Update RDF documentation.

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

1 files changed, 12 insertions, 64 deletions

diff --git a/rdf-documentation/probeset-metadata.md b/rdf-documentation/probeset-metadata.md
index ce51854..fe857b9 100644
--- a/rdf-documentation/probeset-metadata.md
+++ b/rdf-documentation/probeset-metadata.md
@@ -6,7 +6,7 @@
 The following SQL query was executed:
 
 ```sql
-SELECT IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name)) AS ProbeSetIdName, ProbeSet.Id, ProbeSet.Name, ProbeSet.alias, IFNULL(GeneChip.Name, '') AS GeneChipName, NULLIF(TRIM(ProbeSet.TargetId), '') AS TargetId, ProbeSet.Symbol, ProbeSet.description, NULLIF(TRIM(ProbeSet.Probe_set_target_region), '') AS Probe_set_target_region, ProbeSet.Chr, IFNULL(ProbeSet.Mb, '') AS Mb, ProbeSet.Mb, ProbeSet.Chr, ProbeSet.Strand_Probe, ProbeSet.GeneId, ProbeSet.OMIM, ProbeSet.HomoloGeneID, ProbeSet.UniProtID, ProbeSet.Symbol, ProbeSet.Symbol, ProbeSet.Symbol, ProbeSet.Symbol, ProbeSet.Symbol, Species.Name, ProbeSet.RefSeq_TranscriptId, GeneList_rn33.kgId, (GeneList.txStart * 1000000) AS TranscriptStartMm10, (GeneList_rn33.txStart * 1000000) AS TranscriptStartRn7, GeneList.Chromosome, GeneList_rn33.Chromosome, (GeneList.txEnd * 1000000) AS TranscriptEndMm10, (GeneList_rn33.txEnd * 1000000) AS TranscriptEndRn7, ProbeSet.Symbol, ProbeSet.GeneId, Species.FullName, ProbeSet.Symbol, ProbeSet.GeneId, Species.name, ProbeSet.GeneId, ProbeSet.GeneId, Species.Name, ProbeSet.Strand_Probe, IFNULL(ProbeSet.Probe_set_specificity, '') AS Probe_set_specificity, IFNULL(ProbeSet.Probe_set_BLAT_score, '') AS Probe_set_BLAT_score, IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '') AS Probe_set_Blat_Mb_start, IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '') AS Probe_set_Blat_Mb_end, ProbeSet.BlatSeq, ProbeSet.TargetSeq FROM ProbeSet LEFT JOIN GeneChip ON GeneChip.Id = ProbeSet.ChipId LEFT JOIN GeneList ON GeneList.GeneID = ProbeSet.GeneId LEFT JOIN GeneList_rn33 ON GeneList.geneSymbol = ProbeSet.Symbol LEFT JOIN Species ON GeneChip.SpeciesId = Species.Id
+SELECT IF(NULLIF(TRIM(ProbeSet.Name), '') IS NULL, '', TRIM(ProbeSet.Name)) AS ProbeSetIdName, ProbeSet.Id, ProbeSet.Name, ProbeSet.alias, IFNULL(GeneChip.Name, '') AS GeneChipName, NULLIF(TRIM(ProbeSet.TargetId), '') AS TargetId, ProbeSet.Symbol, ProbeSet.description, NULLIF(TRIM(ProbeSet.Probe_set_target_region), '') AS Probe_set_target_region, ProbeSet.Chr, IFNULL(ProbeSet.Mb, '') AS Mb, ProbeSet.Mb, ProbeSet.Chr, ProbeSet.Strand_Probe, ProbeSet.GeneId, ProbeSet.OMIM, ProbeSet.HomoloGeneID, ProbeSet.UniProtID, ProbeSet.Strand_Probe, IFNULL(ProbeSet.Probe_set_specificity, '') AS Probe_set_specificity, IFNULL(ProbeSet.Probe_set_BLAT_score, '') AS Probe_set_BLAT_score, IFNULL(ProbeSet.Probe_set_Blat_Mb_start, '') AS Probe_set_Blat_Mb_start, IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '') AS Probe_set_Blat_Mb_end, ProbeSet.BlatSeq, ProbeSet.TargetSeq FROM ProbeSet LEFT JOIN GeneChip ON GeneChip.Id = ProbeSet.ChipId LEFT JOIN Species ON GeneChip.SpeciesId = Species.Id WHERE ProbeSet.Name IS NOT NULL
 ```
 
