Hi Christoph,
    I may say that our benchmark results coincide (and one thumbs up
from me for "bushiness").

On Fri, 2011-05-27 at 20:04 +0200, Christoph Helma wrote:

> Dear All,
> 
> Some time ago I made some benchmark tests, if I remember correctly the
> main results were
> 
> - the most resource intensive task was to build and maintain the
>   internal RDF tree of the library (this is at least true for redland
>   and RDF.rb libraries). I suppose that a lot of indexing is going on to
>   make tree traversal more efficient. Resource usage (CPU and memory
>   scaled very unfavorable with the size _and_ the "bushiness" (ie.
>   branching degree) of the RDF tree
> 
> - the library implementation (redland in C, RDF.rb in ruby) has a small
>   impact, but both versions were unusable for our datasets
> 


That is expected I think. RDF has a different purpose IMHO, which serves
perfectly. But maybe the time we turned to some other serialization has
come. But to be realistic... not in this project!


> - RDF format (RDF/XML, Turtle, N3, JSON, ...) had only a minor impact
> 


I confirm that too.


> - parsing times was reduced by several orders of magnitude with a custom
>   parser that avoids complex data structures and indexing (not much fun
>   to write and maintain). I am also not sure how well it scales, it has
>   still the limitation that everything has to fit into memory.
> 
> Best regards,
> Christoph
> 
> 
> On Fri, 27 May 2011 19:27:24 +0200, Egon Willighagen <egon.willighagen at gmail.com> wrote:
> > Dear Pantelis,
> > 
> > On Fri, May 27, 2011 at 5:50 PM, chung <chvng at mail.ntua.gr> wrote:
> > > Some criticism on RDF from the experience we've gained in OpenTox :
> > > http://is.gd/qLJG3h . The article is not complete yet and will be
> > > enriched with more facts and diagrams.
> > 
> > Please do, because right now you left out so much detail on what you
> > are in fact doing. I do appreciate your frustration, and the
> > difference is unacceptable.
> > 
> > I have these questions:
> > 
> > * RDF is not a format, while ARFF is for file format? you mix RDF and
> > RDF/XML as if they are the same thing; why?
> > * what RDF file format have you used? RDF/XML, as you later refer to?
> > * are you using reasoning, and if so why? moreover, you should not
> > compare a reasoning environment with a non-reasoning one (of course,
> > you'd see differences)
> > * what information is specified in the ARFF header?
> > * why aren't you using a vector annotation in RDF?
> > * how large is the file, and what are you doing to use 2GB of heap space?
> > * how large is your data set?
> > * what does your code look like?
> > 
> > A fair comment would be take ARFF takes a short cut: it imposes
> > additional structure on the data, something you identify in your
> > report. RDF does not do that by itself. A vector environment does.
> > That does not mean that such is not possible with RDF. Have you
> > consider what options there are to introduce this vector restriction
> > into the computational framework, forced to use RDF? Do you believe it
> > is impossible to achieve that with RDF? Would you see it impossible to
> > define an ontology to capture vector notation, allowing you to specify
> > what each column in that vector represents?
> > 
> > Now, given that you do see that option too, you would probably end up
> > with a ontology looking very much like the ARFF specification, but the
> > in RDF.
> > 
> > In short, based on your report I really cannot judge of RDF is the
> > problem, because your results do not make such conclusion possible.
> > Instead, I rather think that you are running into a highly confounded
> > analysis where it is not possible to assign the slowness to any
> > factor. I think you are comparing two widely different data models,
> > one optimized for computation (ARFF) and one not (your current RDF/XML
> > file). Would that perhaps be the significant factor in the difference
> > in speed?
> > 
> > I am looking forward to a more detailed report on the various involved
> > factors that determine the speed here,
> > 
> > Egon
> > 
> > -- 
> > Dr E.L. Willighagen
> > Postdoctoral Researcher
> > Institutet för miljömedicin
> > Karolinska Institutet (http://ki.se/imm)
> > Homepage: http://egonw.github.com/
> > LinkedIn: http://se.linkedin.com/in/egonw
> > Blog: http://chem-bla-ics.blogspot.com/
> > PubList: http://www.citeulike.org/user/egonw/tag/papers
> > _______________________________________________
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