Oryza Sativa QTLs and genes retrieval from TropGene, Gramene and Ensembl

None

/default:methodResponse/default:return
/default:methodResponse/default:return
/default:methodResponse/default:return
List output=new LinkedList();
List qtl_id=new LinkedList();
for(int i=0;i11){
				if(end-start100){
					if(end-start
/default:methodResponse/default:return
/default:methodResponse/default:return
/default:methodResponse/default:return
/default:methodResponse/default:return
List output=new LinkedList();
List qtl_id=new LinkedList();
for(int i=0;i11){
				if(end-start100){
					if(end-start
String commons_qtl_informations="\"chromosome\" \"gramene_position\" \"tropgene_position\"\n";
String chromosome="";
for(int i=0;igramene_start&&tropgene_stopgramene_stop){
			commons_qtl_informations+=chromosome+" ";
			commons_qtl_informations+=Integer.valueOf(tropgene_start.intValue())+":"+Integer.valueOf(tropgene_stop.intValue())+" ";
			commons_qtl_informations+=Integer.valueOf(gramene_start.intValue())+":"+Integer.valueOf(gramene_stop.intValue())+"\n";
		}
	}
}

Name	Description
Ontology_concept_term
max_qtl_size

Name	Type	Description
gramene_ontology_concept2identifier	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_gramene_marker_ontology_concept_term_identifier?wsdl Wsdl Operation method
gramene_ontology_concept2identifier_input	xmlsplitter
XPath_Service	xpath	Xpath Expression /default:methodResponse/default:return
gramene_identifier2sequence_position	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_gramene_marker_identifier_sequence_position?wsdl Wsdl Operation method
gramene_identifier2sequence_position_input	xmlsplitter
gramene_identifier2chromosome_name	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_gramene_marker_identifier_chromosome_name?wsdl Wsdl Operation method
gramene_identifier2chromosome_name_input	xmlsplitter
XPath_Service_4	xpath	Xpath Expression /default:methodResponse/default:return
XPath_Service_3	xpath	Xpath Expression /default:methodResponse/default:return
gramene_merge_chromosome_and_position	beanshell	Script List output=new LinkedList(); List qtl_id=new LinkedList(); for(int i=0;i11){ if(end-start100){ if(end-start
gramene_identifier2qtl_accession	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_gramene_marker_identifier_sequence_accession?wsdl Wsdl Operation method
gramene_identifier2qtl_accession_input	xmlsplitter
XPath_Service_2	xpath	Xpath Expression /default:methodResponse/default:return
osativa_eg_gene	biomart
tropgeneRice_ontology_concept_term2QTL	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_TROPGENE_RICE_ontology_concept_term_quantitative_trait_locus?wsdl Wsdl Operation method
tropgeneRice_ontology_concept_term2QTL_input	xmlsplitter
tropgeneRice_QTL2chromosome	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_TROPGENE_RICE_quantitative_trait_locus_chromosome_name?wsdl Wsdl Operation method
XPath_Service_5	xpath	Xpath Expression /default:methodResponse/default:return
XPath_Service_2_2	xpath	Xpath Expression /default:methodResponse/default:return
tropgeneRice_QTL2sequence_position	wsdl	Wsdl http://gohelle.cirad.fr:8080/BioSemantic_webapp/services/get_medoc_TROPGENE_RICE_quantitative_trait_locus_sequence_position?wsdl Wsdl Operation method
XPath_Service_4_2	xpath	Xpath Expression /default:methodResponse/default:return
tropgeneRice_QTL2chromosome_input	xmlsplitter
tropgeneRice_QTL2sequence_position_input	xmlsplitter
osativa_eg_gene_2	biomart
tropgene_merge_chromosome_and_position	beanshell	Script List output=new LinkedList(); List qtl_id=new LinkedList(); for(int i=0;i11){ if(end-start100){ if(end-start
qtl_with_common_positions	beanshell	Script String commons_qtl_informations="\"chromosome\" \"gramene_position\" \"tropgene_position\"\n"; String chromosome=""; for(int i=0;igramene_start&&tropgene_stopgramene_stop){ commons_qtl_informations+=chromosome+" "; commons_qtl_informations+=Integer.valueOf(tropgene_start.intValue())+":"+Integer.valueOf(tropgene_stop.intValue())+" "; commons_qtl_informations+=Integer.valueOf(gramene_start.intValue())+":"+Integer.valueOf(gramene_stop.intValue())+"\n"; } } }

