ChEBI mashup from searched string

Created: 2010-04-29 14:09:37

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A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint.

First a full text search query is done, then we do a reverse link query to get all the related topic. Finally with a describe queries we obtain the complete graph of each topic.

The ntriples result is a mashup of what is known about this searched topic form ChEBI. This graph can then be loaded in a triplestore for further exploration.

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Workflow Components

Authors (3)

Titles (1)

Descriptions (2)

Dependencies (0)

Inputs (1)

Name	Description
searched_string	A demo showing hoe to use SOAP services from Bio2RDF ChEBI SPARQL endpoint. search for fructose or keto-d-fructose or whatever you like.

Processors (14)

Name	Type	Description
ChEBI_Describe	wsdl	Wsdl http://quebec.chebi.bio2rdf.org/wsdl Wsdl Operation ChEBI_Describe
ChEBI_Describe_input	xmlsplitter
ChEBI_Describe_output	xmlsplitter
ChEBI_Link	wsdl	Wsdl http://quebec.chebi.bio2rdf.org/wsdl Wsdl Operation ChEBI_Link
ChEBI_Link_input	xmlsplitter
ChEBI_Link_output	xmlsplitter
ChEBI_Search	wsdl	Wsdl http://quebec.chebi.bio2rdf.org/wsdl Wsdl Operation ChEBI_Search
ChEBI_Search_input	xmlsplitter
ChEBI_Search_output	xmlsplitter
Merge_String_List_to_a_String	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();
ntriples2subjects	workflow
ntriples2subjects_2	workflow
Flatten_List	localworker	Script flatten(inputs, outputs, depth) { for (i = inputs.iterator(); i.hasNext();) { element = i.next(); if (element instanceof Collection && depth > 0) { flatten(element, outputs, depth - 1); } else { outputs.add(element); } } } outputlist = new ArrayList(); flatten(inputlist, outputlist, 1);
Merge_String_List_to_a_String_2	localworker	Script String seperatorString = "\n"; if (seperator != void) { seperatorString = seperator; } StringBuffer sb = new StringBuffer(); for (Iterator i = stringlist.iterator(); i.hasNext();) { String item = (String) i.next(); sb.append(item); if (i.hasNext()) { sb.append(seperatorString); } } concatenated = sb.toString();

Beanshells (0)

Outputs (6)

Name	Description
o1
o2
o3
o4
o5
ntriples

Datalinks (21)

Source	Sink
ChEBI_Describe_input:output	ChEBI_Describe:parameters
Flatten_List:outputlist	ChEBI_Describe_input:bm_uri
ChEBI_Describe:parameters	ChEBI_Describe_output:input
ChEBI_Link_input:output	ChEBI_Link:parameters
ntriples2subjects:bmuri_list	ChEBI_Link_input:bm_uri
ChEBI_Link:parameters	ChEBI_Link_output:input
ChEBI_Search_input:output	ChEBI_Search:parameters
searched_string	ChEBI_Search_input:query_text
ChEBI_Search:parameters	ChEBI_Search_output:input
ChEBI_Link_output:CallReturn	Merge_String_List_to_a_String:stringlist
ChEBI_Search_output:CallReturn	ntriples2subjects:ntriples
Merge_String_List_to_a_String:concatenated	ntriples2subjects_2:ntriples
ChEBI_Describe_output:CallReturn	Merge_String_List_to_a_String_2:stringlist
ntriples2subjects:bmuri_list	Flatten_List:inputlist
ntriples2subjects_2:bmuri_list	Flatten_List:inputlist
ChEBI_Search_output:CallReturn	o1
ChEBI_Link_output:CallReturn	o2
ntriples2subjects_2:bmuri_list	o3
Flatten_List:outputlist	o4
ChEBI_Describe_output:CallReturn	o5
Merge_String_List_to_a_String_2:concatenated	ntriples