u74av2 rdf:type gnc:geneChip .
-gn:platform_mg_u74av2 rdfs:label "Affy Mouse Genome U74Av2 (GPL81)" .
-gn:platform_mg_u74av2 skos:prefLabel "MG_U74AV2" .
-gn:platform_mg_u74av2 gnt:hasGOTreeValue "affy_mg_u74av2" .
-gn:platform_mg_u74av2 gnt:belongsToSpecies gn:Mus_musculus .
-gn:platform_mg_u74av2 gnt:hasGeoSeriesId geoSeries:GPL81 .
-```
-
-
-## 'dump-probesetfreeze'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT ProbeSetFreeze.Name, AvgMethod.Name AS AvgMethodName, AvgMethod.Name AS AvgMethodName, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.Name, ProbeSetFreeze.Name2, ProbeSetFreeze.CreateTime, ProbeSetFreeze.DataScale, Tissue.Short_Name, InbredSet.Name AS InbredSetName FROM 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 ON ProbeFreeze.TissueId = Tissue.TissueId WHERE ProbeSetFreeze.public > 0 AND InfoFiles.InfoPageName IS NULL GROUP BY ProbeFreeze.Id
-```
-
-The above query results to triples that have the form:
-
-```text
-gn:Probesetfreeze_name_ -> rdf:type -> gnc:probesetDataset
-gn:Probesetfreeze_name_ -> gnt:usesNormalization -> gn:avgmethod_avgmethod_avgmethodname
-gn:Probesetfreeze_name_ -> dct:title -> ProbeSetFreeze(FullName)
-gn:Probesetfreeze_name_ -> rdfs:label -> ProbeSetFreeze(ShortName)
-gn:Probesetfreeze_name_ -> skos:prefLabel -> ProbeSetFreeze(Name)
-gn:Probesetfreeze_name_ -> skos:altLabel -> ProbeSetFreeze(Name2)
-gn:Probesetfreeze_name_ -> dct:created -> "ProbeSetFreeze(CreateTime)"^^xsd:datetime
-gn:Probesetfreeze_name_ -> gnt:usesDataScale -> ProbeSetFreeze(DataScale)
-gn:Probesetfreeze_name_ -> gnt:hasTissue -> gn:tissue_tissue_short_name
-gn:Probesetfreeze_name_ -> gnt:belongsToInbredSet -> gn:inbredSet_inbredset_inbredsetname
-```
-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 gnc: <http://genenetwork.org/category/>
-PREFIX dct: <http://purl.org/dc/terms/>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
-PREFIX gnt: <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 * WHERE {
- ?s rdf:type gnc:probesetDataset .
- ?s gnt:usesNormalization gn:avgmethod_rankinv .
- ?s dct:title "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
- ?s rdfs:label "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:Cmmtubcbxdp00cerilm0513 rdf:type gnc:probesetDataset .
-gn:Cmmtubcbxdp00cerilm0513 gnt:usesNormalization gn:avgmethod_rankinv .
-gn:Cmmtubcbxdp00cerilm0513 dct:title "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
-gn:Cmmtubcbxdp00cerilm0513 rdfs:label "UBC/CMMT BXD P0 Cerebellum ILM Mouse WG-6 v2.0 (May13) RankInv" .
-gn:Cmmtubcbxdp00cerilm0513 skos:prefLabel "CMMTUBCBXDP00CerILM0513" .
-gn:Cmmtubcbxdp00cerilm0513 skos:altLabel "CMMTUBCBXDP00CerILMMay13" .
-gn:Cmmtubcbxdp00cerilm0513 dct:created "2013-04-22"^^xsd:datetime .
-gn:Cmmtubcbxdp00cerilm0513 gnt:usesDataScale "log2" .
-gn:Cmmtubcbxdp00cerilm0513 gnt:hasTissue gn:tissue_cb .
-gn:Cmmtubcbxdp00cerilm0513 gnt:belongsToInbredSet gn:inbredSet_bxd .
-```
-
diff --git a/rdf-documentation/dump-phenotype.md b/rdf-documentation/dump-phenotype.md
deleted file mode 100644
index c9436a3..0000000
--- a/rdf-documentation/dump-phenotype.md
+++ /dev/null
@@ -1,121 +0,0 @@
-# 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 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 -> 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_ -> 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 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 * WHERE {
- ?s rdf:type gnc:phenotypeDataset .
- ?s rdfs:label "B6D2F2-PSUPublish" .
- ?s skos:prefLabel "B6D2F2 PSU Phenotypes" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-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 gnt:belongsToInbredSet gn:B6d2f2-psupublish .
-```
-
-
-## 'dump-phenotypes'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id) AS Phenotype, CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id) AS Phenotype, Phenotype.Post_publication_description, 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, IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT)) AS pmid, Publication.Id FROM 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 PublishXRef.InbredSetId IN (SELECT PublishFreeze.InbredSetId FROM PublishFreeze)
-```
-
-The above query results to triples that have the form:
-
-```text
-gn:trait_phenotype -> rdf:type -> gnc:phenotype
-gn:trait_phenotype -> rdfs:label -> Phenotype
-gn:trait_phenotype -> dct:description -> PhenotypePost_publication_description
-gn:trait_phenotype -> gnt:abbreviation -> Phenotype(Post_publication_abbreviation)
-gn:trait_phenotype -> gnt:labCode -> Phenotype(Lab_code)
-gn:trait_phenotype -> gnt:submitter -> PhenotypeSubmitter
-gn:trait_phenotype -> gnt:mean -> "mean"^^xsd:double
-gn:trait_phenotype -> gnt:locus -> PublishXRef(Locus)
-gn:trait_phenotype -> gnt:LRS -> "lrs"^^xsd:double
-gn:trait_phenotype -> gnt:additive -> "additive"^^xsd:double
-gn:trait_phenotype -> gnt:sequence -> "PublishXRef(Sequence)"^^xsd:integer
-gn:trait_phenotype -> dct:isReferencedBy -> pubmed:pmid
-gn:trait_phenotype -> dct:contributor -> PhenotypeOwner
-```
-Here's an example query:
-
-```sparql
-PREFIX dct: <http://purl.org/dc/terms/>
-PREFIX gn: <http://genenetwork.org/id/>
-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 * WHERE {
- ?s rdf:type gnc:phenotype .
- ?s rdfs:label "BXD_10001" .
- ?s dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" .
- ?s gnt:abbreviation "CBLWT2" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:trait_bxd_10001 rdf:type gnc:phenotype .
-gn:trait_bxd_10001 rdfs:label "BXD_10001" .
-gn:trait_bxd_10001 dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" .
-gn:trait_bxd_10001 gnt:abbreviation "CBLWT2" .
-gn:trait_bxd_10001 gnt:submitter "robwilliams" .
-gn:trait_bxd_10001 gnt:mean "52.13529418496525"^^xsd:double .
-gn:trait_bxd_10001 gnt:locus "rs48756159" .
-gn:trait_bxd_10001 gnt:LRS "13.4974911471087"^^xsd:double .
-gn:trait_bxd_10001 gnt:additive "2.39444435069444"^^xsd:double .
-gn:trait_bxd_10001 gnt:sequence "1"^^xsd:integer .
-gn:trait_bxd_10001 dct:isReferencedBy pubmed:11438585 .
