Workflow Entry: Sponge into Virtuoso triplestore the needed ressource from PubMed [myexperiment:pubmed_step3_describe]

Created at: 17/11/09 @ 07:09:01 Last updated: 27/11/09 @ 03:32:15

Version 2 (latest) (of 2)

Version created on: 17/11/09 @ 07:09:01 by: Francois Belleau | Revision comments Expand

Last edited on: 27/11/09 @ 03:32:17 by: Francois Belleau

Title: Sponge into Virtuoso triplestore the needed ressource from PubMed [myexperiment:pubmed_step3_describe]

Type: Taverna 2

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query = labrie,f query = labrie

query = labrie,f query = labrie query = h1n1

query = morissette,j query = labrie,f query = labrie query = h1n1

Get a list of paper from pubmed.

Option 1:

Copy and paste this link into File > 'Open workflow location...'
http://www.myexperiment.org/workflows/958/download?version=2
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Authors (1)

Titles (7)

Descriptions (4)

Inputs (3)

Processors (6)

Name	Type	Description
Insert_ntriples	workflow
Pubmed_xml_rdfiser	workflow
SPARQL_query	workflow
Split_string_into_string_list_by_regular_expression	localworker
semicolon	stringconstant
Count	workflow

Beanshells (14)

Name	Inputs	Outputs
SPARQL_insert_ntriples	ntriples graph sparql_host sparql_port	html
Concat_log_message	msg graph sparql_url subject	log
Split_sparql_url	sparql_url	host port
First_subject	ntriples	subject
Create_directory	directory	log directory_copy
Get_NCBI_XML_By_ID_Namespace	id rettype retmode namespace	outputText
split_bmuri	bmuri	namespace id
build_xml_filename	path namespace id	xml_filename
test_if_filename_exist	filename id	id_copy
build_filename_nt	filename_xml	filename_nt
test_file_exists	filename	filename_xml
Filter_list_of_strings_extracting_match_to_a_regex	stringlist regex group	filteredlist count
Build_sparql_url	sparql_query sparql_endpoint graph	sparql_query_url
stringlist_count	in	out

Outputs (3)

Name	Description
o2
bio2rdf_subject_fetch_pubmed_log
o1

Datalinks (13)

Source	Sink
graph	Insert_ntriples:graph
Pubmed_xml_rdfiser:ncbi_pubmed_xml2ntriples	Insert_ntriples:ntriples
sparql_endpoint	Insert_ntriples:sparql_endpoint_url
Count:utility_stringlist_count	Pubmed_xml_rdfiser:pubmed_bmuri
sparql_endpoint	SPARQL_query:sparql_endpoint
graph	SPARQL_query:graph
Split_string_into_string_list_by_regular_expression:split	SPARQL_query:sparql_query
sparql_query	Split_string_into_string_list_by_regular_expression:string
semicolon:value	Split_string_into_string_list_by_regular_expression:regex
SPARQL_query:sparql_query_bmuri_list	Count:stringlist
Pubmed_xml_rdfiser:ncbi_pubmed_xml2ntriples	o2
Insert_ntriples:sparql_insert_ntriples_log	bio2rdf_subject_fetch_pubmed_log
SPARQL_query:sparql_query_bmuri_list	o1