diff options
| -rw-r--r-- | rdf-documentation/dump-genotype.md | 52 | ||||
| -rw-r--r-- | rdf-documentation/dump-phenotype.md | 59 | ||||
| -rw-r--r-- | rdf-documentation/dump-probeset-summary-stats.md | 2 | ||||
| -rw-r--r-- | rdf-documentation/dump-species-metadata.md | 260 |
4 files changed, 184 insertions, 189 deletions
diff --git a/rdf-documentation/dump-genotype.md b/rdf-documentation/dump-genotype.md index 07533f9..2f5edbc 100644 --- a/rdf-documentation/dump-genotype.md +++ b/rdf-documentation/dump-genotype.md @@ -59,25 +59,24 @@ gn:B6d2rigeno gnt:belongsToInbredSet gn:_b6d2ri . The following SQL query was executed: ```sql -SELECT CONCAT(IF(GenoFreeze.Name IS NULL, '', CONCAT(GenoFreeze.Name, '_')), Geno.Name) AS abbrev, Geno.Name, Geno.Chr, IFNULL(Geno.Mb, '') AS Mb, IFNULL(Geno.Mb_mm8, '') AS Mb_mm8, IFNULL(Geno.Mb_2016, '') AS Mb_2016, Geno.Sequence, Geno.Source, IF((Source2 = Source), NULL, Source2) AS Source2, IFNULL(GenoFreeze.Name, '') AS DatasetName, Geno.chr_num, Geno.Comments, GenoXRef.cM FROM Geno LEFT JOIN GenoXRef ON Geno.Id = GenoXRef.GenoId LEFT JOIN GenoFreeze ON GenoFreeze.Id = GenoXRef.GenoFreezeId LEFT JOIN InbredSet ON InbredSet.InbredSetId = GenoFreeze.InbredSetId LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = GenoFreeze.Name +SELECT Geno.Name, Geno.Name, Geno.Chr, IFNULL(Geno.Mb, '') AS Mb, IFNULL(Geno.Mb_mm8, '') AS Mb_mm8, IFNULL(Geno.Mb_2016, '') AS Mb_2016, Geno.Sequence, Geno.Source, IF((Source2 = Source), NULL, Source2) AS Source2, Species.Fullname, Geno.chr_num, Geno.Comments FROM Geno LEFT JOIN Species USING (SpeciesId) ``` The above query results to triples that have the form: ```text -gn:Abbrev -> rdf:type -> gnc:genotype -gn:Abbrev -> skos:prefLabel -> GenoName -gn:Abbrev -> gnt:chr -> Geno(Chr) -gn:Abbrev -> gnt:mb -> "Mb"^^xsd:double -gn:Abbrev -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double -gn:Abbrev -> gnt:mb2016 -> "Mb_2016"^^xsd:double -gn:Abbrev -> gnt:hasSequence -> Geno(Sequence) -gn:Abbrev -> gnt:hasSource -> Geno(Source) -gn:Abbrev -> gnt:hasAltSourceName -> Source2 -gn:Abbrev -> gnt:belongsToDataset -> gn:Datasetname -gn:Abbrev -> gnt:chrNum -> "Geno(chr_num)"^^xsd:int -gn:Abbrev -> rdfs:comments -> Geno(Comments) -gn:Abbrev -> gnt:cM -> "GenoXRef(cM)"^^xsd:int +gn:Geno_name_ -> rdf:type -> gnc:genotype +gn:Geno_name_ -> skos:prefLabel -> GenoName +gn:Geno_name_ -> gnt:chr -> Geno(Chr) +gn:Geno_name_ -> gnt:mb -> "Mb"^^xsd:double +gn:Geno_name_ -> gnt:mbMm8 -> "Mb_mm8"^^xsd:double +gn:Geno_name_ -> gnt:mb2016 -> "Mb_2016"^^xsd:double +gn:Geno_name_ -> gnt:hasSequence -> Geno(Sequence) +gn:Geno_name_ -> gnt:hasSource -> Geno(Source) +gn:Geno_name_ -> gnt:hasAltSourceName -> Source2 +gn:Geno_name_ -> gnt:belongsToSpecies -> gn:Species_fullname +gn:Geno_name_ -> gnt:chrNum -> "Geno(chr_num)"^^xsd:int +gn:Geno_name_ -> rdfs:comments -> Geno(Comments) ``` Here's an example query: @@ -94,9 +93,9 @@ PREFIX xsd: <http://www.w3.org/2001/XMLSchema#> SELECT * WHERE { ?s rdf:type gnc:genotype . - ?s skos:prefLabel "D1Mit118" . + ?s skos:prefLabel "D1Mit296" . ?s gnt:chr "1" . - ?s gnt:mb #{"3.968933"^^xsd:double}# . + ?s gnt:mb #{"9.749729"^^xsd:double}# . ?s ?p ?o . } ``` @@ -104,16 +103,15 @@ SELECT * WHERE { Expected Result: ```rdf -gn:B6d2f2geno_d1mit118 