Galaxy History ' LOAD Queries'


DatasetAnnotation
1: a affy
4 lines
format: txt, database: ?
Info: uploaded txt file
select distinct * where {
?s a <http://bio2rdf.org/ns/affymetrix#Probeset>.
?s ?p ?o .
} LIMIT 100
None
2: SPARQL Query Tool on data 1
101 lines
format: txt, database: ?
Info: Execute SPARQL query. The endpoint is http://open-biomed.org:8890/sparql/.
?s ?p ?o
<http://bio2rdf.org/affymetrix:1007_s_at> <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> <http://bio2rdf.org/ns/affymetrix#Probeset>
<http://bio2rdf.org/affymetrix:1007_s_at> <http://www.w3.org/2000/01/rdf-schema#label> "DDR1"
<http://bio2rdf.org/affymetrix:1007_s_at> <http://bio2rdf.org/affymetrix_resource:xSpecies_Scientific_Name> <http://bio2rdf.org/taxon:9606>
<http://bio2rdf.org/affymetrix:1007_s_at> <http://bio2rdf.org/affymetrix_resource:Sequence_Type> "Exemplar sequence"
<http://bio2rdf.org/affymetrix:1007_s_at> <http://bio2rdf.org/affymetrix_resource:Sequence_Source> "Affymetrix Proprietary Database"
3: Inspecting predicates
3 lines
format: txt, database: ?
Info: uploaded txt file
select distinct ?p where {
<http://bio2rdf.org/affymetrix:1007_s_at> ?p ?o .
} LIMIT 1000
プレディケイトを列挙する。
4: SPARQL Query Tool on data 3
41 lines
format: txt, database: ?
Info: Execute SPARQL query. The endpoint is http://open-biomed.org:8890/sparql/.
?p
<http://www.w3.org/1999/02/22-rdf-syntax-ns#type>
<http://www.w3.org/2000/01/rdf-schema#label>
<http://bio2rdf.org/affymetrix_resource:xSpecies_Scientific_Name>
<http://bio2rdf.org/affymetrix_resource:Sequence_Type>
<http://bio2rdf.org/affymetrix_resource:Sequence_Source>
とある affy probeset の述語
5: casting
5 lines
format: txt, database: ?
Info: uploaded txt file
select * where {
?prob a <http://bio2rdf.org/ns/affymetrix#Probeset> .
?prob <http://open-biomed.org/BH11Ujicha/ExprsFc_Moderate_Control> ?ratio .
FILTER (xsd:float(?ratio) > 2.0)
} LIMIT 1000
型キャストを試す。
6: SPARQL Query Tool on data 5
85 lines
format: txt, database: ?
Info: Execute SPARQL query. The endpoint is http://open-biomed.org:8890/sparql/.
?prob ?ratio
<http://bio2rdf.org/affymetrix:217536_x_at> "2.83694726518681"
<http://bio2rdf.org/affymetrix:206278_at> "2.4879083125559"
<http://bio2rdf.org/affymetrix:202133_at> "2.00782905214837"
<http://bio2rdf.org/affymetrix:217784_at> "2.42790372600543"
<http://bio2rdf.org/affymetrix:222196_at> "2.26550718759286"
7: Query1
7 lines
format: txt, database: ?
Info: uploaded txt file
select * where {
?prob a <http://bio2rdf.org/ns/affymetrix#Probeset> .
?prob <http://open-biomed.org/BH11Ujicha/ExprsFc_Moderate_Control> ?ratio .
FILTER (xsd:float(?ratio) >= 2.0)
?prob <http://open-biomed.org/BH11Ujicha/ExprsPv_Severe_Control> ?pvalue .
FILTER (xsd:float(?pvalue) <= 0.0001)
* 遺伝子発現で深刻なアルツハイマー病死後脳と健常者死後脳で - 2倍以上の倍率変化があるプローブセットで : bh11ujicha:ExprsFc_Severe_Controlで2.0以上 - p < 0.0001以下のプローブセットで : bh11ujicha:ExprsPv_Severe_Controlで0.0001以下
8: SPARQL Query Tool on data 7
4 lines
format: txt, database: ?
Info: Execute SPARQL query. The endpoint is http://open-biomed.org:8890/sparql/.
?prob ?ratio ?pvalue
<http://bio2rdf.org/affymetrix:206278_at> "2.4879083125559" "3.88457568550016E-5"
<http://bio2rdf.org/affymetrix:202018_s_at> "2.21567511382248" "3.04985863662882E-5"
<http://bio2rdf.org/affymetrix:217675_at> "2.36253204455268" "2.89996858591752E-5"
9: Query2
8 lines
format: txt, database: ?
Info: uploaded txt file
select distinct ?prob where {
?prob a <http://bio2rdf.org/ns/affymetrix#Probeset> .
