What is known about HIV using Bio2RDF's SPARQL endpoints ?

Created: 2009-02-05 06:13:53 Last updated: 2009-02-05 06:15:22

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To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched. The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph.

Once the mashup is built, two SPARQL queries analyze the obtained graph. Finally you can submit queries to the RDF mashup about HIV as you like. Enjoy.

This is the queries present in this workflow :

CONSTRUCT {
?s ?p ?o .
}
FROM < geneid,uniprot,omim,pubmed,go >
WHERE {
?s ?p ?o .
?o bif:contains "hiv" .
}

then

SELECT * WHERE {?s ?p ?o}

then

SELECT ?type, count(*)
WHERE {
?s <rdf:type> ?type .
}

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Descriptions (6)

To answer this question Bio2RDF Atlas about mouse and human genome is searched. The selected URIs are then loaded into the local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert into the graph. Once the mashup is built, 2 sparql queries analyse the obtained graph. This is the correspondint queries : CONSTRUCT { ?s ?p ?o . } FROM < geneid,uniprot,omim,pubmed,go> WHERE { ?s ?p ?o . ?o bif:contains "hiv" . } then SELECT * WHERE {?s ?p ?o} then SELECT ?type, count(*) WHERE { ?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . }

SELECT ?type, count(*) WHERE { ?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . }

To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched. The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert into the graph. Once the mashup is built, 2 sparql queries analyse the obtained graph. Finaly you can submit queries to the RDF mashup about HIV as you like. This is the corresponding queries : CONSTRUCT { ?s ?p ?o . } FROM < geneid,uniprot,omim,pubmed,go> WHERE { ?s ?p ?o . ?o bif:contains "hiv" . } then SELECT * WHERE {?s ?p ?o} then SELECT ?type, count(*) WHERE { ?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . }

SELECT * FROM < geneid,uniprot,omim,pubmed,go> WHERE { ?s ?p ?o . ?o bif:contains "hiv" . } then SELECT * WHERE {?s ?p ?o} then SELECT ?type, count(*) WHERE { ?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . } then

To answer this question Bio2RDF Atlas about mouse and human genome sparql endpoint available at http://atlas.bio2rdf.org/sparql is searched. The selected URIs are then loaded into your local Virtuoso triplestore at http://localhost:8890/sparql. You must enable insert mode into the graph. Once the mashup is built, 2 SPARQL queries analyze the obtained graph. Finally you can submit queries to the RDF mashup about HIV as you like. This is the queries present in this workflow : CONSTRUCT { ?s ?p ?o . } FROM < geneid,uniprot,omim,pubmed,go> WHERE { ?s ?p ?o . ?o bif:contains "hiv" . } then SELECT * WHERE {?s ?p ?o} then SELECT ?type, count(*) WHERE { ?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . }

SELECT * FROM < geneid,uniprot,omim,pubmed,go> WHERE { ?s ?p ?o . ?o bif:contains "hiv" . } then SELECT ?type, count(*) WHERE { ?s <http://www.w3.org/1999/02/22-rdf-syntax-ns#type> ?type . } then

Dependencies (0)

Inputs (0)

Processors (12)

Name	Type	Description
Search_Bio2RDF_atlas	workflow
Namespace_list_to_search	stringconstant	Value geneid,uniprot,omim,pubmed,go
Searched_term	stringconstant	Value hiv
Split_string_into_list	localworker	Script List split = new ArrayList(); if (!string.equals("")) { String regexString = ","; if (regex != void) { regexString = regex; } String[] result = string.split(regexString); for (int i = 0; i < result.length; i++) { split.add(result[i]); } }
Result_limit_100	stringconstant	Value 100
Insert_triples_in_local_graph	workflow
Virtuoso_server	stringconstant	Value http://localhost:8890/
Concatenate_two_strings	localworker	Script output = string1 + string2;
Count_triples	stringconstant	Value sparql?default-graph-uri=http%3A%2F%2Flocalhost%3A8890%2Fhiv&should-sponge=&query=SELECT+count(*)+WHERE+{%3Fs+%3Fp+%3Fo}&format=text%2Fhtml&debug=on
SPARQL_query	localworker	Script URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
SPARQL_query_2	localworker	Script URL inputURL = null; if (base != void) { inputURL = new URL(new URL(base), url); } else { inputURL = new URL(url); } URLConnection con = inputURL.openConnection(); InputStream in = con.getInputStream(); InputStreamReader isr = new InputStreamReader(in); Reader inReader = new BufferedReader(isr); StringBuffer buf = new StringBuffer(); int ch; while ((ch = inReader.read()) > -1) { buf.append((char)ch); } inReader.close(); contents = buf.toString(); //String NEWLINE = System.getProperty("line.separator"); // //URL inputURL = null; //if (base != void) { // inputURL = new URL(new URL(base), url); //} else { // inputURL = new URL(url); //} //StringBuffer result = new StringBuffer(); //BufferedReader reader = new BufferedReader(new InputStreamReader(inputURL.openStream())); //String line = null; //while ((line = reader.readLine()) != null) { // result.append(line); // result.append(NEWLINE); //} // //contents = result.toString();
Count_type	stringconstant	Value sparql?default-graph-uri=http%3A%2F%2Flocalhost%3A8890%2Fhiv&should-sponge=&query=SELECT+%3Ftype%2C+count(*)+%0D%0AWHERE+{%0D%0A%3Fs++%3Ftype+.%0D%0A}&format=text%2Fhtml&debug=on

