On 07/11/13 02:55, Adeeb Noor wrote:
On Wed, Nov 6, 2013 at 5:23 AM, Andy Seaborne <a...@apache.org
<mailto:a...@apache.org>> wrote:
On 06/11/13 00:31, Adeeb Noor wrote:
Any help with my question please.
AdeeB
On Mon, Nov 4, 2013 at 1:48 PM, Adeeb Noor
<adeeb.n...@colorado.edu <mailto:adeeb.n...@colorado.edu>> wrote:
Hi Andy:
Thanks for the response.
My TDB is on my hard drive with 15GB size wise.
How many triples?
*The number of triples is: 37397456*
And how much of the DB does the SELECT query match?
What's SELECT (count(*) AS ?c) ....
What's SELECT (count(distinct *) AS ?c) ....
No response?
This is asking what proportion of the DB is being extracted.
On the current information, I'd guess the system starts swapping due to
a large construct graph but that's just a guess.
Streaming the execConstructTriples to a disk file may help.
*Here is the SELECT I want to apply to generate my subgraph:*
Long, incomplete query.
Try reordering the FILTERs putting the || ones last. May make no
difference but without sizing figures, only you can know.
Andy
CONSTRUCT
{
ddidd:C0004057 ?r ?disease1 .
?disease1 ?r10 ddidd:C0004057 .
?disease1 ?r1 ?omim1 .
?omim1 ?r11 ?disease1 .
?omim1 ?r2 ?w .
?w ?r12 ?omim1 .
?omim1 ?r3 ?bp .
?bp ?r13 ?omim1 .
?omim1 ?r4 ?genotypePhenotype .
?genotypePhenotype ?r14 ?omim1 .
?omim1 ?r5 ?gene.
?gene ?r15 ?omim1 .
?w ?r6 ?gene2.
?gene2 ?r16 ?w .
?omim1 ?r7 ?gene3 .
?gene3 ?r17 ?omim1.
?gene3 ?r8 ?bp2 .
?bp2 ?r18 ?gene3 .
?gene3 ?r9 ?genotypePhenotype2 .
?genotypePhenotype2 ?r19 ?gene3 .
?gene a ?gCLASS.
?gene2 a ?g2CLASS.
?gene3 a ?g3CLASS.
?genotypePhenotype a ?genotypePhenotypeCLASS .
?genotypePhenotype2 a ?genotypePhenotype2CLASS.
?w a ?wCLASS .
?omim1 a ?omimt1 .
?bp a ?bpCLASS .
?bp2 a ?bp2CLASS .
ddidd:C0004057 ddids:label ?ldrug1 .
?disease1 ddids:label ?ldisease1 .
?omim1 ddids:label ?lomim1 .
?w ddids:label ?lw .
?bp ddids:label ?lbp .
?genotypePhenotype ddids:label ?lgenotypePhenotype .
?gene ddids:label ?lgene .
?gene2 ddids:label ?lgene2 .
?gene3 ddids:label ?lgene3 .
?bp2 ddids:label ?lbp2 .
?genotypePhenotype2 ddids:label ?lgenotypePhenotype2 .
}WHERE{
ddidd:C0004057 ?r ?disease1 .
?disease1 ?r10 ddidd:C0004057 .
?disease1 ?r1 ?omim1 .
?omim1 ?r11 ?disease1 .
?omim1 ?r2 ?w .
?w ?r12 ?omim1 .
?omim1 ?r3 ?bp .
?bp ?r13 ?omim1 .
?omim1 ?r4 ?genotypePhenotype .
?genotypePhenotype ?r14 ?omim1 .
?omim1 ?r5 ?gene.
?gene ?r15 ?omim1 .
?w ?r6 ?gene2.
?gene2 ?r16 ?w .
?omim1 ?r7 ?gene3 .
?gene3 ?r17 ?omim1.
?gene3 ?r8 ?bp2 .
?bp2 ?r18 ?gene3 .
?gene3 ?r9 ?genotypePhenotype2 .
?genotypePhenotype2 ?r19 ?gene3 .
?gene a ?gCLASS.
?gene2 a ?g2CLASS.