{ ?prob <http://bio2rdf.org/affymetrix_resource:Pathway> "Apoptosis_KEGG". }
UNION
{ ?prob <http://bio2rdf.org/affymetrix_resource:Pathway> "Apoptosis // GenMAPP". }
UNION
* パスウェイでKEGG, GenMAPPのパスウェイデータベースで - アポトーシスのパスウェイにのっているプローブセット : で"Apoptosis_KEGG"、"Apoptosis // GenMAPP", "Apoptosis_GenMAPP"
10: SPARQL Query Tool on data 9
143 lines
format: txt, database: ?
Info: Execute SPARQL query. The endpoint is http://open-biomed.org:8890/sparql/.
?prob
<http://bio2rdf.org/affymetrix:1729_at>
<http://bio2rdf.org/affymetrix:1861_at>
<http://bio2rdf.org/affymetrix:200796_s_at>
<http://bio2rdf.org/affymetrix:200797_s_at>
<http://bio2rdf.org/affymetrix:200798_x_at>
11: Query3
5 lines
format: txt, database: ?
Info: uploaded txt file
select distinct ?prob where {
?prob a <http://bio2rdf.org/ns/affymetrix#Probeset> .
?prob <http://open-biomed.org/BH11Ujicha/PubMed> ?coo .
FILTER (?coo = "0")
}
* PubMedの共起情報で - 共起がない、すなわち共起回数が0のプローブセット : bh11ujicha:PubMedで0
12: SPARQL Query Tool on data 11
10,001 lines
format: txt, database: ?
Info: Execute SPARQL query. The endpoint is http://open-biomed.org:8890/sparql/.
?prob
<http://bio2rdf.org/affymetrix:1053_at>
<http://bio2rdf.org/affymetrix:121_at>
<http://bio2rdf.org/affymetrix:1255_g_at>
<http://bio2rdf.org/affymetrix:1294_at>
<http://bio2rdf.org/affymetrix:1320_at>
13: Query1+2+3
14 lines
format: txt, database: ?
Info: uploaded txt file
select * where {
?prob a <http://bio2rdf.org/ns/affymetrix#Probeset> .
?prob <http://open-biomed.org/BH11Ujicha/ExprsFc_Moderate_Control> ?ratio .
FILTER (xsd:float(?ratio) >= 2.0)
?prob <http://open-biomed.org/BH11Ujicha/ExprsPv_Severe_Control> ?pvalue .
FILTER (xsd:float(?pvalue) <= 0.0001)
SPAQRLクエリ例 * 遺伝子発現で深刻なアルツハイマー病死後脳と健常者死後脳で - 2倍以上の倍率変化があるプローブセットで : bh11ujicha:ExprsFc_Severe_Controlで2.0以上 - p < 0.0001以下のプローブセットで : bh11ujicha:ExprsPv_Severe_Controlで0.0001以下 * パスウェイでKEGG, GenMAPPのパスウェイデータベースで - アポトーシスのパスウェイにのっているプローブセット : で"Apoptosis_KEGG"、"Apoptosis // GenMAPP", "Apoptosis_GenMAPP" * PubMedの共起情報で - 共起がない、すなわち共起回数が0のプローブセット : bh11ujicha:PubMedで0 を同時に満たすプローブセットを抽出する。
14: Query1+2+3 w/o FILTER
11 lines
format: txt, database: ?
Info: uploaded txt file
select * where {
?prob a <http://bio2rdf.org/ns/affymetrix#Probeset> .
?prob <http://open-biomed.org/BH11Ujicha/ExprsFc_Moderate_Control> ?ratio .
?prob <http://open-biomed.org/BH11Ujicha/ExprsPv_Severe_Control> ?pvalue .
{ ?prob <http://bio2rdf.org/affymetrix_resource:Pathway> "Apoptosis_KEGG". }
FILTER無しで値を見るクエリ(100個まで)
15: SPARQL Query Tool on data 13
1 lines
format: txt, database: ?
Info: Execute SPARQL query. The endpoint is http://open-biomed.org:8890/sparql/.
?prob ?ratio ?pvalue ?coo
16: SPARQL Query Tool on data 14
101 lines
format: txt, database: ?
Info: Execute SPARQL query. The endpoint is http://open-biomed.org:8890/sparql/.
?prob ?ratio ?pvalue ?coo
<http://bio2rdf.org/affymetrix:1729_at> "1.0408978933254" "0.613126419243369" "3"
<http://bio2rdf.org/affymetrix:1861_at> "1.09012599151122" "0.318770618857425" "26"
<http://bio2rdf.org/affymetrix:200796_s_at> "1.03061072922342" "0.71660736435848" "1"
<http://bio2rdf.org/affymetrix:200797_s_at> "1.09949395221536" "0.177073791679756" "1"
<http://bio2rdf.org/affymetrix:200798_x_at> "0.91987175381177" "0.949829291388054" "1"