Update RDF documentation.

Signed-off-by: Munyoki Kilyungi <me@bonfacemunyoki.com>

1 files changed, 193 insertions, 0 deletions

diff --git a/rdf-documentation/genelist.md b/rdf-documentation/genelist.md
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+# Gene Metadata
+## 'genelist-rn33'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT GeneList_rn33.id AS GENE_UID, GeneList_rn33.geneSymbol, GeneList_rn33.chromosome, GeneList_rn33.txStart, GeneList_rn33.txEnd, GeneList_rn33.strand, GeneList_rn33.NM_ID, GeneList_rn33.kgID, GeneList_rn33.geneSymbol, GeneList_rn33.geneSymbol, GeneList_rn33.geneSymbol, GeneList_rn33.geneSymbol, GeneList_rn33.geneSymbol FROM GeneList_rn33
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:gene_rn33Genelist_rn33_gene_uid -> rdf:type -> gnc:Gene 
+gn:gene_rn33Genelist_rn33_gene_uid -> gnt:belongsToSpecies -> gn:Rattus_norvegicus 
+gn:gene_rn33Genelist_rn33_gene_uid -> gnt:geneSymbol -> GeneList_rn33(geneSymbol) 
+gn:gene_rn33Genelist_rn33_gene_uid -> gnt:chromosome -> GeneList_rn33(chromosome) 
+gn:gene_rn33Genelist_rn33_gene_uid -> gnt:TxStart -> "GeneList_rn33(txStart)"^^xsd:double 
+gn:gene_rn33Genelist_rn33_gene_uid -> gnt:TxEnd -> "GeneList_rn33(txEnd)"^^xsd:double 
+gn:gene_rn33Genelist_rn33_gene_uid -> gnt:Strand -> GeneList_rn33(strand) 
+gn:gene_rn33Genelist_rn33_gene_uid -> gnt:transcript -> transcript:GeneList_rn33(NM_ID) 
+gn:gene_rn33Genelist_rn33_gene_uid -> gnt:hasKgID -> GeneList_rn33(kgID) 
+gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=GeneList_rn33(geneSymbol)> .
+<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=GeneList_rn33(geneSymbol)> a gnc:PantherLink 
+gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <https://www.ebi.ac.uk/gwas/search?query=GeneList_rn33(geneSymbol)> .
+<https://www.ebi.ac.uk/gwas/search?query=GeneList_rn33(geneSymbol)> a gnc:ebiGwasLink 
+gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=GeneList_rn33%28geneSymbol%29> .
+<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=GeneList_rn33%28geneSymbol%29> a gnc:stringLink 
+gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <https://www.gtexportal.org/home/gene/GeneList_rn33%28geneSymbol%29> .
+<https://www.gtexportal.org/home/gene/GeneList_rn33%28geneSymbol%29> a gnc:gtexLink 
+gn:gene_rn33Genelist_rn33_gene_uid -> dct:references -> <http://www.proteinatlas.org/search/GeneList_rn33%28geneSymbol%29> .
+<http://www.proteinatlas.org/search/GeneList_rn33%28geneSymbol%29> a gnc:proteinAtlasLink 
+```
+Here's an example query:
+
+```sparql
+PREFIX gn: <http://genenetwork.org/id/> 
+PREFIX probeset: <http://genenetwork.org/probeset/> 
+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 dct: <http://purl.org/dc/terms/> 
+PREFIX owl: <http://www.w3.org/2002/07/owl#> 
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 
+PREFIX qb: <http://purl.org/linked-data/cube#> 
+PREFIX gene: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=> 
+PREFIX sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#> 
+PREFIX transcript: <https://portals.broadinstitute.org/gpp/public/trans/details?transName=> 
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#> 
+
+SELECT * WHERE { 
+    ?s rdf:type gnc:Gene .
+    ?s gnt:belongsToSpecies gn:Rattus_norvegicus .
+    ?s gnt:geneSymbol "0610031j06rik" .
+    ?s gnt:chromosome "2" .
+    ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:gene_rn331 rdf:type gnc:Gene .
+gn:gene_rn331 gnt:belongsToSpecies gn:Rattus_norvegicus .
+gn:gene_rn331 gnt:geneSymbol "0610031j06rik" .
+gn:gene_rn331 gnt:chromosome "2" .
+gn:gene_rn331 gnt:TxStart "180.388175"^^xsd:double .
+gn:gene_rn331 gnt:TxEnd "180.391765"^^xsd:double .
+gn:gene_rn331 gnt:Strand "+" .
+gn:gene_rn331 gnt:transcript transcript:NM_001004226 .