rdf:type gnc:genotype . -gn:B6d2f2geno_d1mit118 skos:prefLabel "D1Mit118" . -gn:B6d2f2geno_d1mit118 gnt:chr "1" . -gn:B6d2f2geno_d1mit118 gnt:mb "3.968933"^^xsd:double . -gn:B6d2f2geno_d1mit118 gnt:mbMm8 "3.959096"^^xsd:double . -gn:B6d2f2geno_d1mit118 gnt:mb2016 "3.959014"^^xsd:double . -gn:B6d2f2geno_d1mit118 gnt:hasSequence "TAATACGACTCNCTATAGGGCGAATTGAGGCCCTCTAGATGCATGCTCGANCGGCCGCCAGTGTGCTGGAAAGCCAGCCTGGNCTACAGAGCTCAAGAGACCACATGTGATACTTGCCTTTCTGAGTCTAACATATATAGAATGATCTAATGGTCTCTAATCACACACTTTTTTTTGTGAATGAAACTTATTAAGAGTTTTATATTTGTGTGTGTGTGTGTGTGTGTGTGTGTCTGTGTGTCTCTGTGTGTGTGT" . -gn:B6d2f2geno_d1mit118 gnt:hasSource "Mit" . -gn:B6d2f2geno_d1mit118 gnt:belongsToDataset gn:B6d2f2geno . -gn:B6d2f2geno_d1mit118 gnt:chrNum "1"^^xsd:int . -gn:B6d2f2geno_d1mit118 gnt:cM "0.0"^^xsd:int . +gn:D1mit296 rdf:type gnc:genotype . +gn:D1mit296 skos:prefLabel "D1Mit296" . +gn:D1mit296 gnt:chr "1" . +gn:D1mit296 gnt:mb "9.749729"^^xsd:double . +gn:D1mit296 gnt:mbMm8 "9.734943"^^xsd:double . +gn:D1mit296 gnt:mb2016 "9.73981"^^xsd:double . +gn:D1mit296 gnt:hasSequence "CTTGCATGCCTGCGGNTNCGNACTCTAGAGGATCTCCCTATTATTNTNACATNACTTTNAATTAAAATAATAATCAGATAACTTCAACNNNNTGNNCACTTCTGTCAAGTGGACAGAAATAAACATAGAGCCTAATTATCCTGAATTTNAGAGAAAAGAGTGTGTTTANCACAANAGAACAGTTATAGATCTACACACACACACACACACACACACACACACACATACAGTTTGAAAAATGCATCAGTTGAGACC" . +gn:D1mit296 gnt:hasSource "Mit" . +gn:D1mit296 gnt:belongsToSpecies gn:Mus_musculus . +gn:D1mit296 gnt:chrNum "1"^^xsd:int . ``` diff --git a/rdf-documentation/dump-phenotype.md b/rdf-documentation/dump-phenotype.md index dc9b6dd..c9436a3 100644 --- a/rdf-documentation/dump-phenotype.md +++ b/rdf-documentation/dump-phenotype.md @@ -60,28 +60,25 @@ gn:B6d2f2_psupublish gnt:belongsToInbredSet gn:B6d2f2-psupublish . The following SQL query was executed: ```sql -SELECT CONCAT(IF(PublishFreeze.Name IS NULL, '', CONCAT(PublishFreeze.Name, '_')), IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation)) AS abbrev, IF(Phenotype.Post_publication_abbreviation IS NULL, IF(Phenotype.Pre_publication_abbreviation IS NULL, Phenotype.Id, Phenotype.Pre_publication_abbreviation), Phenotype.Post_publication_abbreviation) AS PhenotypeName, CONCAT(InbredSet.Name, '_', PublishXRef.Id) AS phenotypeAltName, Phenotype.Post_publication_description, Phenotype.Post_publication_abbreviation, Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Owner, IFNULL(PublishXRef.mean, '') AS mean, PublishXRef.Locus, IFNULL(PublishXRef.LRS, '') AS lrs, IFNULL(PublishXRef.additive, '') AS additive, PublishXRef.Sequence, InfoFiles.InfoPageName, IF(Publication.PubMed_ID IS NULL, '', CONVERT(Publication.PubMed_Id, INT)) AS pmid, Publication.Id FROM Phenotype LEFT JOIN PublishXRef ON Phenotype.Id = PublishXRef.PhenotypeId LEFT JOIN Publication ON Publication.Id = PublishXRef.PublicationId LEFT JOIN InbredSet ON InbredSet.InbredSetId = PublishXRef.InbredSetId LEFT JOIN PublishFreeze ON PublishFreeze.InbredSetId = PublishXRef.InbredSetId LEFT JOIN InfoFiles ON InfoFiles.InfoPageName = PublishFreeze.Name WHERE PublishFreeze.public > 0 AND PublishFreeze.confidentiality < 1 AND PublishFreeze.Id IS NOT NULL +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:Abbrev -> rdf:type -> gnc:phenotype -gn:Abbrev -> skos:prefLabel -> PhenotypeName -gn:Abbrev -> skos:altLabel -> phenotypeAltName -gn:Abbrev -> dct:description -> PhenotypePost_publication_description -gn:Abbrev -> gnt:abbreviation -> Phenotype(Post_publication_abbreviation) -gn:Abbrev -> gnt:labCode -> Phenotype(Lab_code) -gn:Abbrev -> gnt:submitter -> PhenotypeSubmitter -gn:Abbrev -> dct:contributor -> PhenotypeOwner -gn:Abbrev -> gnt:mean -> "mean"^^xsd:double -gn:Abbrev -> gnt:locus -> PublishXRef(Locus) -gn:Abbrev -> gnt:LRS -> "lrs"^^xsd:double -gn:Abbrev -> gnt:additive -> "additive"^^xsd:double -gn:Abbrev -> gnt:sequence -> "PublishXRef(Sequence)"^^xsd:integer -gn:Abbrev -> gnt:belongsToDataset -> gn:Infofiles_infopagename_ -gn:Abbrev -> dct:isReferencedBy -> pubmed:pmid -gn:Abbrev -> dct:contributor -> PhenotypeOwner +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: @@ -99,9 +96,9 @@ PREFIX pubmed: <http://rdf.ncbi.nlm.nih.gov/pubmed/> SELECT * WHERE { ?s rdf:type gnc:phenotype . - ?s skos:prefLabel "CBLWT2" . - ?s skos:altLabel "BXD_10001" . + ?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 . } ``` @@ -109,18 +106,16 @@ SELECT * WHERE { Expected Result: ```rdf -gn:Bxdpublish_cblwt2 rdf:type gnc:phenotype . -gn:Bxdpublish_cblwt2 skos:prefLabel "CBLWT2" . -gn:Bxdpublish_cblwt2 skos:altLabel "BXD_10001" . -gn:Bxdpublish_cblwt2 dct:description "Central nervous system, morphology: Cerebellum weight, whole, bilateral in adults of both sexes [mg]" . -gn:Bxdpublish_cblwt2 gnt:abbreviation "CBLWT2" . -gn:Bxdpublish_cblwt2 gnt:submitter "robwilliams" . -gn:Bxdpublish_cblwt2 gnt:mean "52.13529418496525"^^xsd:double . -gn:Bxdpublish_cblwt2 gnt:locus "rs48756159" . -gn:Bxdpublish_cblwt2 gnt:LRS "13.4974911471087"^^xsd:double . -gn:Bxdpublish_cblwt2 gnt:additive "2.39444435069444"^^xsd:double . -gn:Bxdpublish_cblwt2 gnt:sequence "1"^^xsd:integer . -gn:Bxdpublish_cblwt2 gnt:belongsToDataset gn:Bxdpublish . -gn:Bxdpublish_cblwt2 dct:isReferencedBy pubmed:11438585 . +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-summary-stats.md b/rdf-documentation/dump-probeset-summary-stats.md index 55771ab..422513b 100644 --- a/rdf-documentation/dump-probeset-summary-stats.md +++ b/rdf-documentation/dump-probeset-summary-stats.md @@ -29,6 +29,8 @@ Here's an example query: 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#> diff --git a/rdf-documentation/dump-species-metadata.md b/rdf-documentation/dump-species-metadata.md index 495905a..160cf44 100644 --- a/rdf-documentation/dump-species-metadata.md +++ b/rdf-documentation/dump-species-metadata.md @@ -18,10 +18,10 @@ 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:species -> gn:Species_fullname +gn:Inbredset_name -> gnt:belongsToSpecies -> gn:Species_fullname gn:Inbredset_name -> gnt:genotype -> genotypeP gn:Inbredset_name -> gnt:phenotype -> phenotypeP -gn:Inbredset_name -> gnt:molecularTrait -> gn:tissue_moleculartrait +gn:Inbredset_name -> gnt:hasTissue -> gn:tissue_moleculartrait ``` Here's an example query: @@ -53,133 +53,133 @@ 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:species gn:Mus_musculus . +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:molecularTrait gn:tissue_a1c . -gn:Bxd gnt:molecularTrait gn:tissue_acc . -gn:Bxd gnt:molecularTrait gn:tissue_adr . -gn:Bxd gnt:molecularTrait gn:tissue_amg . -gn:Bxd