-```
-
diff --git a/rdf-documentation/dump-probeset-metadata.md b/rdf-documentation/dump-probeset-metadata.md
deleted file mode 100644
index 37aa2c5..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 ProbeSetFreeze.Name, 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:Probesetfreeze_name_ -> rdf:type -> gnc:probesetData
-gn:Probesetfreeze_name_ -> gnt:hasProbeset -> probeset:name
-gn:Probesetfreeze_name_ -> gnt:probesetOfDataset -> probeset:ProbeSetFreeze_Name_
-gn:Probesetfreeze_name_ -> gnt:mean -> "mean"^^xsd:double
-gn:Probesetfreeze_name_ -> gnt:se -> "se"^^xsd:double
-gn:Probesetfreeze_name_ -> gnt:locus -> ProbeSetXRef(Locus)
-gn:Probesetfreeze_name_ -> gn:LRS -> "LRS"^^xsd:double
-gn:Probesetfreeze_name_ -> gnt:pValue -> "pValue"^^xsd:double
-gn:Probesetfreeze_name_ -> gnt:additive -> "additive"^^xsd:double
-gn:Probesetfreeze_name_ -> gnt:h2 -> "h2"^^xsd:float
-```
-Here's an example query:
-
-```sparql
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX gnt: <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 * WHERE {
- ?s rdf:type gnc:probesetData .
- ?s gnt:hasProbeset probeset:100001_at .
- ?s gnt:probesetOfDataset probeset:HC_U_0304_R .
- ?s gnt:mean #{"8.14033666666667"^^xsd:double}# .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:Hc_u_0304_r rdf:type gnc:probesetData .
-gn:Hc_u_0304_r gnt:hasProbeset probeset:100001_at .
-gn:Hc_u_0304_r gnt:probesetOfDataset probeset:HC_U_0304_R .
-gn:Hc_u_0304_r gnt:mean "8.14033666666667"^^xsd:double .
-gn:Hc_u_0304_r gnt:se "0.023595817125580502"^^xsd:double .
-gn:Hc_u_0304_r gnt:locus "rsm10000021399" .
-gn:Hc_u_0304_r gn:LRS "12.2805314427567"^^xsd:double .
-gn:Hc_u_0304_r gnt:pValue "0.118"^^xsd:double .
-gn:Hc_u_0304_r gnt:additive "0.0803547619047631"^^xsd:double .
-```
-
diff --git a/rdf-documentation/dump-probeset-summary-stats.md b/rdf-documentation/dump-probeset-summary-stats.md
deleted file mode 100644
index 422513b..0000000
--- a/rdf-documentation/dump-probeset-summary-stats.md
+++ /dev/null
@@ -1,60 +0,0 @@
-# Probeset Summary Statistics
-## 'dump-probeset-data'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT CONCAT(ProbeSetFreeze.Name, '_', IF(NULLIF(TRIM(ProbeSet.Name), ProbeSet.Id) IS NULL, '', TRIM(ProbeSet.Name))) AS probesetData, IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name)) AS ProbeSetIdName, ProbeSet.Id, IFNULL(ProbeSetXRef.mean, '') AS mean, ProbeSetXRef.Locus, IFNULL(ProbeSetXRef.LRS, '') AS lrs, IFNULL(ProbeSetXRef.additive, '') AS additive, IFNULL(ProbeSetXRef.se, '') AS stdErr, IFNULL(ProbeSetXRef.pValue, '') AS pValue, IFNULL(ProbeSetXRef.h2, '') AS h2, ProbeSetFreeze.Name 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 -> rdf:type -> gnc:probesetStatistics
-gn:Probesetdata -> gnt:hasProbeSet -> gn:probeset_probesetidname
-gn:Probesetdata -> gnt:mean -> "mean"^^xsd:double
-gn:Probesetdata -> gnt:locus -> ProbeSetXRef(Locus)
-gn:Probesetdata -> gnt:LRS -> "lrs"^^xsd:double
-gn:Probesetdata -> gnt:additive -> "additive"^^xsd:double
-gn:Probesetdata -> gnt:stdErr -> "stdErr"^^xsd:double
-gn:Probesetdata -> gnt:pValue -> "pValue"^^xsd:double
-gn:Probesetdata -> gnt:h2 -> "h2"^^xsd:double
-gn:Probesetdata -> gnt:belongsToDataset -> gn:Probesetfreeze_name_
-```
-Here's an example query:
-
-```sparql
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX gnt: <http://genenetwork.org/id/>
-PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-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 * WHERE {
- ?s rdf:type gnc:probesetStatistics .
- ?s gnt:hasProbeSet gn:probeset_100001_at .
- ?s gnt:mean #{"8.14033666666667"^^xsd:double}# .
- ?s gnt:locus "rsm10000021399" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:Hc_u_0304_r_100001_at rdf:type gnc:probesetStatistics .
-gn:Hc_u_0304_r_100001_at gnt:hasProbeSet gn:probeset_100001_at .
-gn:Hc_u_0304_r_100001_at gnt:mean "8.14033666666667"^^xsd:double .
-gn:Hc_u_0304_r_100001_at gnt:locus "rsm10000021399" .
-gn:Hc_u_0304_r_100001_at gnt:LRS "12.2805314427567"^^xsd:double .
-gn:Hc_u_0304_r_100001_at gnt:additive "0.0803547619047631"^^xsd:double .
-gn:Hc_u_0304_r_100001_at gnt:stdErr "0.023595817125580502"^^xsd:double .
-gn:Hc_u_0304_r_100001_at gnt:pValue "0.118"^^xsd:double .
-gn:Hc_u_0304_r_100001_at gnt:belongsToDataset gn:Hc_u_0304_r .
-```
-
diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md
deleted file mode 100644
index 160cf44..0000000
--- a/rdf-documentation/dump-species-metadata.md
+++ /dev/null
@@ -1,373 +0,0 @@
-# Species Metadata
-## 'dump-inbred-set'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT InbredSet.Name, InbredSet.FullName, InbredSet.GeneticType, InbredSet.Family, MappingMethod.Name, InbredSet.InbredSetCode, Species.Fullname, IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '') AS genotypeP, IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '') AS phenotypeP, (SELECT GROUP_CONCAT(DISTINCT Tissue.Short_Name SEPARATOR'||') AS MolecularTraits FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species WHERE ProbeFreeze.TissueId = Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id ORDER BY Tissue.Name) AS molecularTrait FROM InbredSet LEFT JOIN Species ON InbredSet.SpeciesId=Species.Id LEFT JOIN MappingMethod ON InbredSet.MappingMethodId=MappingMethod.Id
-```
-
-The above query results to triples that have the form:
-
-```text
-gn:Inbredset_name -> rdf:type -> gnc:inbredSet
-gn:Inbredset_name -> rdfs:label -> InbredSet(FullName)
-gn:Inbredset_name -> gnt:geneticType -> InbredSet(GeneticType)
-gn:Inbredset_name -> gnt:family -> InbredSet(Family)
-gn:Inbredset_name -> gnt:mappingMethod -> MappingMethod(Name)
-gn:Inbredset_name -> gnt:code -> InbredSet(InbredSetCode)
-gn:Inbredset_name -> gnt:belongsToSpecies -> gn:Species_fullname
-gn:Inbredset_name -> gnt:genotype -> genotypeP
-gn:Inbredset_name -> gnt:phenotype -> phenotypeP
-gn:Inbredset_name -> gnt:hasTissue -> gn:tissue_moleculartrait
-```
-Here's an example query:
-
-```sparql
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX gnt: <http://genenetwork.org/term/>
-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 taxon: <http://purl.uniprot.org/taxonomy/>
-
-SELECT * WHERE {
- ?s rdf:type gnc:inbredSet .