Name	Inputs	Outputs
gramene_merge_chromosome_and_position	positions_input chromosome_input max_qtl_size qtl_id_input	output qtl_id
tropgene_merge_chromosome_and_position	positions_input chromosome_input max_qtl_size qtl_id_input	output qtl_id
qtl_with_common_positions	gramene_data tropgene_data	commons_qtl_informations

Name	Description
qtl_accession_gramene
Ensembl_gene_gramene
Ensembl_gene_tropgene
qtl_accession_tropgene
common_qtl_informations
qtl_position_tropgene
qtl_position_gramene

Source	Sink
gramene_ontology_concept2identifier_input:output	gramene_ontology_concept2identifier:parameters
Ontology_concept_term	gramene_ontology_concept2identifier_input:input
gramene_ontology_concept2identifier:parameters	XPath_Service:xml_text
gramene_identifier2sequence_position_input:output	gramene_identifier2sequence_position:parameters
XPath_Service:nodelist	gramene_identifier2sequence_position_input:input
gramene_identifier2chromosome_name_input:output	gramene_identifier2chromosome_name:parameters
XPath_Service:nodelist	gramene_identifier2chromosome_name_input:input
gramene_identifier2chromosome_name:parameters	XPath_Service_4:xml_text
gramene_identifier2sequence_position:parameters	XPath_Service_3:xml_text
XPath_Service_3:nodelist	gramene_merge_chromosome_and_position:positions_input
XPath_Service_4:nodelist	gramene_merge_chromosome_and_position:chromosome_input
max_qtl_size	gramene_merge_chromosome_and_position:max_qtl_size
XPath_Service_2:nodelist	gramene_merge_chromosome_and_position:qtl_id_input
gramene_identifier2qtl_accession_input:output	gramene_identifier2qtl_accession:parameters
XPath_Service:nodelist	gramene_identifier2qtl_accession_input:input
gramene_identifier2qtl_accession:parameters	XPath_Service_2:xml_text
gramene_merge_chromosome_and_position:output	osativa_eg_gene:osativa_eg_gene.chromosomal_region_filter
tropgeneRice_ontology_concept_term2QTL_input:output	tropgeneRice_ontology_concept_term2QTL:parameters
Ontology_concept_term	tropgeneRice_ontology_concept_term2QTL_input:input
tropgeneRice_QTL2chromosome_input:output	tropgeneRice_QTL2chromosome:parameters
tropgeneRice_ontology_concept_term2QTL:parameters	XPath_Service_5:xml_text
tropgeneRice_QTL2chromosome:parameters	XPath_Service_2_2:xml_text
tropgeneRice_QTL2sequence_position_input:output	tropgeneRice_QTL2sequence_position:parameters
tropgeneRice_QTL2sequence_position:parameters	XPath_Service_4_2:xml_text
XPath_Service_5:nodelist	tropgeneRice_QTL2chromosome_input:input
XPath_Service_5:nodelist	tropgeneRice_QTL2sequence_position_input:input
tropgene_merge_chromosome_and_position:output	osativa_eg_gene_2:osativa_eg_gene.chromosomal_region_filter
XPath_Service_2_2:nodelist	tropgene_merge_chromosome_and_position:chromosome_input
XPath_Service_4_2:nodelist	tropgene_merge_chromosome_and_position:positions_input
max_qtl_size	tropgene_merge_chromosome_and_position:max_qtl_size
XPath_Service_5:nodelist	tropgene_merge_chromosome_and_position:qtl_id_input
gramene_merge_chromosome_and_position:output	qtl_with_common_positions:gramene_data
tropgene_merge_chromosome_and_position:output	qtl_with_common_positions:tropgene_data
gramene_merge_chromosome_and_position:qtl_id	qtl_accession_gramene
osativa_eg_gene:osativa_eg_gene	Ensembl_gene_gramene
osativa_eg_gene_2:osativa_eg_gene	Ensembl_gene_tropgene
tropgene_merge_chromosome_and_position:qtl_id	qtl_accession_tropgene
qtl_with_common_positions:commons_qtl_informations	common_qtl_informations
tropgene_merge_chromosome_and_position:output	qtl_position_tropgene
gramene_merge_chromosome_and_position:output	qtl_position_gramene

Oryza Sativa QTLs and genes retrieval from TropGene, Gramene and Ensembl

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