?gene3 a ?g3CLASS.
?genotypePhenotype a ?genotypePhenotypeCLASS .
?genotypePhenotype2 a ?genotypePhenotype2CLASS.
?w a ?wCLASS .
?omim1 a ?omimt1 .
?bp a ?bpCLASS .
?bp2 a ?bp2CLASS .
ddidd:C0004057 ddids:label ?ldrug1 .
?disease1 ddids:label ?ldisease1 .
?omim1 ddids:label ?lomim1 .
?w ddids:label ?lw .
?bp ddids:label ?lbp .
?genotypePhenotype ddids:label ?lgenotypePhenotype .
?gene ddids:label ?lgene .
?gene2 ddids:label ?lgene2 .
?gene3 ddids:label ?lgene3 .
?bp2 ddids:label ?lbp2 .
?genotypePhenotype2 ddids:label ?lgenotypePhenotype2 .
FILTER ( ?r = ddids:may_treat || ?r = ddids:may_prevent )
FILTER (?omimt1 = ddids:gene || ?omimt1 = ddids:genotypePhenotype )
FILTER (?wCLASS = ddids:pathway || ?r2 = ddids:gene_is_element_in_pathway )
FILTER (?bpCLASS = ddids:biologicalProcess )
FILTER (?bp2CLASS = ddids:biologicalProcess )
FILTER (?genotypePhenotypeCLASS = ddids:genotypePhenotype )
FILTER (?genotypePhenotype2CLASS = ddids:genotypePhenotype )
FILTER (?gCLASS = ddids:gene )
FILTER (?g2CLASS = ddids:gene )
FILTER (?g3CLASS = ddids:gene )
}
We still know little about your setup.
and my PC is Mac Pro with
2.4 GHZ and 4GB of memory.
Java 32 bit or 64 bit?
*java version "1.6.0_65"*
*Java(TM) SE Runtime Environment (build 1.6.0_65-b14-462-11M4609)*
*Java HotSpot(TM) 64-Bit Server VM (build 20.65-b04-462, mixed mode)*
I was not able to use QueryExecution.__execConstructTriples as
it returnees an iterator and I want to save the subgraph
into a new TDB .
Why is that a problem? Add them to a TDB database.
* I will try it and let you know. *
Or even use a SPARQL Update operation.
*SPARQL update if I am not wrong will not work in my case as I want to
create a subgraph from the whole data and store it in a new TDB. We can
use only the SPARQL update if we can add data on the original TDB; AM I
right ? *
**
Here is my code below:
FileLoader fileLoader = new
FileLoader("src/DDICONSTRUCT.__tql");
String q = fileLoader.loadAll();
Query query = QueryFactory.create(q) ;
QueryExecution qexec =
QueryExecutionFactory.create(__query, data.tdb);
Model constructModel = qexec.execConstruct();
The program has been running for almost a day now, let me
know if there is
something wrong or if there is an alternative to CONSTRUCT
thing.
On Sun, Nov 3, 2013 at 12:59 PM, Andy Seaborne
<a...@apache.org <mailto:a...@apache.org>> wrote:
On 03/11/13 07:05, Adeeb Noor wrote:
Hi Andy:
I did figure it out, however it takes to much time
(CONSTRUCT) to finish
as
my query is complex. Is that something normal ? in
fact, it is still
running
Hard to tell - it depends on many factors such as
machine setup, where
the data is stored, structure and volume of your data
Try
QueryExecution.__execConstructTriples
Andy
AdeeB
On Sat, Nov 2, 2013 at 9:56 AM, Adeeb Noor
<adeeb.n...@colorado.edu
<mailto:adeeb.n...@colorado.edu>>
wrote:
Hi Andy:
Thanks for the quick response. I tried CONSTRUCT
and it did work out.
But
how can I reformat such a query to CONSTRUCT one:
SELECT DISTINCT *
{
?ddi ddids:has_association ?c .
?ddi ddids:has_association ?c2 .
?c ddids:chemical_or_drug___affects_gene_product
?omim .
?omim ddids:gene_product_encoded_by___gene ?g .