- ?s rdfs:label "BXD Family" .
- ?s gnt:geneticType "riset" .
- ?s gnt:family "Reference Populations (replicate average, SE, N)" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:Bxd rdf:type gnc:inbredSet .
-gn:Bxd rdfs:label "BXD Family" .
-gn:Bxd gnt:geneticType "riset" .
-gn:Bxd gnt:family "Reference Populations (replicate average, SE, N)" .
-gn:Bxd gnt:mappingMethod "BXD" .
-gn:Bxd gnt:code "BXD" .
-gn:Bxd gnt:belongsToSpecies gn:Mus_musculus .
-gn:Bxd gnt:genotype "Traits and Cofactors" .
-gn:Bxd gnt:phenotype "DNA Markers and SNPs" .
-gn:Bxd gnt:hasTissue gn:tissue_a1c .
-gn:Bxd gnt:hasTissue gn:tissue_acc .
-gn:Bxd gnt:hasTissue gn:tissue_adr .
-gn:Bxd gnt:hasTissue gn:tissue_amg .
-gn:Bxd gnt:hasTissue gn:tissue_bebv .
-gn:Bxd gnt:hasTissue gn:tissue_bla .
-gn:Bxd gnt:hasTissue gn:tissue_brmet .
-gn:Bxd gnt:hasTissue gn:tissue_brmicrorna .
-gn:Bxd gnt:hasTissue gn:tissue_brn .
-gn:Bxd gnt:hasTissue gn:tissue_cart .
-gn:Bxd gnt:hasTissue gn:tissue_cb .
-gn:Bxd gnt:hasTissue gn:tissue_cbc .
-gn:Bxd gnt:hasTissue gn:tissue_ctx .
-gn:Bxd gnt:hasTissue gn:tissue_dfc .
-gn:Bxd gnt:hasTissue gn:tissue_drg .
-gn:Bxd gnt:hasTissue gn:tissue_ec .
-gn:Bxd gnt:hasTissue gn:tissue_emb .
-gn:Bxd gnt:hasTissue gn:tissue_eye .
-gn:Bxd gnt:hasTissue gn:tissue_fat .
-gn:Bxd gnt:hasTissue gn:tissue_fecmet .
-gn:Bxd gnt:hasTissue gn:tissue_femur .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_aor .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_atr .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_blo .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_bonm .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_bre .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_cau .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_cer .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_cerv .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_cml .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_col .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_colsig .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_cor .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_ebv .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_eso .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_esogas .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_fal .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_fro .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_muc .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_ner .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_pan .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_put .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_sintter .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_skinex .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_skisex .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_sn .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_sto .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_sub .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_tf .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_thy .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_tib .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_vag .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_ven .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_vis .
-gn:Bxd gnt:hasTissue gn:tissue_gtex_who .
-gn:Bxd gnt:hasTissue gn:tissue_gut .
-gn:Bxd gnt:hasTissue gn:tissue_hea .
-gn:Bxd gnt:hasTissue gn:tissue_hip .
-gn:Bxd gnt:hasTissue gn:tissue_hippreccel .
-gn:Bxd gnt:hasTissue gn:tissue_hipprot .
-gn:Bxd gnt:hasTissue gn:tissue_hip_mirna .
-gn:Bxd gnt:hasTissue gn:tissue_hsc .
-gn:Bxd gnt:hasTissue gn:tissue_hyp .
-gn:Bxd gnt:hasTissue gn:tissue_ifra_ctx .
-gn:Bxd gnt:hasTissue gn:tissue_ipc .
-gn:Bxd gnt:hasTissue gn:tissue_isl .
-gn:Bxd gnt:hasTissue gn:tissue_itc .
-gn:Bxd gnt:hasTissue gn:tissue_kid .
-gn:Bxd gnt:hasTissue gn:tissue_lathab .
-gn:Bxd gnt:hasTissue gn:tissue_lcm_brreg .
-gn:Bxd gnt:hasTissue gn:tissue_leaf .
-gn:Bxd gnt:hasTissue gn:tissue_liv .
-gn:Bxd gnt:hasTissue gn:tissue_livdnam .
-gn:Bxd gnt:hasTissue gn:tissue_livmet .
-gn:Bxd gnt:hasTissue gn:tissue_livpro .
-gn:Bxd gnt:hasTissue gn:tissue_lung .
-gn:Bxd gnt:hasTissue gn:tissue_m1c .
-gn:Bxd gnt:hasTissue gn:tissue_mam .
-gn:Bxd gnt:hasTissue gn:tissue_mamtum .
-gn:Bxd gnt:hasTissue gn:tissue_mbr .
-gn:Bxd gnt:hasTissue gn:tissue_md .
-gn:Bxd gnt:hasTissue gn:tissue_methyl .
-gn:Bxd gnt:hasTissue gn:tissue_mfc .
-gn:Bxd gnt:hasTissue gn:tissue_musmet .
-gn:Bxd gnt:hasTissue gn:tissue_nac .
-gn:Bxd gnt:hasTissue gn:tissue_nbcb .
-gn:Bxd gnt:hasTissue gn:tissue_neutrophil .
-gn:Bxd gnt:hasTissue gn:tissue_ocl .
-gn:Bxd gnt:hasTissue gn:tissue_ofc .
-gn:Bxd gnt:hasTissue gn:tissue_of_ctx .
-gn:Bxd gnt:hasTissue gn:tissue_ova .
-gn:Bxd gnt:hasTissue gn:tissue_pcg .
-gn:Bxd gnt:hasTissue gn:tissue_pfc .
-gn:Bxd gnt:hasTissue gn:tissue_pg .
-gn:Bxd gnt:hasTissue gn:tissue_pln .
-gn:Bxd gnt:hasTissue gn:tissue_pl_ctx .
-gn:Bxd gnt:hasTissue gn:tissue_pons .
-gn:Bxd gnt:hasTissue gn:tissue_pro .
-gn:Bxd gnt:hasTissue gn:tissue_ret .
-gn:Bxd gnt:hasTissue gn:tissue_ret_mirna .
-gn:Bxd gnt:hasTissue gn:tissue_ret_sc-rna-s .
-gn:Bxd gnt:hasTissue gn:tissue_s1c .
-gn:Bxd gnt:hasTissue gn:tissue_sal .
-gn:Bxd gnt:hasTissue gn:tissue_sg .
-gn:Bxd gnt:hasTissue gn:tissue_skm .
-gn:Bxd gnt:hasTissue gn:tissue_spi .
-gn:Bxd gnt:hasTissue gn:tissue_spl .
-gn:Bxd gnt:hasTissue gn:tissue_stc .
-gn:Bxd gnt:hasTissue gn:tissue_str .
-gn:Bxd gnt:hasTissue gn:tissue_tc .
-gn:Bxd gnt:hasTissue gn:tissue_tes .
-gn:Bxd gnt:hasTissue gn:tissue_tes_dna_met .
-gn:Bxd gnt:hasTissue gn:tissue_thelp .
-gn:Bxd gnt:hasTissue gn:tissue_thy .
-gn:Bxd gnt:hasTissue gn:tissue_treg .
-gn:Bxd gnt:hasTissue gn:tissue_ute .
-gn:Bxd gnt:hasTissue gn:tissue_v1 .
