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Posted to users@jena.apache.org by Marko Pance <mp...@chemaxon.com> on 2015/08/05 14:28:51 UTC
Convert .ttl turtle format file into .rdf file
Hi...
I have a .ttl file and I would like to use jena to convert it to an rdf file. Can you please advise on how to do so? Thanks!
Re: Convert .ttl turtle format file into .rdf file
Posted by "ajs6f@virginia.edu" <aj...@virginia.edu>.
Can you say a little more about these files? How large are they, and what kind of RDF is in them? Also, when you say "an rdf file", to what format are you referring? RDF/XML?
I don't know very much about the workings of 'riot', but there's not too much state involved with reading and writing RDF, although there is some.
---
A. Soroka
The University of Virginia Library
On Aug 5, 2015, at 10:30 AM, Marko Pance <mp...@chemaxon.com> wrote:
> Thanks for your response. I am using the riot utility successfully on smaller file sizes. But for large ones I get a "
>
> java.lang.OutOfMemoryError: GC overhead limit exceeded" error message. Is there a way I can increase the heap size allocated to the JVM with a command line option?
>
>
>
>
> Best,
>
> Marko
>
>
> From: ajs6f@virginia.edu
> To: users@jena.apache.org
> Sent: Wednesday, August 5, 2015 2:35:33 PM
> Subject: Re: Convert .ttl turtle format file into .rdf file
>
> You can use the utility 'riot' for this:
>
> https://jena.apache.org/documentation/io/#command-line-tools
>
> ---
> A. Soroka
> The University of Virginia Library
>
> On Aug 5, 2015, at 8:28 AM, Marko Pance <mp...@chemaxon.com> wrote:
>
>> Hi...
>>
>> I have a .ttl file and I would like to use jena to convert it to an rdf file. Can you please advise on how to do so? Thanks!
Re: Convert .ttl turtle format file into .rdf file
Posted by Andy Seaborne <an...@apache.org>.
On 06/08/15 11:00, Damian Steer wrote:
>
>> On 6 Aug 2015, at 10:13, Marko Pance <mp...@chemaxon.com> wrote:
>>
>> I'm sorry, I don't quite understand your response. Are you saying if I'd like to stream I should try using a format other than rdf/xml? In oder to do so, could I use the command of:
>>
>>
>>
>> bin/riot --out rdfthrift ~/Downloads/chembl_20.0_molecule.ttl > ~/Downloads/chembl_20.0_molecule.rdf
>
> Essentially yes.
>
> My reading of ‘—stream’ is that it is the same as ‘—out’ but with the additional requirement that the format should support streaming.
>
>> What would go in place of "rdfthrift”?
>
> Depends on what you want to do with the result. If you want rdf/xml then you can’t stream (currently). If you want another format, well, you already have turtle of course.
>
> ntriples is a solid format generally.
>
> Damian
>
Yes - that's about it.
--stream guarantees a streaming setup or says "no"
--out will stream if possible but will fall back to non-streaming
--pretty always chooses pretty.
for example, Turtle can be printed subject-block-by-subject-block
(streaming) or more pretty with embedded bnodes and lists. Some of the
pretty forms require looking through the data before starting to print.
RDF/XML, especially the RDF/XML-ABBREV is very much in the latter
category as well. It requires looking in the data first for striping,
for lists and sorting out namespace for properties. Even Jena's Basic
RDF/XML is non-streaming.
There could be a streaming RDF/XML (per triple or per subject block) but
it's going to look ugly. No RDF/XML striping (nested triples like bnode
objects), namespace attributes will need to be written on each block.
I agree with Damian - at scale N-Triples, N-Quads are useful.
(Compressed if necessary.) Everything supports them.
Andy
Re: Convert .ttl turtle format file into .rdf file
Posted by Damian Steer <d....@bris.ac.uk>.
> On 6 Aug 2015, at 10:13, Marko Pance <mp...@chemaxon.com> wrote:
>
> I'm sorry, I don't quite understand your response. Are you saying if I'd like to stream I should try using a format other than rdf/xml? In oder to do so, could I use the command of:
>
>
>
> bin/riot --out rdfthrift ~/Downloads/chembl_20.0_molecule.ttl > ~/Downloads/chembl_20.0_molecule.rdf
Essentially yes.
My reading of ‘—stream’ is that it is the same as ‘—out’ but with the additional requirement that the format should support streaming.
> What would go in place of "rdfthrift”?
