Bio2RDF: CPath search, rdfise and load demo (step 2)
Created: 2009-02-19 07:14:23
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Authors (1)
Titles (5)
| Bio2RDF: CPath search, rdfise and load demo (step 2) |
| Bio2RDF: Bind search, rdfise and load demo |
| Bio2RDF: CPath search, rdfise and load demo |
| Bind search and rdfiser demo |
| Bio2RDF Bind search and rdfiser demo |
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 . }
} |
Dependencies (0)
Processors (11)
| Name |
Type |
Description |
| genes_list |
stringconstant |
Valueakt1s1,bad,bcl2l11,cdc25c,gab1,grb7 |
| Split_string_into_string_list |
localworker |
ScriptList 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]);
}
}
|
| CPath_search |
workflow |
|
| CPath_describe |
workflow |
|
| Sesame_load_triples |
workflow |
|
| mem_rdf_db |
stringconstant |
Valuemem-rdf-db |
| from_cpath |
stringconstant |
Valuecpath: |
| cdc25c |
stringconstant |
Valuecdc25c |
| mouse |
stringconstant |
Value10090 |
| rdfxml |
stringconstant |
Valuerdfxml |
| CPath_links |
workflow |
|
Beanshells (12)
| Name |
Description |
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:string |
| genes_list:value |
Split_string_into_string_list:string |
| CPath_search:cpath_bmuris |
o1 |
| CPath_links:cpath_bmuris |
o2 |
| Sesame_load_triples:number_of_uploaded_triples |
03 |
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licensed under:
Version 1
(of 1)
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