-gn:Bxd gnt:hasTissue gn:tissue_vfc .
-gn:Bxd gnt:hasTissue gn:tissue_vta .
-gn:Bxd gnt:hasTissue gn:tissue_wb .
-gn:Bxd gnt:hasTissue gn:tissue_wbc .
-gn:Bxd gnt:hasTissue gn:tissue_wbpr .
-gn:Bxd gnt:hasTissue gn:tissue_wfat .
-gn:Bxd gnt:hasTissue gn:tissue_wfat_pro .
-```
-
-
-## 'dump-species'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT Species.Fullname, Species.SpeciesName, Species.Name, Species.MenuName, Species.FullName, Species.Family, Species.TaxonomyId FROM Species
-```
-
-The above query results to triples that have the form:
-
-```text
-gn:Species_fullname -> rdf:type -> gnc:species
-gn:Species_fullname -> skos:label -> Species(SpeciesName)
-gn:Species_fullname -> skos:altLabel -> Species(Name)
-gn:Species_fullname -> rdfs:label -> Species(MenuName)
-gn:Species_fullname -> gnt:binomialName -> Species(FullName)
-gn:Species_fullname -> gnt:family -> Species(Family)
-gn:Species_fullname -> gnt:organism -> taxon:Species(TaxonomyId)
-```
-Here's an example query:
-
-```sparql
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX gnt: <http://genenetwork.org/term/>
-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 taxon: <http://purl.uniprot.org/taxonomy/>
-
-SELECT * WHERE {
- ?s rdf:type gnc:species .
- ?s skos:label "Mouse" .
- ?s skos:altLabel "mouse" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:Mus_musculus rdf:type gnc:species .
-gn:Mus_musculus skos:label "Mouse" .
-gn:Mus_musculus skos:altLabel "mouse" .
-gn:Mus_musculus rdfs:label "Mouse (Mus musculus, mm10)" .
-gn:Mus_musculus gnt:binomialName "Mus musculus" .
-gn:Mus_musculus gnt:family "Vertebrates" .
-gn:Mus_musculus gnt:organism taxon:10090 .
-```
-
-
-## 'dump-strain'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT Strain.Name, Species.Fullname, Strain.Name, IF ((Strain.Name2 != Strain.Name), Strain.Name2, '') AS Name2, IF ((Strain.Alias != Strain.Name), Strain.Alias, '') AS Alias, IF ((Strain.Symbol != Strain.Name), Strain.Symbol, '') AS Symbol FROM Strain LEFT JOIN Species ON Strain.SpeciesId = Species.SpeciesId
-```
-
-The above query results to triples that have the form:
-
-```text
-gn:Strain_name_ -> rdf:type -> gnc:strain
-gn:Strain_name_ -> gnt:belongsToSpecies -> gn:Species_fullname
-gn:Strain_name_ -> rdfs:label -> StrainName
-gn:Strain_name_ -> rdfs:label -> Name2
-gn:Strain_name_ -> gnt:alias -> Alias
-gn:Strain_name_ -> gnt:symbol -> Symbol
-```
-Here's an example query:
-
-```sparql
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX gnt: <http://genenetwork.org/term/>
-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 taxon: <http://purl.uniprot.org/taxonomy/>
-
-SELECT * WHERE {
- ?s rdf:type gnc:strain .
- ?s gnt:belongsToSpecies gn:Mus_musculus .
- ?s rdfs:label "B6D2F1" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:B6d2f1 rdf:type gnc:strain .
-gn:B6d2f1 gnt:belongsToSpecies gn:Mus_musculus .
-gn:B6d2f1 rdfs:label "B6D2F1" .
-```
-
-
-## 'dump-mapping-method'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT MappingMethod.Name, MappingMethod.Name FROM MappingMethod
-```
-
-The above query results to triples that have the form:
-
-```text
-gn:mappingMethod_mappingmethod_name -> rdf:type -> gnc:mappingMethod
-gn:mappingMethod_mappingmethod_name -> rdfs:label -> MappingMethod(Name)
-```
-Here's an example query:
-
-```sparql
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX gnt: <http://genenetwork.org/term/>
-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 taxon: <http://purl.uniprot.org/taxonomy/>
-
-SELECT * WHERE {
- ?s rdf:type gnc:mappingMethod .
- ?s rdfs:label "qtlreaper" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:mappingMethod_qtlreaper rdf:type gnc:mappingMethod .
-gn:mappingMethod_qtlreaper rdfs:label "qtlreaper" .
-```
-
-
-## 'dump-avg-method'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT AvgMethod.Name, AvgMethod.Normalization FROM AvgMethod
-```
-
-The above query results to triples that have the form:
-
-```text
-gn:avgmethod_avgmethod_name -> rdf:type -> gnc:avgMethod
-gn:avgmethod_avgmethod_name -> rdfs:label -> AvgMethod(Normalization)
-```
-Here's an example query:
-
-```sparql
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX owl: <http://www.w3.org/2002/07/owl#>
-PREFIX gnt: <http://genenetwork.org/term/>
-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 taxon: <http://purl.uniprot.org/taxonomy/>
-
-SELECT * WHERE {
- ?s rdf:type gnc:avgMethod .
- ?s rdfs:label "MAS5" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:avgmethod_mas5 rdf:type gnc:avgMethod .
-gn:avgmethod_mas5 rdfs:label "MAS5" .
-```
-
diff --git a/rdf-documentation/generif-metadata.md b/rdf-documentation/generif-metadata.md
new file mode 100644
index 0000000..fc058bc
--- /dev/null
+++ b/rdf-documentation/generif-metadata.md
@@ -0,0 +1,170 @@
+# GeneRIF Metadata
+## 'genewiki-symbols'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT GeneRIF_BASIC.GeneId, GROUP_CONCAT(DISTINCT symbol) AS symbol, GROUP_CONCAT(DISTINCT Species.SpeciesName) AS species, GROUP_CONCAT(DISTINCT TaxID) AS taxId FROM GeneRIF_BASIC LEFT JOIN Species USING (SpeciesId) GROUP BY GeneId ORDER BY BINARY symbol
+```
+
+The above query results to triples that have the form:
+
+```text
+generif:GeneRIF_BASIC(GeneId) -> gnt:symbol -> symbol
+generif:GeneRIF_BASIC(GeneId) -> gnt:belongsToSpecies -> species
+generif:GeneRIF_BASIC(GeneId) -> dct:relation -> ncbiTaxon:taxId
+```
+Here's an example query:
+
+```sparql
+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 gnc: <http://genenetwork.org/category/>
+PREFIX gnt: <http://genenetwork.org/term/>
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
+PREFIX ncbiTaxon: <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>
+PREFIX generif: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT * WHERE {
+ ?s gnt:belongsToSpecies "Human" .
+ ?s dct:relation ncbiTaxon:9606 .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+generif:233 gnt:belongsToSpecies "Human" .
+generif:233 dct:relation ncbiTaxon:9606 .