Depends on what you want to do with the result. If you want rdf/xml then you can’t stream (currently). If you want another format, well, you already have turtle of course.
ntriples is a solid format generally.
Damian
--
Damian Steer
Senior Technical Researcher
Research IT
+44 (0) 117 928 7057
Re: Convert .ttl turtle format file into .rdf file
Posted by Marko Pance <mp...@chemaxon.com>.
I'm sorry, I don't quite understand your response. Are you saying if I'd like to stream I should try using a format other than rdf/xml? In oder to do so, could I use the command of:
bin/riot --out rdfthrift ~/Downloads/chembl_20.0_molecule.ttl > ~/Downloads/chembl_20.0_molecule.rdf
What would go in place of "rdfthrift"?
From: "Damian Steer" <d....@bris.ac.uk>
To: users@jena.apache.org
Sent: Wednesday, August 5, 2015 5:05:48 PM
Subject: Re: Convert .ttl turtle format file into .rdf file
> On 5 Aug 2015, at 15:30, Marko Pance <mp...@chemaxon.com> wrote:
>
> Thanks for your response. I am using the riot utility successfully on smaller file sizes. But for large ones I get a "
>
> java.lang.OutOfMemoryError: GC overhead limit exceeded" error message.
I think you’re converting to rdf/xml? That doesn’t stream, so it will take memory.
You can use —stream <format> to ensure steaming:
$ bin/riot --stream rdfxml input.rdf
Language 'RDF/XML' not registered for streaming.
Streaming languages:
TriX
Turtle
N-Quads
RDF-THRIFT
TriG
N-Triples
Non-streaming languages:
RDF/JSON
JSON-LD
RDF/XML
> Is there a way I can increase the heap size allocated to the JVM with a command line option?
$ export JVM_ARGS=-Xmx1G # or whatever you want
$ riot ….
Damian
--
Damian Steer
Senior Technical Researcher
Research IT
+44 (0) 117 928 7057
Re: Convert .ttl turtle format file into .rdf file
Posted by Damian Steer <d....@bris.ac.uk>.
> On 5 Aug 2015, at 15:30, Marko Pance <mp...@chemaxon.com> wrote:
>
> Thanks for your response. I am using the riot utility successfully on smaller file sizes. But for large ones I get a "
>
> java.lang.OutOfMemoryError: GC overhead limit exceeded" error message.
I think you’re converting to rdf/xml? That doesn’t stream, so it will take memory.
You can use —stream <format> to ensure steaming:
$ bin/riot --stream rdfxml input.rdf
Language 'RDF/XML' not registered for streaming.
Streaming languages:
TriX
Turtle
N-Quads
RDF-THRIFT
TriG
N-Triples
Non-streaming languages:
RDF/JSON
JSON-LD
RDF/XML
> Is there a way I can increase the heap size allocated to the JVM with a command line option?
$ export JVM_ARGS=-Xmx1G # or whatever you want
$ riot ….
Damian
--
Damian Steer
Senior Technical Researcher
Research IT
+44 (0) 117 928 7057
Re: Convert .ttl turtle format file into .rdf file
Posted by Marko Pance <mp...@chemaxon.com>.
Thanks for your response. I am using the riot utility successfully on smaller file sizes. But for large ones I get a "
java.lang.OutOfMemoryError: GC overhead limit exceeded" error message. Is there a way I can increase the heap size allocated to the JVM with a command line option?
Best,
Marko
From: ajs6f@virginia.edu
To: users@jena.apache.org
Sent: Wednesday, August 5, 2015 2:35:33 PM
Subject: Re: Convert .ttl turtle format file into .rdf file
You can use the utility 'riot' for this:
https://jena.apache.org/documentation/io/#command-line-tools
---
A. Soroka
The University of Virginia Library
On Aug 5, 2015, at 8:28 AM, Marko Pance <mp...@chemaxon.com> wrote:
> Hi...
>
> I have a .ttl file and I would like to use jena to convert it to an rdf file. Can you please advise on how to do so? Thanks!
Re: Convert .ttl turtle format file into .rdf file
Posted by "ajs6f@virginia.edu" <aj...@virginia.edu>.
You can use the utility 'riot' for this:
https://jena.apache.org/documentation/io/#command-line-tools
---
A. Soroka
The University of Virginia Library
On Aug 5, 2015, at 8:28 AM, Marko Pance <mp...@chemaxon.com> wrote:
> Hi...
>
> I have a .ttl file and I would like to use jena to convert it to an rdf file. Can you please advise on how to do so? Thanks!