Workflow Entry: Bio2RDF: CPath search, rdfise and load demo (step 2)

Created at: 19/02/09 @ 07:14:23

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Version created on: 19/02/09 @ 07:14:24 by: Francois Belleau | Revision comments Expand

Title: Bio2RDF: CPath search, rdfise and load demo (step 2)

Type: Taverna 2

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Workflow Components

Authors (1)

Titles (5)

Descriptions (6)

Search for a list of genes into the Pathway Commons interaction database and load the fetched triples into a triplestore. INSERT IN GRAPH <http://localhost/sesame/mem_rdf_db> { CONSTRUCT{ ?s, ?p, ?o . } FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { SELECT ?s FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { ?s, ?p, ?o . FILTER ( regex(?o, "query")) . } , ?p, ?o . } }

Search for a list of genes into the Bind interaction database and load the fetched triples into a triplestore. INSERT IN GRAPH <http://localhost/sesame/mem_rdf_db> { CONSTRUCT{ ?s, ?p, ?o . } FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { SELECT ?s FROM <http://soap.bind.ca/wsdl/bind.wsdl> WHERE { ?s, ?p, ?o . FILTER ( regex(?o, "query")) . } , ?p, ?o . } }

Search for a list of genes at Bind interaction database and load the fetched triples into a triplestore.

Search for a list of genes into the Bind interaction database and load the fetched triples into a triplestore.

Search for a list of genes into the Pathway Commons interaction database and load the fetched triples into a triplestore. INSERT IN GRAPH <http://localhost/sesame/mem_rdf_db> { CONSTRUCT{ ?s2, ?p2, ?o2 . } FROM <http://www.pathwaycommons.org/pc/webservice.do> WHERE { SELECT ?s FROM <http://www.pathwaycommons.org/pc/webservice.do> WHERE { ?s2, ?p2, ?o2 . ?s, ?p, ?o2 . FILTER ( regex(?o, "QUERY")) . } , ?p, ?o . } }

Search for a list of genes into the Pathway Commons interaction database and load the fetched triples into a triplestore. INSERT IN GRAPH <http://localhost/sesame/mem_rdf_db> { CONSTRUCT{ ?s, ?p, ?o . } FROM <http://www.pathwaycommons.org/pc/webservice.do> WHERE { SELECT ?s FROM <http://www.pathwaycommons.org/pc/webservice.do> WHERE { ?s, ?p, ?o . FILTER ( regex(?o, "QUERY")) . } , ?p, ?o . } }

Inputs (0)

Processors (11)

Name	Type	Description
genes_list	stringconstant
Split_string_into_string_list	localworker
CPath_search	workflow
CPath_describe	workflow
Sesame_load_triples	workflow
mem_rdf_db	stringconstant
from_cpath	stringconstant
cdc25c	stringconstant
mouse	stringconstant
rdfxml	stringconstant
CPath_links	workflow

Beanshells (12)

Name	Inputs	Outputs
Concatenate_pc_search_url	taxon_id query	pc_url
Filter_list_of_pc_bmuri	stringlist	cpath_bmuris
Concatenate_cpath_get_record_by_cpath_id_url	query	cpath_url
Split_bmuri	bmuri	namespace_id namespace id
Replace_namespace	string	stringReplaced
Sesame_upload_triples	triples repository input_format	html
Split_string_into_string_list	string	split
Filter_list_of_strings_extracting_msg	stringlist	filteredlist
Concatenate_two_strings	string1 string2	output
Concatenate_cpath_parents_url	query	cpath_url
Filter_list_of_pc_bmuri	stringlist	cpath_bmuris
Split_bmuri	bmuri	namespace_id namespace id

Outputs (3)

Name	Description
o1
o2
03

Datalinks (13)

Source	Sink
Split_string_into_string_list:split	CPath_search:query
mouse:value	CPath_search:taxon_id
CPath_links:cpath_bmuris	CPath_describe:cpath_bmuri
mem_rdf_db:value	Sesame_load_triples:repository
from_cpath:value	Sesame_load_triples:bmuri
rdfxml:value	Sesame_load_triples:ntriples_or_rdfxml
CPath_describe:cpath_rdf_biopax	Sesame_load_triples:triples
CPath_search:cpath_bmuris	CPath_links:cpath_bmuri
cdc25c:value	Split_string_into_string_list
genes_list:value	Split_string_into_string_list
CPath_search:cpath_bmuris	o1
CPath_links:cpath_bmuris	o2
Sesame_load_triples:number_of_uploaded_triples	03