+gn:gene_rn331 dct:references <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=0610031j06rik> .
+<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=0610031j06rik> a gnc:PantherLink .
+gn:gene_rn331 dct:references <https://www.ebi.ac.uk/gwas/search?query=0610031j06rik> .
+<https://www.ebi.ac.uk/gwas/search?query=0610031j06rik> a gnc:ebiGwasLink .
+gn:gene_rn331 dct:references <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=0610031j06rik> .
+<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=0610031j06rik> a gnc:stringLink .
+gn:gene_rn331 dct:references <https://www.gtexportal.org/home/gene/0610031j06rik> .
+<https://www.gtexportal.org/home/gene/0610031j06rik> a gnc:gtexLink .
+gn:gene_rn331 dct:references <http://www.proteinatlas.org/search/0610031j06rik> .
+<http://www.proteinatlas.org/search/0610031j06rik> a gnc:proteinAtlasLink .
+```
+
+
+## 'genelist'
+
+## Generated Triples:
+
+The following SQL query was executed:
+
+```sql
+SELECT CONCAT_WS('_', GeneSymbol, GeneID, AlignID) AS GENE_UID, GeneList.GeneSymbol, GeneList.GeneDescription, GeneList.GeneId, GeneList.GeneSymbol, GeneList.GeneSymbol, GeneList.GeneID, Species.Name, GeneList.GeneSymbol, Species.Name, GeneList.GeneID, Species.Name, GeneList.GeneID, GeneList.GeneSymbol, Species.FullName, GeneList.GeneSymbol, GeneList.GeneSymbol, GeneList.GeneSymbol, GeneList.GeneSymbol, GeneList.Chromosome, GeneList.TxStart, GeneList.TxEnd, GeneList.Strand, Species.Name, GeneList.NM_ID, GeneList.kgID, GeneList.UnigenID, GeneList.ProteinID, GeneList.AlignID, IFNULL(RGD_ID, '') AS RGD_ID FROM GeneList LEFT JOIN Species USING (SpeciesId)
+```
+
+The above query results to triples that have the form:
+
+```text
+gn:geneGENE_UID -> rdf:type -> gnc:Gene 
+gn:geneGENE_UID -> gnt:geneSymbol -> GeneList(GeneSymbol) 
+gn:geneGENE_UID -> dct:description -> GeneListGeneDescription 
+gn:geneGENE_UID -> gnt:hasGeneId -> gene:GeneList(GeneId) 
+gn:geneGENE_UID -> dct:references -> <https://www.ebi.ac.uk/gwas/search?query=GeneList%28GeneSymbol%29> .
+<https://www.ebi.ac.uk/gwas/search?query=GeneList%28GeneSymbol%29> a gnc:ebiGwasLink 
+gn:geneGENE_UID -> dct:references ->  
+gn:geneGENE_UID -> dct:references ->  
+gn:geneGENE_UID -> dct:references ->  
+gn:geneGENE_UID -> dct:references -> <http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=GeneList(GeneID)> .
+<http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=GeneList(GeneID)> a gnc:gemmaLink 
+gn:geneGENE_UID -> dct:references ->  
+gn:geneGENE_UID -> dct:references -> <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=GeneList%28GeneSymbol%29> .
+<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=GeneList%28GeneSymbol%29> a gnc:pantherLink 
+gn:geneGENE_UID -> dct:references -> <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=GeneList%28GeneSymbol%29> .
+<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=GeneList%28GeneSymbol%29> a gnc:stringLink 
+gn:geneGENE_UID -> dct:references -> <https://www.gtexportal.org/home/gene/GeneList%28GeneSymbol%29> .
+<https://www.gtexportal.org/home/gene/GeneList%28GeneSymbol%29> a gnc:gtexLink 
+gn:geneGENE_UID -> dct:references -> <http://www.proteinatlas.org/search/GeneList%28GeneSymbol%29> .