gnt:molecularTrait gn:tissue_bebv . -gn:Bxd gnt:molecularTrait gn:tissue_bla . -gn:Bxd gnt:molecularTrait gn:tissue_brmet . -gn:Bxd gnt:molecularTrait gn:tissue_brmicrorna . -gn:Bxd gnt:molecularTrait gn:tissue_brn . -gn:Bxd gnt:molecularTrait gn:tissue_cart . -gn:Bxd gnt:molecularTrait gn:tissue_cb . -gn:Bxd gnt:molecularTrait gn:tissue_cbc . -gn:Bxd gnt:molecularTrait gn:tissue_ctx . -gn:Bxd gnt:molecularTrait gn:tissue_dfc . -gn:Bxd gnt:molecularTrait gn:tissue_drg . -gn:Bxd gnt:molecularTrait gn:tissue_ec . -gn:Bxd gnt:molecularTrait gn:tissue_emb . -gn:Bxd gnt:molecularTrait gn:tissue_eye . -gn:Bxd gnt:molecularTrait gn:tissue_fat . -gn:Bxd gnt:molecularTrait gn:tissue_fecmet . -gn:Bxd gnt:molecularTrait gn:tissue_femur . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_aor . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_atr . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_blo . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_bonm . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_bre . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_cau . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_cer . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_cerv . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_cml . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_col . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_colsig . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_cor . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_ebv . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_eso . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_esogas . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_fal . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_fro . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_muc . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_ner . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_pan . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_put . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_sintter . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_skinex . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_skisex . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_sn . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_sto . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_sub . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_tf . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_thy . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_tib . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_vag . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_ven . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_vis . -gn:Bxd gnt:molecularTrait gn:tissue_gtex_who . -gn:Bxd gnt:molecularTrait gn:tissue_gut . -gn:Bxd gnt:molecularTrait gn:tissue_hea . -gn:Bxd gnt:molecularTrait gn:tissue_hip . -gn:Bxd gnt:molecularTrait gn:tissue_hippreccel . -gn:Bxd gnt:molecularTrait gn:tissue_hipprot . -gn:Bxd gnt:molecularTrait gn:tissue_hip_mirna . -gn:Bxd gnt:molecularTrait gn:tissue_hsc . -gn:Bxd gnt:molecularTrait gn:tissue_hyp . -gn:Bxd gnt:molecularTrait gn:tissue_ifra_ctx . -gn:Bxd gnt:molecularTrait gn:tissue_ipc . -gn:Bxd gnt:molecularTrait gn:tissue_isl . -gn:Bxd gnt:molecularTrait