diff options
Diffstat (limited to 'rdf-documentation/probeset-metadata.md')
| -rw-r--r-- | rdf-documentation/probeset-metadata.md | 102 |
1 files changed, 63 insertions, 39 deletions
diff --git a/rdf-documentation/probeset-metadata.md b/rdf-documentation/probeset-metadata.md index cde4e43..ce51854 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, IFNULL(ProbeSet.Mb_mm8, '') AS Mb_mm8, IFNULL(ProbeSet.Mb_2016, '') AS Mb_2016, 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_start_2016, '') AS Probe_set_Blat_Mb_start_2016, IFNULL(ProbeSet.Probe_set_Blat_Mb_end, '') AS Probe_set_Blat_Mb_end, IFNULL(ProbeSet.Probe_set_Blat_Mb_start_2016, '') AS Probe_set_Blat_Mb_start_2016, ProbeSet.BlatSeq, ProbeSet.TargetSeq, IFNULL(ProbeSet.HomoloGeneID, '') AS HomoloGeneID, IFNULL(ProbeSet.UniProtID, '') AS UniProtID, IFNULL(ProbeSet.PubChem_ID, '') AS PubChem_ID, IFNULL(ProbeSet.KEGG_ID, '') AS KEGG_ID, IFNULL(ProbeSet.OMIM, '') AS OMIM, IFNULL(ProbeSet.ChEBI_ID, '') AS ChEBI_ID FROM ProbeSet LEFT JOIN GeneChip ON GeneChip.Id = ProbeSet.ChipId +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 ``` The above query results to triples that have the form: @@ -22,22 +22,38 @@ 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:mbMm8 -> "Mb_mm8"^^xsd:double -gn:probesetProbesetidname -> gnt:mb2016 -> "Mb_2016"^^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:strandProbe -> ProbeSet(Strand_Probe) gn:probesetProbesetidname -> gnt:hasSpecificity -> Probe_set_specificity gn:probesetProbesetidname -> gnt:hasBlatScore -> Probe_set_BLAT_score gn:probesetProbesetidname -> gnt:hasBlatMbStart -> "Probe_set_Blat_Mb_start"^^xsd:double -gn:probesetProbesetidname -> gnt:hasBlatMbStart2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double gn:probesetProbesetidname -> gnt:hasBlatMbEnd -> "Probe_set_Blat_Mb_end"^^xsd:double -gn:probesetProbesetidname -> gnt:hasBlatMbEnd2016 -> "Probe_set_Blat_Mb_start_2016"^^xsd:double gn:probesetProbesetidname -> gnt:hasBlatSeq -> ProbeSetBlatSeq gn:probesetProbesetidname -> gnt:hasTargetSeq -> ProbeSetTargetSeq -gn:probesetProbesetidname -> gnt:hasHomologeneId -> homologene:HomoloGeneID -gn:probesetProbesetidname -> gnt:hasUniprotId -> uniprot:UniProtID -gn:probesetProbesetidname -> gnt:hasPubChemId -> pubchem:PubChem_ID -gn:probesetProbesetidname -> gnt:hasKeggId -> kegg:KEGG_ID -gn:probesetProbesetidname -> gnt:hasOmimId -> -gn:probesetProbesetidname -> gnt:hasChebiId -> chebi:ChEBI_ID ``` Here's an example query: @@ -47,15 +63,9 @@ 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 kegg: <http://bio2rdf.org/ns/kegg#> -PREFIX pubchem: <https://pubchem.ncbi.nlm.nih.gov/> -PREFIX omim: <https://www.omim.org/entry/> PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> -PREFIX uniprot: <http://purl.uniprot.org/uniprot/> -PREFIX chebi: <http://purl.obolibrary.org/obo/CHEBI_> PREFIX dct: <http://purl.org/dc/terms/> PREFIX owl: <http://www.w3.org/2002/07/owl#> -PREFIX homologene: <https://bio2rdf.org/homologene:> PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> PREFIX qb: <http://purl.org/linked-data/cube#> PREFIX sdmx-measure: <http://purl.org/linked-data/sdmx/2009/measure#> @@ -63,8 +73,8 @@ PREFIX skos: <http://www.w3.org/2004/02/skos/core#> SELECT * WHERE { ?s rdf:type gnc:Probeset . - ?s rdfs:label "100001_at" . - ?s skos:altLabel "T3g; Ctg3; Ctg-3" . + ?s rdfs:label "100322_at" . + ?s skos:altLabel "IGHG2A; AU044919; MGC102604; MGC102659; Ighg" . ?s gnt:hasChip gn:platformMg_u74av2 . ?s ?p ?o . } @@ -73,25 +83,39 @@ SELECT * WHERE { Expected Result: ```rdf -gn:probeset100001_at rdf:type gnc:Probeset . -gn:probeset100001_at rdfs:label "100001_at" . -gn:probeset100001_at skos:altLabel "T3g; Ctg3; Ctg-3" . -gn:probeset100001_at gnt:hasChip gn:platformMg_u74av2 . -gn:probeset100001_at gnt:symbol "Cd3g" . -gn:probeset100001_at dct:description "CD3d antigen, gamma polypeptide" . -gn:probeset100001_at gnt:chr "9" . -gn:probeset100001_at gnt:mb "44.970689"^^xsd:double . -gn:probeset100001_at gnt:mbMm8 "44.721684"^^xsd:double . -gn:probeset100001_at gnt:mb2016 "44.778772"^^xsd:double . -gn:probeset100001_at gnt:hasSpecificity "9.3" . -gn:probeset100001_at gnt:hasBlatScore "186" . -gn:probeset100001_at gnt:hasBlatMbStart "44.970689"^^xsd:double . -gn:probeset100001_at gnt:hasBlatMbStart2016 "44.778772"^^xsd:double . -gn:probeset100001_at gnt:hasBlatMbEnd "44.971291"^^xsd:double . -gn:probeset100001_at gnt:hasBlatMbEnd2016 "44.778772"^^xsd:double . -gn:probeset100001_at gnt:hasBlatSeq "CTCTGTTGCAAAATGAACAGCTGTACAGCCCCTCAAGGACCGGGAATATGACCAGTACAGCCATCTCCAAGGAAACCAACTGAGGAAGAAGTGAACTCAGCAGGACTCAGGGTGTCCCCACAATGCATTTTGGAGAGAGCCCAGACTGCAAGCAGAGAGGAAGAACTGAGGAAAACAAGCACAGCGTGGTGTT" . -gn:probeset100001_at gnt:hasTargetSeq "ctctgttgcaaaatgaacagctgtaccagcccctcaaggaccgggaatatgaccagtacagccatctccaaggaaaccaactgaggaagaagtgaactcagcaggactcagggtgtccccccttntatccagcacccagaatcaaaacaatgcattttggagagagcccagtagagagattttcaaccctacaggtagactgcaagcagagaggaagaactgtcaaagaaattttggtcttttttttttttttnncaaaataaaataaaagcttggaggagccagtggtatgantnnnnnntgnancanttgtcaaccttgtttggggttnncagcaccccacccccagaccccccaaaaaaattcagtgaaggaaaacaagcacagcgtggtgtt" . -gn:probeset100001_at gnt:hasHomologeneId homologene:55 . -gn:probeset100001_at gnt:hasOmimId omim:186740 . +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" . ``` |