diff options
Diffstat (limited to 'rdf-documentation/generif-metadata.md')
| -rw-r--r-- | rdf-documentation/generif-metadata.md | 72 |
1 files changed, 19 insertions, 53 deletions
diff --git a/rdf-documentation/generif-metadata.md b/rdf-documentation/generif-metadata.md index fc058bc..7e3c4d6 100644 --- a/rdf-documentation/generif-metadata.md +++ b/rdf-documentation/generif-metadata.md @@ -6,35 +6,33 @@ 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 +SELECT GeneRIF_BASIC.symbol, GeneRIF_BASIC.symbol FROM GeneRIF_BASIC GROUP 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 +gn:symbolGeneRIF_BASIC_symbol_ -> rdfs:label -> GeneRIF_BASIC(symbol) ``` 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 skos: <http://www.w3.org/2004/02/skos/core#> +PREFIX xkos: <http://rdf-vocabulary.ddialliance.org/xkos#> 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 taxon: <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 . } ``` @@ -42,8 +40,6 @@ SELECT * WHERE { Expected Result: ```rdf -generif:233 gnt:belongsToSpecies "Human" . -generif:233 dct:relation ncbiTaxon:9606 . ``` @@ -54,43 +50,34 @@ generif:233 dct:relation ncbiTaxon:9606 . 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 '$$') AS GeneCategory, Species.Fullname, IFNULL(GeneRIF.PubMed_ID, '') AS PubMed_ID, GeneRIF.createtime, GeneRIF.email, Investigators.Email, Investigators.FirstName, Investigators.LastName, Investigators.Email, GeneRIF.weburl FROM GeneRIF LEFT JOIN Species ON Species.SpeciesId = GeneRIF.SpeciesId LEFT JOIN GeneRIFXRef ON GeneRIFXRef.GeneRIFId = GeneRIF.Id LEFT JOIN GeneCategory ON GeneRIFXRef.GeneCategoryId = GeneCategory.Id LEFT JOIN Investigators ON Investigators.Email = GeneRIF.email WHERE GeneRIF.display > 0 AND GeneRIF.VersionId = 0 AND GeneRIF.comment IS NOT NULL GROUP BY GeneRIF.comment, GeneRIF.createtime +SELECT GeneRIF.symbol, GeneRIF.comment, GeneRIF.createtime AS EntryCreateTime, GeneRIF.PubMed_ID AS PMID, GeneRIF.weburl, Species.Fullname, GROUP_CONCAT(DISTINCT GeneCategory.Name SEPARATOR '$$') AS GeneCategory, GeneRIF.email, Investigators.Email, Investigators.FirstName, Investigators.LastName, Investigators.Email 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, BINARY GeneRIF.symbol ``` 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 +gn:symbolGeneRIF_symbol_ -> rdfs:comment -> [ rdf:type gnc:GNWikiEntry ; xkos:classifiedUnder gn:Species_fullname ; rdfs:comment "GeneRIFcomment"^^xsd:string ; dct:references pubmed:GeneRIF(PMID) ; dct:creator gn:investigatorInvestigators_firstname_investigators_lastname_investigators_email ; gnt:belongsToCategory "GeneCategory" ; foaf:homepage "GeneRIF(weburl)" ; ] ``` 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 skos: <http://www.w3.org/2004/02/skos/core#> +PREFIX xkos: <http://rdf-vocabulary.ddialliance.org/xkos#> 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 taxon: <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 rdfs:comment #{\x5b; rdf:type gnc:GNWikiEntry ; xkos:classifiedUnder gn:Mus_musculus ; rdfs:comment "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."