gn:tissue_itc . -gn:Bxd gnt:molecularTrait gn:tissue_kid . -gn:Bxd gnt:molecularTrait gn:tissue_lathab . -gn:Bxd gnt:molecularTrait gn:tissue_lcm_brreg . -gn:Bxd gnt:molecularTrait gn:tissue_leaf . -gn:Bxd gnt:molecularTrait gn:tissue_liv . -gn:Bxd gnt:molecularTrait gn:tissue_livdnam . -gn:Bxd gnt:molecularTrait gn:tissue_livmet . -gn:Bxd gnt:molecularTrait gn:tissue_livpro . -gn:Bxd gnt:molecularTrait gn:tissue_lung . -gn:Bxd gnt:molecularTrait gn:tissue_m1c . -gn:Bxd gnt:molecularTrait gn:tissue_mam . -gn:Bxd gnt:molecularTrait gn:tissue_mamtum . -gn:Bxd gnt:molecularTrait gn:tissue_mbr . -gn:Bxd gnt:molecularTrait gn:tissue_md . -gn:Bxd gnt:molecularTrait gn:tissue_methyl . -gn:Bxd gnt:molecularTrait gn:tissue_mfc . -gn:Bxd gnt:molecularTrait gn:tissue_musmet . -gn:Bxd gnt:molecularTrait gn:tissue_nac . -gn:Bxd gnt:molecularTrait gn:tissue_nbcb . -gn:Bxd gnt:molecularTrait gn:tissue_neutrophil . -gn:Bxd gnt:molecularTrait gn:tissue_ocl . -gn:Bxd gnt:molecularTrait gn:tissue_ofc . -gn:Bxd gnt:molecularTrait gn:tissue_of_ctx . -gn:Bxd gnt:molecularTrait gn:tissue_ova . -gn:Bxd gnt:molecularTrait gn:tissue_pcg . -gn:Bxd gnt:molecularTrait gn:tissue_pfc . -gn:Bxd gnt:molecularTrait gn:tissue_pg . -gn:Bxd gnt:molecularTrait gn:tissue_pln . -gn:Bxd gnt:molecularTrait gn:tissue_pl_ctx . -gn:Bxd gnt:molecularTrait gn:tissue_pons . -gn:Bxd gnt:molecularTrait gn:tissue_pro . -gn:Bxd gnt:molecularTrait gn:tissue_ret . -gn:Bxd gnt:molecularTrait gn:tissue_ret_mirna . -gn:Bxd gnt:molecularTrait gn:tissue_ret_sc-rna-s . -gn:Bxd gnt:molecularTrait gn:tissue_s1c . -gn:Bxd gnt:molecularTrait gn:tissue_sal . -gn:Bxd gnt:molecularTrait gn:tissue_sg . -gn:Bxd gnt:molecularTrait gn:tissue_skm . -gn:Bxd gnt:molecularTrait gn:tissue_spi . -gn:Bxd gnt:molecularTrait gn:tissue_spl . -gn:Bxd gnt:molecularTrait gn:tissue_stc . -gn:Bxd gnt:molecularTrait gn:tissue_str . -gn:Bxd gnt:molecularTrait gn:tissue_tc . -gn:Bxd gnt:molecularTrait gn:tissue_tes . -gn:Bxd gnt:molecularTrait gn:tissue_tes_dna_met . -gn:Bxd gnt:molecularTrait gn:tissue_thelp . -gn:Bxd gnt:molecularTrait gn:tissue_thy . -gn:Bxd gnt:molecularTrait gn:tissue_treg . -gn:Bxd gnt:molecularTrait gn:tissue_ute . -gn:Bxd gnt:molecularTrait gn:tissue_v1 . -gn:Bxd gnt:molecularTrait gn:tissue_vfc . -gn:Bxd gnt:molecularTrait gn:tissue_vta . -gn:Bxd gnt:molecularTrait gn:tissue_wb . -gn:Bxd gnt:molecularTrait gn:tissue_wbc . -gn:Bxd gnt:molecularTrait gn:tissue_wbpr . -gn:Bxd gnt:molecularTrait gn:tissue_wfat . -gn:Bxd gnt:molecularTrait gn:tissue_wfat_pro . +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 . ``` @@ -251,7 +251,7 @@ The above query results to triples that have the form: ```text gn:Strain_name_ -> rdf:type -> gnc:strain -gn:Strain_name_ -> gnt:species -> gn:Species_fullname +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 @@ -271,7 +271,7 @@ PREFIX taxon: <http://purl.uniprot.org/taxonomy/> SELECT * WHERE { ?s rdf:type gnc:strain . - ?s gnt:species gn:Mus_musculus . + ?s gnt:belongsToSpecies gn:Mus_musculus . ?s rdfs:label "B6D2F1" . ?s ?p ?o . } @@ -281,7 +281,7 @@ Expected Result: ```rdf gn:B6d2f1 rdf:type gnc:strain . -gn:B6d2f1 gnt:species gn:Mus_musculus . +gn:B6d2f1 gnt:belongsToSpecies gn:Mus_musculus . gn:B6d2f1 rdfs:label "B6D2F1" . ``` |