 The above query results to triples that have the form:
@@ -17,36 +17,18 @@ gn:probesetProbesetidname -> rdfs:label -> ProbeSet(Name)
 gn:probesetProbesetidname -> skos:altLabel -> ProbeSet(alias) 
 gn:probesetProbesetidname -> gnt:hasChip -> gn:platformGenechipname 
 gn:probesetProbesetidname -> gnt:hasTargetId -> TargetId 
-gn:probesetProbesetidname -> gnt:symbol -> ProbeSet(Symbol) 
+gn:probesetProbesetidname -> gnt:geneSymbol -> ProbeSet(Symbol) 
 gn:probesetProbesetidname -> dct:description -> ProbeSetdescription 
 gn:probesetProbesetidname -> gnt:targetsRegion -> Probe_set_target_region 
 gn:probesetProbesetidname -> gnt:chr -> ProbeSet(Chr) 
 gn:probesetProbesetidname -> gnt:mb -> "Mb"^^xsd:double 
-gn:probesetProbesetidname -> gnt:location -> Chr ProbeSet(Chr) @ ProbeSet(Mb) 
-gn:probesetProbesetidname -> dct:references -> <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=ProbeSet(GeneId)> .
-<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=ProbeSet(GeneId)> a gnc:NCBIGeneLink 
-gn:probesetProbesetidname -> dct:references -> <http://www.ncbi.nlm.nih.gov/omim/ProbeSet(OMIM)> .
-<http://www.ncbi.nlm.nih.gov/omim/ProbeSet(OMIM)> a gnc:omimLink 
-gn:probesetProbesetidname -> dct:references -> <http://www.ncbi.nlm.nih.gov/homologene/?term=ProbeSet(HomoloGeneID)> .
-<http://www.ncbi.nlm.nih.gov/homologene/?term=ProbeSet(HomoloGeneID)> a gnc:homologeneLink 
-gn:probesetProbesetidname -> dct:references -> <https://www.uniprot.org/uniprot/ProbeSet(UniProtID)> .
-<https://www.uniprot.org/uniprot/ProbeSet(UniProtID)> a gnc:uniprotLink 
-gn:probesetProbesetidname -> dct:references -> <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=ProbeSet(Symbol)> .
-<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=ProbeSet(Symbol)> a gnc:stringLink 
-gn:probesetProbesetidname -> dct:references -> <https://www.gtexportal.org/home/gene/ProbeSet(Symbol)> .
-<https://www.gtexportal.org/home/gene/ProbeSet(Symbol)> a gnc:gtexLink 
-gn:probesetProbesetidname -> dct:references -> <https://www.ebi.ac.uk/gwas/search?query=ProbeSet(Symbol)> .
-<https://www.ebi.ac.uk/gwas/search?query=ProbeSet(Symbol)> a gnc:ebiGwasLink 
-gn:probesetProbesetidname -> dct:references -> <http://www.proteinatlas.org/search/ProbeSet(Symbol)> .
-<http://www.proteinatlas.org/search/ProbeSet(Symbol)> a gnc:proteinAtlasLink 
-gn:probesetProbesetidname -> dct:references ->  
-gn:probesetProbesetidname -> dct:references -> <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=ProbeSet(Symbol)> .
-<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=ProbeSet(Symbol)> a gnc:PantherLink 
-gn:probesetProbesetidname -> dct:references ->  
-gn:probesetProbesetidname -> dct:references ->  
-gn:probesetProbesetidname -> dct:references -> <http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=ProbeSet(GeneId)> .
-<http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=ProbeSet(GeneId)> a gnc:gemmaLink 
-gn:probesetProbesetidname -> dct:references ->  
+gn:probesetProbesetidname -> gnt:location -> Chr ProbeSet(Chr) @ ProbeSet(Mb) Mb  
+gn:probesetProbesetidname -> gnt:hasGeneId -> gene:ProbeSet(GeneId) 
+gn:probesetProbesetidname -> dct:references -> <http://www.ncbi.nlm.nih.gov/omim/ProbeSet%28OMIM%29> .
+<http://www.ncbi.nlm.nih.gov/omim/ProbeSet%28OMIM%29> a gnc:omimLink 
+gn:probesetProbesetidname -> dct:references -> <http://www.ncbi.nlm.nih.gov/homologene/?term=ProbeSet%28HomoloGeneID%29> .
+<http://www.ncbi.nlm.nih.gov/homologene/?term=ProbeSet%28HomoloGeneID%29> a gnc:homologeneLink 
+gn:probesetProbesetidname -> gnt:uniprot -> uniprot:ProbeSet(UniProtID) 
 gn:probesetProbesetidname -> gnt:strandProbe -> ProbeSet(Strand_Probe) 
 gn:probesetProbesetidname -> gnt:hasSpecificity -> Probe_set_specificity 
 gn:probesetProbesetidname -> gnt:hasBlatScore -> Probe_set_BLAT_score 
@@ -61,6 +43,7 @@ Here's an example query:
 PREFIX gn: <http://genenetwork.org/id/> 
 PREFIX probeset: <http://genenetwork.org/probeset/> 
 PREFIX gnc: <http://genenetwork.org/category/> 
+PREFIX gene: <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=> 
 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#> 
@@ -73,9 +56,6 @@ PREFIX skos: <http://www.w3.org/2004/02/skos/core#>
 
