RelEx to extract relations from papers

[Rushdi]

Hello! I have seven papers from biomedical domain in .txt format. I
would like to have the relations extracted from these papers using
RelEx for comparing its result with another relation extractor. Can
anybody help me by running RelEx over the papers and sending me the
extracted relations?

Thank you.

[Linas Vepstas]

What do you expect to do with the relations, once you have them?

--linas

[Rushdi Shams]

Hi, if I have the relations from the seven papers extracted by RelEx,
then I will compare this result with the one with my relation
extractor. I executed my relation extractor on these seven papers as
well.

Thanks for your query.

Rushdi

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[Arya Tafvizi]

We asked this on stackoverflow.com as well (http://stackoverflow.com/questions/6997576/sigsegv-when-accessing-link-parser-through-jni). Not sure which forum is best to address this question. Thanks.

 

The server I'm trying to set this up on has Red Hat Enterprise Linux Server 5.4 64-bit. We've compiled and installed Link Parser 4.6.7 (64-bit) as well as both JDK5 and JDK6 64-bit.

When calling on the library, this is the error returned:

A fatal error has been detected by the Java Runtime Environment:

SIGSEGV (0xb) at pc=0x00002aaaaefeb180, pid=24955, tid=1103116608

JRE version: 6.0_24-b07

Java VM: Java HotSpot(TM) 64-Bit Server VM (19.1-b02 mixed mode linux-amd64 compressed oops)

Problematic frame:

C [liblink-grammar.so.4+0xa180] linkage_get_num_words+0x0

This hasn't been encountered with the same Java code running on Windows, OS X, and other Linux distributions.

Also, Link Parser works fine through the provided executables (link-parser), so it doesn't appear to be a problem with compiling and installing the package.

[Linas Vepstas]

On 9 August 2011 09:18, Arya Tafvizi <arya.t...@gmail.com> wrote:
> We asked this on stackoverflow.com as well
> (http://stackoverflow.com/questions/6997576/sigsegv-when-accessing-link-parser-through-jni).
> Not sure which forum is best to address this question. Thanks.
>
> The server I'm trying to set this up on has Red Hat Enterprise Linux Server
> 5.4 64-bit. We've compiled and installed Link Parser 4.6.7 (64-bit) as well
> as both JDK5 and JDK6 64-bit.
>
> When calling on the library, this is the error returned:
>
> A fatal error has been detected by the Java Runtime Environment:
>
> SIGSEGV (0xb) at pc=0x00002aaaaefeb180, pid=24955, tid=1103116608
>
> JRE version: 6.0_24-b07
>
> Java VM: Java HotSpot(TM) 64-Bit Server VM (19.1-b02 mixed mode linux-amd64
> compressed oops)
>
> Problematic frame:
>
> C [liblink-grammar.so.4+0xa180] linkage_get_num_words+0x0

Would you have the rest of the stack trace handy? Who called this?
Was it called by the jni wrappers directly, or by something else
within link-grammar?

Any clue what the arguments to linkage_get_num_words were?

The first arg to inkage_get_num_words should be a pointer; I figure
that its either zero, or some corrupt value: e.g. 32-bit instead of
64-bit, or v.v.

did you recompile link-grammar to be 64-bit? Is it possible that
the liblink_grammar_java is sending 64-bit pointers to a 32-bit lib, or v.v?

> This hasn't been encountered with the same Java code running on Windows, OS
> X, and other Linux distributions.
>
> Also, Link Parser works fine through the provided executables (link-parser),
> so it doesn't appear to be a problem with compiling and installing the
> package.
>

[Arya Tafvizi]

I have attached one of the log files to this email. We checked and the
binaries are LGP 64bit. The get_words function is being called from
inside the LGP by org.linkgrammar.LGService.getAsParseResult. I'm not
sure what the input to the function was.

I run the Java code with -D"java.library.path=/usr/local/lib"

-Arya Tafvizi