very slow owl import with paxtools-4.0.1

[Zhihua Li]

Hi all,

This is more of a paxtools question than biopax but I couldn't find a
paxtools mailing list......

Basically I'm writing my own java programs to manipulate owl files. I
tried two paxtools jar archives: the latest
"official" version (paxtools-4.0.1.jar) and the file used by
cytoscape biopax plugin (biopax.jar). I can see they are different
because paxtools-4.0.1 uses SimpleIOHandler to import owl files (into
a model) while biopax.jar uses
SimpleReader.

I constantly found that SimpleReader from biopax.jar is far quicker in
reading an owl file than SimpleIOHandler from paxtools-4.0.1 by a
factor of almost 10 fold. The difference can be seen with a simple
code:
Model model = (new SimpleReader()).convertFromOWL(new
FileInputStream(infile));
vs
Model model = (new SimpleIOHandler()).convertFromOWL(new
FileInputStream(infile));

Recently I came across this gigantic owl file (1.2G) that needs to be
processed by paxtools-4.0.1. After running overnight it's still not
done. Given the huge speed difference between paxtools-4.0.1 and
biopax.jar, I suspect
that there's some room to expedite the way SimpleIOHandler imports owl
file. Does anyone have an idea
related to this issue?

Thanks a lot!

Zhihua Li

[Emek Demir]

Zhihua -

In fact there was an unfortunate bug that caused n^2 reads to the
model's object table- this was fixed several weeks ago in the latest
Paxtools.

Best,
ED

[Zhihua Li]

ED,

Thank you very much. I guess the fix hasn't gone to the distribution paxtools-4.0.1 yet.
and I'll need the latest source code?
I try to download the source code by doing

hg clone http://biopax.hg.sourceforge.net:8000/hgroot/biopax/paxtools
but I kept getting a message saying the remote host does not respond.

It could be that our firework has blocked some of the transfer. Is there any
other way I can get and use the fixed version of SimpleIOHandler?

Thanks again!

Zhihua Li

[IgorRodchenkov]

Hi Zhihua,

Please wait for the v4.1.0 release; it is happening right now ;)

Igor.

[Emek Demir]

Zhihua - we will make a release today. Igor is currently working on it.

I have just checked the hg repo at sf and it works fine, I think it is a firewall issue. Did you try the instructions here :

http://sourceforge.net/apps/trac/sourceforge/wiki/CVS%20client%20instructions

?

Best,
ED

[IgorRodchenkov]

Just released; see: https://groups.google.com/d/msg/biopax-discuss/zwtwDG23T1E/Lb0qpruH7RQJ topic.

PS:

For some reason "fat" JARs are now bigger 12M than before... We should probably find why and release v4.1.1 ;)

[Zhihua Li]

Ignor and Emek

Just downloaded v4.1.0 and it works great! Finished the processing of the 1.2G owl file in minutes.
Thanks so much for the help!

Zhihua Li