?g ddids:gene_plays_role_in___process ?w .
?g ddids:gene_plays_role_in___process ?bp .
?bp ddids:process_involves_gene ?g2 .
?g2 ddids:gene_plays_role_in___process ?bp2 .
where I need each variable ( for example ?w, ?bp
, etc) to be a new
resources.
Thanks
On Sat, Nov 2, 2013 at 6:41 AM, Andy Seaborne
<a...@apache.org <mailto:a...@apache.org>> wrote:
You need to use a CONSTRUCT query, not a
SELECT one.
outputAsRDF encodes the result set (i.e. the
table) as RDF - it is not
the datamodel of the original data.
CONSTRUCT allows you to create one RDF graph
from data from another.
See also SPARQL Update for doign that from
one graph to another in the
same database.
Andy
On 02/11/13 05:35, Adeeb Noor wrote:
Hi guys:
I would like to save my SPARQL result
coming from ResultSet into new
rdf.
(new rdf resources) cause I want to do
more work on this subgraph and
it
has to be in the original rdf format.
I tried outputAsRDF function and it
worked however the result I got
the
following:
<rdf:Description rdf:nodeID="A5">
<rs:value rdf:resource="
https://csel.cs.colorado.edu/~__noor/Drug_Disease_ontology/
<https://csel.cs.colorado.edu/~noor/Drug_Disease_ontology/>
DDID.owl#genotypePhenotype
"/>
<rs:variable>omimt</rs:__variable>
</rdf:Description>
<rdf:Description rdf:nodeID="A6">
<rs:value rdf:resource="
https://csel.cs.colorado.edu/~__noor/Drug_Disease_ontology/
<https://csel.cs.colorado.edu/~noor/Drug_Disease_ontology/>
DDID.rdf#C0007589
"/>
<rs:variable>w</rs:variable>
</rdf:Description>
<rdf:Description rdf:nodeID="A7">
<rs:binding rdf:nodeID="A8"/>
<rs:binding rdf:nodeID="A9"/>
<rs:binding rdf:nodeID="A10"/>
<rs:binding rdf:nodeID="A11"/>
<rs:binding rdf:nodeID="A12"/>
<rs:binding rdf:nodeID="A13"/>
<rs:binding rdf:nodeID="A14"/>
<rs:binding rdf:nodeID="A15"/>
<rs:binding rdf:nodeID="A16"/>
<rs:binding rdf:nodeID="A17"/>
<rs:binding rdf:nodeID="A18"/>
<rs:binding rdf:nodeID="A19"/>
<rs:binding rdf:nodeID="A20"/>
<rs:binding rdf:nodeID="A21"/>
<rs:binding rdf:nodeID="A22"/>
<rs:binding rdf:nodeID="A23"/>
<rs:binding rdf:nodeID="A24"/>
<rs:binding rdf:nodeID="A25"/>
<rs:binding rdf:nodeID="A26"/>
<rs:binding rdf:nodeID="A27"/>
</rdf:Description>
how I can remove this nodes things and
make it something like:
<rdf:Description rdf:about="
https://csel.cs.colorado.edu/~__noor/Drug_Disease_ontology/
<https://csel.cs.colorado.edu/~noor/Drug_Disease_ontology/>
DDID.rdf#C3229174">
<j.0:label>Cytra-K Oral
Product</j.0:label>
<rdf:type rdf:resource="
https://csel.cs.colorado.edu/~__noor/Drug_Disease_ontology/
<https://csel.cs.colorado.edu/~noor/Drug_Disease_ontology/>
DDID.owl#chemical
"/>
</rdf:Description>
please help me out
--
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303 <tel:571-484-3303>
Email: adeeb.n...@colorado.edu
<mailto:adeeb.n...@colorado.edu>
--
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303 <tel:571-484-3303>
Email: adeeb.n...@colorado.edu <mailto:adeeb.n...@colorado.edu>
--
Adeeb Noor
Ph.D. Candidate
Dept of Computer Science
University of Colorado at Boulder
Cell: 571-484-3303
Email: adeeb.n...@colorado.edu <mailto:adeeb.n...@colorado.edu>