Beanshells (4)

Name	Inputs	Outputs
Search_Atlas	sparql_endpoint term namespace limit	sparql_xml
insert_n3_into_graph	host port n3 graph	html
describe_uri	sparql_endpoint bmuri	n3
triples_inserted	string bmuri	result

Outputs (4)

Name	Description
bmuris
inserted
count
type_count

Datalinks (16)

Source	Sink
Split_string_into_list:split	Search_Bio2RDF_atlas:namespace
Searched_term:value	Search_Bio2RDF_atlas:term
Result_limit_100:value	Search_Bio2RDF_atlas:limit
Namespace_list_to_search:value	Split_string_into_list:string
Search_Bio2RDF_atlas:bmuris	Insert_triples_in_local_graph:bmuri
Concatenate_two_strings:output	Insert_triples_in_local_graph:graph
Searched_term:value	Concatenate_two_strings:string2
Virtuoso_server:value	Concatenate_two_strings:string1
Virtuoso_server:value	SPARQL_query:base
Count_triples:value	SPARQL_query:url
Count_type:value	SPARQL_query_2:url
Virtuoso_server:value	SPARQL_query_2:base
Search_Bio2RDF_atlas:bmuris	bmuris
Insert_triples_in_local_graph:triples_inserted	inserted
SPARQL_query:contents	count
SPARQL_query_2:contents	type_count

Coordinations (2)

Controller	Target
SPARQL_query	SPARQL_query_2
Insert_triples_in_local_graph	SPARQL_query

Information Workflow Type

Taverna 2

Information Uploader

Francois Belleau

Information License

All versions of this Workflow are licensed under:

Information Version 2 (latest) (of 2)

Information Credits (1)

(People/Groups)

Francois Belleau

Information Attributions (0)

(Workflows/Files)

None

Information Tags (8)

Uploader tags

bio2rdf
|
geneid
|
hiv
|
OMIM
|
pubmed
|
sparql
|
uniprot
|
virtuoso

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Information Favourited By (1)

David De Roure

Information Statistics

4380 viewings

2521 downloads

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Version History

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What is known about HIV using Bio2RDF's SPARQL endpoints ?

Created by Francois Belleau on Thursday 05 February 2009 05:32:49 (UTC)

Last edited by Francois Belleau on Thursday 05 February 2009 05:45:31 (UTC)
What is known about HIV using Bio2RDF's SPARQL endpoints ?

Created by Francois Belleau on Thursday 05 February 2009 06:13:53 (UTC)

Last edited by Francois Belleau on Thursday 05 February 2009 06:15:23 (UTC)

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Jun Zhao

Dear Francois,

Firstly, congratulation on the great job! I have been looking forward to this for a long time, a binding between Bio2RDF and Taverna.

I have download your workflow and tried to run it using Taverna 2.0. However, no results were ever returned to me. I digged into the workflow and found that the value given to the string processor "virtuoso_server" is http://localhost:8890. Is this the reason why I got no results back? What should I fix to make the workflow run on my local desktop?

Thanks,

Jun

Benjamin Good

Jun,

I think the workflow assumes that you have a triple-store running locally. Basically it goes and gets the data for you, sticks it into your server, and then lets you query it.

Anyone have this working?

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What is known about HIV using Bio2RDF's SPARQL endpoints ?

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