^^xsd:string ; dct:created "2011-06-10T12:06:30"^^xsd:datetime ; dct:references pubmed:094369 ; dct:references pubmed:8016086 ; dct:references pubmed:8550102 ; dct:creator gn:investigatorGrant_morahan_gem_waimr.uwa.edu.au ; gnt:belongsToCategory "Biochemistry" ; gnt:belongsToCategory "Genetic variation and alleles" ; gnt:belongsToCategory "Physiology and function" ; \x5d; }# . ?s ?p ?o . } ``` @@ -98,18 +85,7 @@ SELECT * WHERE { 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 . +gn:symbolSlc9a1 rdfs:comment [ rdf:type gnc:GNWikiEntry ; xkos:classifiedUnder gn:Mus_musculus ; rdfs:comment "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."^^xsd:string ; dct:created "2011-06-10T12:06:30"^^xsd:datetime ; dct:references pubmed:094369 ; dct:references pubmed:8016086 ; dct:references pubmed:8550102 ; dct:creator gn:investigatorGrant_morahan_gem_waimr.uwa.edu.au ; gnt:belongsToCategory "Biochemistry" ; gnt:belongsToCategory "Genetic variation and alleles" ; gnt:belongsToCategory "Physiology and function" ; ] . ``` @@ -120,39 +96,34 @@ gn:generif_beb6fe8c-d5bc-36b7-9a9f-9030f19e605f dct:references pubmed:8550102 . 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 +SELECT GeneRIF_BASIC.symbol AS GeneRIFSymbol, GeneRIF_BASIC.comment, Species.Fullname AS SpeciesFullName, GeneRIF_BASIC.TaxID AS TaxonomicId, GeneRIF_BASIC.createtime AS EntryCreateTime, GeneRIF_BASIC.PubMed_ID AS PMID, GeneRIF_BASIC.GeneId, GeneRIF_BASIC.VersionId FROM GeneRIF_BASIC LEFT JOIN Species USING (SpeciesId) WHERE GeneRIF_BASIC.comment IS NOT NULL AND TRIM(GeneRIF_BASIC.comment) != '' AND TRIM(GeneRIF_BASIC.symbol) != '' GROUP BY GeneRIF_BASIC.comment, GeneRIF_BASIC.createtime, GeneRIF_BASIC.VersionId, GeneRIF_BASIC.SpeciesId, GeneRIF_BASIC.TaxID ``` 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 +gn:symbolGeneRIF_BASIC_GeneRIFSymbol_ -> rdfs:comment -> [ rdf:type gnc:NCBIWikiEntry ; rdfs:comment "GeneRIF_BASICcomment"^^xsd:string ; xkos:classifiedUnder gn:Species_speciesfullname ; skos:notation taxon:GeneRIF_BASIC(TaxonomicId) ; gnt:hasGeneId generif:GeneRIF_BASIC(GeneId) ; gnt:hasVersionId 'GeneRIF_BASIC(VersionId)'^^xsd:integer ; dct:references pubmed:GeneRIF_BASIC(PMID) ; ] ``` 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 skos: <http://www.w3.org/2004/02/skos/core#> +PREFIX xkos: <http://rdf-vocabulary.ddialliance.org/xkos#> 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 taxon: <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 rdfs:comment #{\x5b; rdf:type gnc:NCBIWikiEntry ; rdfs:comment "he results demonstrate that apoM-S1P inhibits ox-LDL-induced inflammation in HUVECs via the S1PR2-mediated PI3K/Akt signaling pathway."^^xsd:string ; xkos:classifiedUnder gn:Homo_sapiens ; skos:notation taxon:9606 ; gnt:hasGeneId generif:55937 ; gnt:hasVersionId '1'^^xsd:integer ; dct:created "2019-08-03T07:43:00"^^xsd:datetime ; \x5d;}# . ?s ?p ?o . } ``` @@ -160,11 +131,6 @@ SELECT * WHERE { 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 . +gn:symbolAPOM rdfs:comment [ rdf:type gnc:NCBIWikiEntry ; rdfs:comment "he results demonstrate that apoM-S1P inhibits ox-LDL-induced inflammation in HUVECs via the S1PR2-mediated PI3K/Akt signaling pathway."^^xsd:string ; xkos:classifiedUnder gn:Homo_sapiens ; skos:notation taxon:9606 ; gnt:hasGeneId generif:55937 ; gnt:hasVersionId '1'^^xsd:integer ; dct:created "2019-08-03T07:43:00"^^xsd:datetime ; ] . ``` |