+```
+
+
+## 'gn-genewiki-entries'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT Species.FullName, GeneRIF.comment, GeneRIF.symbol, GeneRIF.createtime, GeneRIF.comment, GeneRIF.symbol, GROUP_CONCAT(DISTINCT GeneCategory.Name SEPARATOR '$$') AS GeneCategory, Species.Fullname, IFNULL(GeneRIF.PubMed_ID, '') AS PubMed_ID, GeneRIF.createtime, GeneRIF.email, Investigators.Email, Investigators.FirstName, Investigators.LastName, Investigators.Email, GeneRIF.weburl FROM GeneRIF LEFT JOIN Species ON Species.SpeciesId = GeneRIF.SpeciesId LEFT JOIN GeneRIFXRef ON GeneRIFXRef.GeneRIFId = GeneRIF.Id LEFT JOIN GeneCategory ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id LEFT JOIN Investigators ON Investigators.Email = GeneRIF.email WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 AND GeneRIF.comment IS NOT NULL GROUP BY GeneRIF.comment, GeneRIF.createtime
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:generif_e72e92f4-59b5-3bbd-ac46-a39a23f25e55 -> rdf:type -> gnc:GNWikiEntry
+gn:generif_e72e92f4-59b5-3bbd-ac46-a39a23f25e55 -> rdfs:label -> GeneRIFcomment
+gn:generif_e72e92f4-59b5-3bbd-ac46-a39a23f25e55 -> gnt:symbol -> GeneRIF(symbol)
+gn:generif_e72e92f4-59b5-3bbd-ac46-a39a23f25e55 -> gnt:belongsToSpecies -> gn:Species_fullname
+gn:generif_e72e92f4-59b5-3bbd-ac46-a39a23f25e55 -> dct:created ->
+gn:generif_e72e92f4-59b5-3bbd-ac46-a39a23f25e55 -> dct:creator -> gn:investigator_investigators_firstname_investigators_lastname_investigators_email
+gn:generif_e72e92f4-59b5-3bbd-ac46-a39a23f25e55 -> foaf:homepage -> GeneRIF(weburl)
+gn:generif_e72e92f4-59b5-3bbd-ac46-a39a23f25e55 -> gnt:belongsToCategory -> GeneCategory
+gn:generif_e72e92f4-59b5-3bbd-ac46-a39a23f25e55 -> dct:references -> pubmed:PubMed_ID
+```
+Here's an example query:
+
+```sparql
+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 gnc: <http://genenetwork.org/category/>
+PREFIX gnt: <http://genenetwork.org/term/>
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
+PREFIX ncbiTaxon: <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>
+PREFIX generif: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT * WHERE {
+ ?s rdf:type gnc:GNWikiEntry .
+ ?s rdfs:label "Part 2 of the Slc9a1 wiki.\r\n\r\nThe human SLC9A1 gene was cloned and mapped to human chromosome 1p Lifton et al., 1990.\r\n\r\nThe mouse Slc9a1 gene maps to chromosome 4. Morahan et al., 1993. There are three common alleles of Slc9a1, originally detected by RFLP analyses. Each of these allelic SLC9A1 proteins have different levels of antiporter activity. Morahan et al. 1994 Remarkably, intracellular pH varies between strains based on their Slc9a1 alleles. McClive et al. 1996." .
+ ?s gnt:symbol "Slc9a1" .
+ ?s gnt:belongsToSpecies gn:Mus_musculus .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f rdf:type gnc:GNWikiEntry .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f rdfs:label "Part 2 of the Slc9a1 wiki.\r\n\r\nThe human SLC9A1 gene was cloned and mapped to human chromosome 1p Lifton et al., 1990.\r\n\r\nThe mouse Slc9a1 gene maps to chromosome 4. Morahan et al., 1993. There are three common alleles of Slc9a1, originally detected by RFLP analyses. Each of these allelic SLC9A1 proteins have different levels of antiporter activity. Morahan et al. 1994 Remarkably, intracellular pH varies between strains based on their Slc9a1 alleles. McClive et al. 1996." .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f gnt:symbol "Slc9a1" .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f gnt:belongsToSpecies gn:Mus_musculus .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f dct:created "2011-06-10T12:06:30"^^xsd:datetime .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f dct:creator gn:investigator_grant_morahan_gem_waimr.uwa.edu.au .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f gnt:belongsToCategory "Biochemistry" .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f gnt:belongsToCategory "Genetic variation and alleles" .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f gnt:belongsToCategory "Physiology and function" .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f dct:references pubmed:094369 .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f dct:references pubmed:8016086 .
+gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f dct:references pubmed:8550102 .
+```
+
+
+## 'ncbi-genewiki-entries'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT GeneRIF_BASIC.GeneId, GeneRIF_BASIC.VersionId, GeneRIF_BASIC.comment, GeneRIF_BASIC.symbol, GeneRIF_BASIC.createtime, GeneRIF_BASIC.comment, GeneRIF_BASIC.symbol, GROUP_CONCAT(PubMed_ID) AS pmids, GeneRIF_BASIC.VersionId, GeneRIF_BASIC.createtime FROM GeneRIF_BASIC GROUP BY GeneId, comment, createtime
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:generif_d6552bcc-c798-34ab-a533-e23323255d1b -> rdf:type -> gnc:NCBIWikiEntry
+gn:generif_d6552bcc-c798-34ab-a533-e23323255d1b -> rdfs:label -> "GeneRIF_BASIC(comment)"^^xsd:string
+gn:generif_d6552bcc-c798-34ab-a533-e23323255d1b -> gnt:symbol -> GeneRIF_BASIC(symbol)
+gn:generif_d6552bcc-c798-34ab-a533-e23323255d1b -> gnt:hasVersion -> GeneRIF_BASIC(VersionId)
+gn:generif_d6552bcc-c798-34ab-a533-e23323255d1b -> dct:created ->
+gn:generif_d6552bcc-c798-34ab-a533-e23323255d1b -> dct:references -> pubmed:pmids
+```
+Here's an example query:
+
+```sparql
+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 gnc: <http://genenetwork.org/category/>
+PREFIX gnt: <http://genenetwork.org/term/>
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX foaf: <http://xmlns.com/foaf/0.1/>
+PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/>
+PREFIX ncbiTaxon: <https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=>
+PREFIX generif: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=>
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+
+SELECT * WHERE {
+ ?s rdf:type gnc:NCBIWikiEntry .
+ ?s rdfs:label #{"A1BG-cysteine-rich secretory protein 3 complex displays a similar function in protecting the circulation from a potentially harmful effect of free CRISP-3"^^xsd:string}# .
+ ?s gnt:symbol "A1BG" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:generif_fc8da76d-e68e-3622-b23a-d5a5daf06c99 rdf:type gnc:NCBIWikiEntry .
+gn:generif_fc8da76d-e68e-3622-b23a-d5a5daf06c99 rdfs:label "A1BG-cysteine-rich secretory protein 3 complex displays a similar function in protecting the circulation from a potentially harmful effect of free CRISP-3"^^xsd:string .
+gn:generif_fc8da76d-e68e-3622-b23a-d5a5daf06c99 gnt:symbol "A1BG" .
+gn:generif_fc8da76d-e68e-3622-b23a-d5a5daf06c99 gnt:hasVersion "1" .
+gn:generif_fc8da76d-e68e-3622-b23a-d5a5daf06c99 dct:created "2010-01-20T18:00:00"^^xsd:datetime .
+gn:generif_fc8da76d-e68e-3622-b23a-d5a5daf06c99 dct:references pubmed:15461460 .