+<http://www.proteinatlas.org/search/GeneList%28GeneSymbol%29> a gnc:proteinAtlasLink 
+gn:geneGENE_UID -> gnt:chromosome -> GeneList(Chromosome) 
+gn:geneGENE_UID -> gnt:TxStart -> "GeneList(TxStart)"^^xsd:double 
+gn:geneGENE_UID -> gnt:TxEnd -> "GeneList(TxEnd)"^^xsd:double 
+gn:geneGENE_UID -> gnt:Strand -> GeneList(Strand) 
+gn:geneGENE_UID -> gnt:belongsToSpecies -> gn:Species_name 
+gn:geneGENE_UID -> gnt:transcript -> transcript:GeneList(NM_ID) 
+gn:geneGENE_UID -> gnt:hasKgID -> GeneList(kgID) 
+gn:geneGENE_UID -> gnt:hasUnigenID -> GeneList(UnigenID) 
+gn:geneGENE_UID -> gnt:hasProteinID -> GeneList(ProteinID) 
+gn:geneGENE_UID -> gnt:hasAlignID -> GeneList(AlignID) 
+gn:geneGENE_UID -> gnt:hasRgdID -> RGD_ID 
+```
+Here's an example query:
+
+```sparql
+PREFIX gn: <http://genenetwork.org/id/> 
+PREFIX probeset: <http://genenetwork.org/probeset/> 
+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 dct: <http://purl.org/dc/terms/> 
+PREFIX owl: <http://www.w3.org/2002/07/owl#> 
+PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> 
+PREFIX qb: <http://purl.org/linked-data/cube#> 
+PREFIX gene: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=> 
+PREFIX sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#> 
+PREFIX transcript: <https://portals.broadinstitute.org/gpp/public/trans/details?transName=> 
+PREFIX skos: <http://www.w3.org/2004/02/skos/core#> 
+
+SELECT * WHERE { 
+    ?s rdf:type gnc:Gene .
+    ?s gnt:geneSymbol "OTTMUSG00000007" .
+    ?s dct:description "predicted gene, OTTMUSG00000007987" .
+    ?s gnt:hasGeneId gene:100137011 .
+    ?s ?p ?o .
+}
+```
+
+Expected Result:
+
+```rdf
+gn:geneOTTMUSG00000007_100137011_G211062 rdf:type gnc:Gene .
+gn:geneOTTMUSG00000007_100137011_G211062 gnt:geneSymbol "OTTMUSG00000007" .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:description "predicted gene, OTTMUSG00000007987" .
+gn:geneOTTMUSG00000007_100137011_G211062 gnt:hasGeneId gene:100137011 .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <https://www.ebi.ac.uk/gwas/search?query=OTTMUSG00000007> .
+<https://www.ebi.ac.uk/gwas/search?query=OTTMUSG00000007> a gnc:ebiGwasLink .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://mouse.brain-map.org/search/show?search_type=gene&search_term=> .
+<http://mouse.brain-map.org/search/show?search_type=gene&search_term=> a gnc:abaLink .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <https://rgd.mcw.edu/rgdweb/elasticResults.html?term=OTTMUSG00000007&category=Gene&species=Mouse> .
+<https://rgd.mcw.edu/rgdweb/elasticResults.html?term=OTTMUSG00000007&category=Gene&species=Mouse> a gnc:rgdLink .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://biogps.org/?org=mouse#goto=genereport&id=100137011> .
+<http://biogps.org/?org=mouse#goto=genereport&id=100137011> a gnc:biogpsLink .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=100137011> .
+<http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=100137011> a gnc:gemmaLink .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <https://genemania.org/search/mus-musculus/OTTMUSG00000007> .
+<https://genemania.org/search/mus-musculus/OTTMUSG00000007> a gnc:genemaniaLink .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=OTTMUSG00000007> .
+<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=OTTMUSG00000007> a gnc:pantherLink .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=OTTMUSG00000007> .
+<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=OTTMUSG00000007> a gnc:stringLink .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <https://www.gtexportal.org/home/gene/OTTMUSG00000007> .
+<https://www.gtexportal.org/home/gene/OTTMUSG00000007> a gnc:gtexLink .
+gn:geneOTTMUSG00000007_100137011_G211062 dct:references <http://www.proteinatlas.org/search/OTTMUSG00000007> .
+<http://www.proteinatlas.org/search/OTTMUSG00000007> a gnc:proteinAtlasLink .
+gn:geneOTTMUSG00000007_100137011_G211062 gnt:chromosome "11" .
+gn:geneOTTMUSG00000007_100137011_G211062 gnt:TxStart "60.630829"^^xsd:double .
+gn:geneOTTMUSG00000007_100137011_G211062 gnt:TxEnd "60.632734"^^xsd:double .
+gn:geneOTTMUSG00000007_100137011_G211062 gnt:belongsToSpecies gn:Mouse .
+gn:geneOTTMUSG00000007_100137011_G211062 gnt:transcript transcript:AK046412 .
+gn:geneOTTMUSG00000007_100137011_G211062 gnt:hasProteinID "Q8BQU9" .
+gn:geneOTTMUSG00000007_100137011_G211062 gnt:hasAlignID "G211062" .
+```
+