 SELECT * WHERE { 
     ?s rdf:type gnc:Probeset .
-    ?s rdfs:label "100322_at" .
-    ?s skos:altLabel "IGHG2A; AU044919; MGC102604; MGC102659; Ighg" .
-    ?s gnt:hasChip gn:platformMg_u74av2 .
     ?s ?p ?o .
 }
 ```
@@ -83,39 +63,7 @@ SELECT * WHERE {
 Expected Result:
 
 ```rdf
-gn:probeset100322_at rdf:type gnc:Probeset .
-gn:probeset100322_at rdfs:label "100322_at" .
-gn:probeset100322_at skos:altLabel "IGHG2A; AU044919; MGC102604; MGC102659; Ighg" .
-gn:probeset100322_at gnt:hasChip gn:platformMg_u74av2 .
-gn:probeset100322_at gnt:symbol "Ighg" .
-gn:probeset100322_at dct:description "immunoglobulin heavy chain gamma polypeptide" .
-gn:probeset100322_at gnt:chr "12" .
-gn:probeset100322_at gnt:mb "114.322406"^^xsd:double .
-gn:probeset100322_at gnt:location "Chr 12 @ 114.322406 on the minus strand" .
-gn:probeset100322_at dct:references <http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=380794> .
-<http://www.ncbi.nlm.nih.gov/gene?cmd=Retrieve&dopt=Graphics&list_uids=380794> a gnc:NCBIGeneLink .
-gn:probeset100322_at dct:references <http://string-db.org/newstring_cgi/show_network_section.pl?identifier=Ighg> .
-<http://string-db.org/newstring_cgi/show_network_section.pl?identifier=Ighg> a gnc:stringLink .
-gn:probeset100322_at dct:references <https://www.gtexportal.org/home/gene/Ighg> .
-<https://www.gtexportal.org/home/gene/Ighg> a gnc:gtexLink .
-gn:probeset100322_at dct:references <https://www.ebi.ac.uk/gwas/search?query=Ighg> .
-<https://www.ebi.ac.uk/gwas/search?query=Ighg> a gnc:ebiGwasLink .
-gn:probeset100322_at dct:references <http://www.proteinatlas.org/search/Ighg> .
-<http://www.proteinatlas.org/search/Ighg> a gnc:proteinAtlasLink .
-gn:probeset100322_at dct:references <http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=Ighg> .
-<http://www.pantherdb.org/genes/geneList.do?searchType=basic&fieldName=all&organism=all&listType=1&fieldValue=Ighg> a gnc:PantherLink .
-gn:probeset100322_at dct:references <https://genemania.org/search/mus-musculus/380794> .
-<https://genemania.org/search/mus-musculus/380794> a gnc:genemaniaLink .
-gn:probeset100322_at 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=> Ighg .
-gn:probeset100322_at dct:references <http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=380794> .
-<http://www.chibi.ubc.ca/Gemma/gene/showGene.html?ncbiid=380794> a gnc:gemmaLink .
-gn:probeset100322_at gnt:strandProbe "-" .
-gn:probeset100322_at gnt:hasSpecificity "3.1" .
-gn:probeset100322_at gnt:hasBlatScore "62" .
-gn:probeset100322_at gnt:hasBlatMbStart "114.322406"^^xsd:double .
-gn:probeset100322_at gnt:hasBlatMbEnd "114.322571"^^xsd:double .
-gn:probeset100322_at gnt:hasBlatSeq "TGGTCACAGCTTTCCGCTCACGTTCACTGAAACGGGCTGATGCTGCACCAACTGTATCTTCCCACCATCCAGTAAGCTTGGGCCCGGTGGTTACTGGAACTGGATCCGGAAATTCCCAGGGAATATTACCTGCAGTTGAATTCTGTGACTACT" .
-gn:probeset100322_at gnt:hasTargetSeq "tggtcacagctttccgctcacgttcggtgctgggaccaagctggaactgaaacgggctgatgctgcaccaactgtatccatcttcccaccatccagtaagcttgggcccggtgggggcnnnnngnnnngnnnnnnntnnnnnnngnnngncnnnnngnnnnncnnntcngaggtgcagcttcaggagtcaggacctngcctngnnaaaccttctcagactctgtccctcacctgttctgtcactggcnactccatcaccagtgnttactggaactggatccggaaattcccagggaataaacttgantacatgggntacataanctacagtggtnncacttactacaatccatctctcaaaagtcgaatctccatnactnnagacacatccaagaaccantattacctgcagttgaattctgtgactact" .
+gn:probeset1824795 rdf:type gnc:Probeset .
+gn:probeset1824795 gnt:location "Not available" .
 ```