+```
+
diff --git a/rdf-documentation/dump-genotype.md b/rdf-documentation/genotype-metadata.md
index 2f5edbc..fc2682c 100644
--- a/rdf-documentation/dump-genotype.md
+++ b/rdf-documentation/genotype-metadata.md
@@ -1,58 +1,5 @@
# Genotype Metadata
-## 'dump-genofreeze'
-
-## Generated Triples:
-
-The following SQL query was executed:
-
-```sql
-SELECT GenoFreeze.Name, GenoFreeze.Name, GenoFreeze.FullName, GenoFreeze.ShortName, GenoFreeze.CreateTime, InbredSet.Name AS InbredSetName FROM GenoFreeze LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = GenoFreeze.Name LEFT JOIN InbredSet ON GenoFreeze.InbredSetId = InbredSet.InbredSetId WHERE GenoFreeze.public > 0 AND GenoFreeze.confidentiality < 1 AND InfoFiles.InfoPageName IS NULL
-```
-
-The above query results to triples that have the form:
-
-```text
-gn:Genofreeze_name_ -> rdf:type -> gnc:genotypeDataset
-gn:Genofreeze_name_ -> rdfs:label -> GenoFreeze(Name)
-gn:Genofreeze_name_ -> skos:prefLabel -> GenoFreeze(FullName)
-gn:Genofreeze_name_ -> skos:altLabel -> GenoFreeze(ShortName)
-gn:Genofreeze_name_ -> dct:created -> "GenoFreeze(CreateTime)"^^xsd:date
-gn:Genofreeze_name_ -> gnt:belongsToInbredSet -> gn:_inbredset_inbredsetname
-```
-Here's an example query:
-
-```sparql
-PREFIX dct: <http://purl.org/dc/terms/>
-PREFIX gn: <http://genenetwork.org/id/>
-PREFIX gnc: <http://genenetwork.org/category/>
-PREFIX gnt: <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 owl: <http://www.w3.org/2002/07/owl#>
-PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
-PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
-
-SELECT * WHERE {
- ?s rdf:type gnc:genotypeDataset .
- ?s rdfs:label "B6D2RIGeno" .
- ?s skos:prefLabel "B6D2RI Genotypes" .
- ?s ?p ?o .
-}
-```
-
-Expected Result:
-
-```rdf
-gn:B6d2rigeno rdf:type gnc:genotypeDataset .
-gn:B6d2rigeno rdfs:label "B6D2RIGeno" .
-gn:B6d2rigeno skos:prefLabel "B6D2RI Genotypes" .
-gn:B6d2rigeno skos:altLabel "B6D2RIGeno" .
-gn:B6d2rigeno dct:created "2022-10-24"^^xsd:date .
-gn:B6d2rigeno gnt:belongsToInbredSet gn:_b6d2ri .
-```
-
-
-## 'dump-genotypes'
+## 'genotypes'
## Generated Triples:
diff --git a/rdf-documentation/phenotype-metadata.md b/rdf-documentation/phenotype-metadata.md
new file mode 100644
index 0000000..b673bb1
--- /dev/null
+++ b/rdf-documentation/phenotype-metadata.md
@@ -0,0 +1,71 @@
+# Phenotypes Metadata
+## 'phenotypes'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id) AS Phenotype, InbredSet.Name, PublishXRef.Id, CONCAT(IFNULL(InbredSet.Name, PublishXRef.InbredSetId), '_', PublishXRef.Id) AS Phenotype, Phenotype.Post_publication_description, 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, IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT)) AS pmid, Publication.Id FROM 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 PublishXRef.InbredSetId IN (SELECT PublishFreeze.InbredSetId FROM PublishFreeze)
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:trait_phenotype -> rdf:type -> gnc:phenotype
+gn:trait_phenotype -> gnt:belongsToSet -> gn:setInbredset_name
+gn:trait_phenotype -> rdfs:label -> PublishXRef(Id)
+gn:trait_phenotype -> skos:altLabel -> Phenotype
+gn:trait_phenotype -> dct:description -> PhenotypePost_publication_description
+gn:trait_phenotype -> gnt:abbreviation -> Phenotype(Post_publication_abbreviation)
+gn:trait_phenotype -> gnt:labCode -> Phenotype(Lab_code)
+gn:trait_phenotype -> gnt:submitter -> PhenotypeSubmitter
+gn:trait_phenotype -> gnt:mean -> "mean"^^xsd:double
+gn:trait_phenotype -> gnt:locus -> PublishXRef(Locus)
+gn:trait_phenotype -> gnt:LRS -> "lrs"^^xsd:double
+gn:trait_phenotype -> gnt:additive -> "additive"^^xsd:double
+gn:trait_phenotype -> gnt:sequence -> "PublishXRef(Sequence)"^^xsd:integer
+gn:trait_phenotype -> dct:isReferencedBy -> pubmed:pmid
+gn:trait_phenotype -> dct:contributor -> PhenotypeOwner
+```
+Here's an example query:
+
+```sparql
+PREFIX dct: <http://purl.org/dc/terms/>
+PREFIX gn: <http://genenetwork.org/id/>
+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 * WHERE {
+ ?s rdf:type gnc:phenotype .
+ ?s gnt:belongsToSet gn:setBxd .
+ ?s rdfs:label "10001" .
+ ?s skos:altLabel "BXD_10001" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:trait_bxd_10001 rdf:type gnc:phenotype .
+gn:trait_bxd_10001 gnt:belongsToSet gn:setBxd .
+gn:trait_bxd_10001 rdfs:label "10001" .
+gn:trait_bxd_10001 skos:altLabel "BXD_10001" .
+gn:trait_bxd_10001 dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" .
+gn:trait_bxd_10001 gnt:abbreviation "CBLWT2" .
+gn:trait_bxd_10001 gnt:submitter "robwilliams" .
+gn:trait_bxd_10001 gnt:mean "52.13529418496525"^^xsd:double .
+gn:trait_bxd_10001 gnt:locus "rs48756159" .
+gn:trait_bxd_10001 gnt:LRS "13.4974911471087"^^xsd:double .
+gn:trait_bxd_10001 gnt:additive "2.39444435069444"^^xsd:double .
+gn:trait_bxd_10001 gnt:sequence "1"^^xsd:integer .
+gn:trait_bxd_10001 dct:isReferencedBy pubmed:11438585 .
+```
+
diff --git a/rdf-documentation/dump-probeset.md b/rdf-documentation/probeset-metadata.md
index d5729cf..2387145 100644
--- a/rdf-documentation/dump-probeset.md
+++ b/rdf-documentation/probeset-metadata.md
@@ -1,5 +1,5 @@
# ProbeSet Metadata
-## 'dump-probeset'
+## 'probeset'
## Generated Triples:
diff --git a/rdf-documentation/dump-publication.md b/rdf-documentation/publication-metadata.md
index 708e47f..018f6da 100644
--- a/rdf-documentation/dump-publication.md
+++ b/rdf-documentation/publication-metadata.md
@@ -1,5 +1,5 @@
# Publications Metadata
-## 'dump-publication'
+## 'publication'
## Generated Triples:
diff --git a/rdf-documentation/species-metadata.md b/rdf-documentation/species-metadata.md
new file mode 100644
index 0000000..79e897c
--- /dev/null
+++ b/rdf-documentation/species-metadata.md
@@ -0,0 +1,375 @@
+# Species Metadata
+## 'inbred-set'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT InbredSet.Name, InbredSet.FullName, InbredSet.Name, InbredSet.GeneticType, InbredSet.Family, MappingMethod.Name, InbredSet.InbredSetCode, Species.Fullname, IF ((SELECT PublishFreeze.Name FROM PublishFreeze WHERE PublishFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'Traits and Cofactors', '') AS genotypeP, IF ((SELECT GenoFreeze.Name FROM GenoFreeze WHERE GenoFreeze.InbredSetId = InbredSet.Id LIMIT 1) IS NOT NULL, 'DNA Markers and SNPs', '') AS phenotypeP, (SELECT GROUP_CONCAT(DISTINCT Tissue.Short_Name SEPARATOR'||') AS MolecularTraits FROM ProbeFreeze, ProbeSetFreeze, InbredSet, Tissue, Species WHERE ProbeFreeze.TissueId = Tissue.Id AND ProbeFreeze.InbredSetId = InbredSet.Id AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id ORDER BY Tissue.Name) AS molecularTrait FROM InbredSet LEFT JOIN Species ON InbredSet.SpeciesId=Species.Id LEFT JOIN MappingMethod ON InbredSet.MappingMethodId=MappingMethod.Id
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:setInbredset_name -> rdf:type -> gnc:set
+gn:setInbredset_name -> rdfs:label -> InbredSet(FullName)
+gn:setInbredset_name -> skos:altLabel -> InbredSet(Name)
+gn:setInbredset_name -> gnt:geneticType -> InbredSet(GeneticType)
+gn:setInbredset_name -> gnt:family -> InbredSet(Family)
+gn:setInbredset_name -> gnt:mappingMethod -> MappingMethod(Name)
+gn:setInbredset_name -> gnt:code -> InbredSet(InbredSetCode)
+gn:setInbredset_name -> gnt:belongsToSpecies -> gn:Species_fullname
+gn:setInbredset_name -> gnt:genotype -> genotypeP
+gn:setInbredset_name -> gnt:phenotype -> phenotypeP
+gn:setInbredset_name -> gnt:hasTissue -> gn:tissue_moleculartrait
+```
+Here's an example query:
+
+```sparql
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX gnt: <http://genenetwork.org/term/>
+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 taxon: <http://purl.uniprot.org/taxonomy/>
+
+SELECT * WHERE {
+ ?s rdf:type gnc:set .
+ ?s rdfs:label "BXD Family" .
+ ?s skos:altLabel "BXD" .
+ ?s gnt:geneticType "riset" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:setBxd rdf:type gnc:set .
+gn:setBxd rdfs:label "BXD Family" .
+gn:setBxd skos:altLabel "BXD" .
+gn:setBxd gnt:geneticType "riset" .
+gn:setBxd gnt:family "Reference Populations (replicate average, SE, N)" .
+gn:setBxd gnt:mappingMethod "BXD" .
+gn:setBxd gnt:code "BXD" .
+gn:setBxd gnt:belongsToSpecies gn:Mus_musculus .
+gn:setBxd gnt:genotype "Traits and Cofactors" .
+gn:setBxd gnt:phenotype "DNA Markers and SNPs" .
+gn:setBxd gnt:hasTissue gn:tissue_a1c .
+gn:setBxd gnt:hasTissue gn:tissue_acc .
+gn:setBxd gnt:hasTissue gn:tissue_adr .
+gn:setBxd gnt:hasTissue gn:tissue_amg .
+gn:setBxd gnt:hasTissue gn:tissue_bebv .
+gn:setBxd gnt:hasTissue gn:tissue_bla .
+gn:setBxd gnt:hasTissue gn:tissue_brmet .
+gn:setBxd gnt:hasTissue gn:tissue_brmicrorna .
+gn:setBxd gnt:hasTissue gn:tissue_brn .
+gn:setBxd gnt:hasTissue gn:tissue_cart .
+gn:setBxd gnt:hasTissue gn:tissue_cb .
+gn:setBxd gnt:hasTissue gn:tissue_cbc .
+gn:setBxd gnt:hasTissue gn:tissue_ctx .
+gn:setBxd gnt:hasTissue gn:tissue_dfc .
+gn:setBxd gnt:hasTissue gn:tissue_drg .
+gn:setBxd gnt:hasTissue gn:tissue_ec .
+gn:setBxd gnt:hasTissue gn:tissue_emb .
+gn:setBxd gnt:hasTissue gn:tissue_eye .
+gn:setBxd gnt:hasTissue gn:tissue_fat .
+gn:setBxd gnt:hasTissue gn:tissue_fecmet .
+gn:setBxd gnt:hasTissue gn:tissue_femur .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_aor .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_atr .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_blo .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_bonm .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_bre .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_cau .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_cer .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_cerv .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_cml .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_col .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_colsig .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_cor .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_ebv .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_eso .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_esogas .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_fal .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_fro .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_muc .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_ner .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_pan .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_put .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_sintter .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_skinex .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_skisex .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_sn .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_sto .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_sub .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_tf .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_thy .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_tib .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_vag .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_ven .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_vis .
+gn:setBxd gnt:hasTissue gn:tissue_gtex_who .
+gn:setBxd gnt:hasTissue gn:tissue_gut .
+gn:setBxd gnt:hasTissue gn:tissue_hea .
+gn:setBxd gnt:hasTissue gn:tissue_hip .
+gn:setBxd gnt:hasTissue gn:tissue_hippreccel .
+gn:setBxd gnt:hasTissue gn:tissue_hipprot .
+gn:setBxd gnt:hasTissue gn:tissue_hip_mirna .
+gn:setBxd gnt:hasTissue gn:tissue_hsc .
+gn:setBxd gnt:hasTissue gn:tissue_hyp .
+gn:setBxd gnt:hasTissue gn:tissue_ifra_ctx .
+gn:setBxd gnt:hasTissue gn:tissue_ipc .
+gn:setBxd gnt:hasTissue gn:tissue_isl .
+gn:setBxd gnt:hasTissue gn:tissue_itc .
+gn:setBxd gnt:hasTissue gn:tissue_kid .
+gn:setBxd gnt:hasTissue gn:tissue_lathab .
+gn:setBxd gnt:hasTissue gn:tissue_lcm_brreg .
+gn:setBxd gnt:hasTissue gn:tissue_leaf .
+gn:setBxd gnt:hasTissue gn:tissue_liv .
+gn:setBxd gnt:hasTissue gn:tissue_livdnam .
+gn:setBxd gnt:hasTissue gn:tissue_livmet .
+gn:setBxd gnt:hasTissue gn:tissue_livpro .
+gn:setBxd gnt:hasTissue gn:tissue_lung .
+gn:setBxd gnt:hasTissue gn:tissue_m1c .
+gn:setBxd gnt:hasTissue gn:tissue_mam .
+gn:setBxd gnt:hasTissue gn:tissue_mamtum .
+gn:setBxd gnt:hasTissue gn:tissue_mbr .
+gn:setBxd gnt:hasTissue gn:tissue_md .
+gn:setBxd gnt:hasTissue gn:tissue_methyl .
+gn:setBxd gnt:hasTissue gn:tissue_mfc .
+gn:setBxd gnt:hasTissue gn:tissue_musmet .
+gn:setBxd gnt:hasTissue gn:tissue_nac .
+gn:setBxd gnt:hasTissue gn:tissue_nbcb .
+gn:setBxd gnt:hasTissue gn:tissue_neutrophil .
+gn:setBxd gnt:hasTissue gn:tissue_ocl .
+gn:setBxd gnt:hasTissue gn:tissue_ofc .
+gn:setBxd gnt:hasTissue gn:tissue_of_ctx .
+gn:setBxd gnt:hasTissue gn:tissue_ova .
+gn:setBxd gnt:hasTissue gn:tissue_pcg .
+gn:setBxd gnt:hasTissue gn:tissue_pfc .
+gn:setBxd gnt:hasTissue gn:tissue_pg .
+gn:setBxd gnt:hasTissue gn:tissue_pln .
+gn:setBxd gnt:hasTissue gn:tissue_pl_ctx .
+gn:setBxd gnt:hasTissue gn:tissue_pons .
+gn:setBxd gnt:hasTissue gn:tissue_pro .
+gn:setBxd gnt:hasTissue gn:tissue_ret .
+gn:setBxd gnt:hasTissue gn:tissue_ret_mirna .
+gn:setBxd gnt:hasTissue gn:tissue_ret_sc-rna-s .
+gn:setBxd gnt:hasTissue gn:tissue_s1c .
+gn:setBxd gnt:hasTissue gn:tissue_sal .
+gn:setBxd gnt:hasTissue gn:tissue_sg .
+gn:setBxd gnt:hasTissue gn:tissue_skm .
+gn:setBxd gnt:hasTissue gn:tissue_spi .
+gn:setBxd gnt:hasTissue gn:tissue_spl .
+gn:setBxd gnt:hasTissue gn:tissue_stc .
+gn:setBxd gnt:hasTissue gn:tissue_str .
+gn:setBxd gnt:hasTissue gn:tissue_tc .
+gn:setBxd gnt:hasTissue gn:tissue_tes .
+gn:setBxd gnt:hasTissue gn:tissue_tes_dna_met .
+gn:setBxd gnt:hasTissue gn:tissue_thelp .
+gn:setBxd gnt:hasTissue gn:tissue_thy .
+gn:setBxd gnt:hasTissue gn:tissue_treg .
+gn:setBxd gnt:hasTissue gn:tissue_ute .
+gn:setBxd gnt:hasTissue gn:tissue_v1 .
+gn:setBxd gnt:hasTissue gn:tissue_vfc .
+gn:setBxd gnt:hasTissue gn:tissue_vta .
+gn:setBxd gnt:hasTissue gn:tissue_wb .
+gn:setBxd gnt:hasTissue gn:tissue_wbc .
+gn:setBxd gnt:hasTissue gn:tissue_wbpr .
+gn:setBxd gnt:hasTissue gn:tissue_wfat .
+gn:setBxd gnt:hasTissue gn:tissue_wfat_pro .
+```
+
+
+## 'species'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT Species.Fullname, Species.SpeciesName, Species.Name, Species.MenuName, Species.FullName, Species.Family, Species.TaxonomyId FROM Species
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:Species_fullname -> rdf:type -> gnc:species
+gn:Species_fullname -> skos:label -> Species(SpeciesName)
+gn:Species_fullname -> skos:altLabel -> Species(Name)
+gn:Species_fullname -> rdfs:label -> Species(MenuName)
+gn:Species_fullname -> gnt:binomialName -> Species(FullName)
+gn:Species_fullname -> gnt:family -> Species(Family)
+gn:Species_fullname -> gnt:organism -> taxon:Species(TaxonomyId)
+```
+Here's an example query:
+
+```sparql
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX gnt: <http://genenetwork.org/term/>
+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 taxon: <http://purl.uniprot.org/taxonomy/>
+
+SELECT * WHERE {
+ ?s rdf:type gnc:species .
+ ?s skos:label "Mouse" .
+ ?s skos:altLabel "mouse" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:Mus_musculus rdf:type gnc:species .
+gn:Mus_musculus skos:label "Mouse" .
+gn:Mus_musculus skos:altLabel "mouse" .
+gn:Mus_musculus rdfs:label "Mouse (Mus musculus, mm10)" .
+gn:Mus_musculus gnt:binomialName "Mus musculus" .
+gn:Mus_musculus gnt:family "Vertebrates" .
+gn:Mus_musculus gnt:organism taxon:10090 .
+```
+
+
+## 'strain'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT Strain.Name, Species.Fullname, Strain.Name, IF ((Strain.Name2 != Strain.Name), Strain.Name2, '') AS Name2, IF ((Strain.Alias != Strain.Name), Strain.Alias, '') AS Alias, IF ((Strain.Symbol != Strain.Name), Strain.Symbol, '') AS Symbol FROM Strain LEFT JOIN Species ON Strain.SpeciesId = Species.SpeciesId
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:Strain_name_ -> rdf:type -> gnc:strain
+gn:Strain_name_ -> gnt:belongsToSpecies -> gn:Species_fullname
+gn:Strain_name_ -> rdfs:label -> StrainName
+gn:Strain_name_ -> rdfs:label -> Name2
+gn:Strain_name_ -> gnt:alias -> Alias
+gn:Strain_name_ -> gnt:symbol -> Symbol
+```
+Here's an example query:
+
+```sparql
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX gnt: <http://genenetwork.org/term/>
+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 taxon: <http://purl.uniprot.org/taxonomy/>
+
+SELECT * WHERE {
+ ?s rdf:type gnc:strain .
+ ?s gnt:belongsToSpecies gn:Mus_musculus .
+ ?s rdfs:label "B6D2F1" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:B6d2f1 rdf:type gnc:strain .
+gn:B6d2f1 gnt:belongsToSpecies gn:Mus_musculus .
+gn:B6d2f1 rdfs:label "B6D2F1" .
+```
+
+
+## 'mapping-method'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT MappingMethod.Name, MappingMethod.Name FROM MappingMethod
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:mappingMethod_mappingmethod_name -> rdf:type -> gnc:mappingMethod
+gn:mappingMethod_mappingmethod_name -> rdfs:label -> MappingMethod(Name)
+```
+Here's an example query:
+
+```sparql
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX gnt: <http://genenetwork.org/term/>
+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 taxon: <http://purl.uniprot.org/taxonomy/>
+
+SELECT * WHERE {
+ ?s rdf:type gnc:mappingMethod .
+ ?s rdfs:label "qtlreaper" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:mappingMethod_qtlreaper rdf:type gnc:mappingMethod .
+gn:mappingMethod_qtlreaper rdfs:label "qtlreaper" .
+```
+
+
+## 'avg-method'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT AvgMethod.Name, AvgMethod.Normalization FROM AvgMethod
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:avgmethod_avgmethod_name -> rdf:type -> gnc:avgMethod
+gn:avgmethod_avgmethod_name -> rdfs:label -> AvgMethod(Normalization)
+```
+Here's an example query:
+
+```sparql
+PREFIX gn: <http://genenetwork.org/id/>
+PREFIX gnc: <http://genenetwork.org/category/>
+PREFIX owl: <http://www.w3.org/2002/07/owl#>
+PREFIX gnt: <http://genenetwork.org/term/>
+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 taxon: <http://purl.uniprot.org/taxonomy/>
+
+SELECT * WHERE {
+ ?s rdf:type gnc:avgMethod .
+ ?s rdfs:label "MAS5" .
+ ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:avgmethod_mas5 rdf:type gnc:avgMethod .
+gn:avgmethod_mas5 rdfs:label "MAS5" .
+```
+
diff --git a/rdf-documentation/dump-tissue.md b/rdf-documentation/tissue-metadata.md
index b7f45d7..3c4fae9 100644
--- a/rdf-documentation/dump-tissue.md
+++ b/rdf-documentation/tissue-metadata.md
@@ -1,5 +1,5 @@
# Tissue Metadata
-## 'dump-tissue'
+## 'tissue'
## Generated Triples:
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-09 23:08:25 +0000