Well, this (FMA) is a very unusual model - everything is an instance of
some other instance (many levels deep) and the root of all that
(dl:Anatomical_entity_template) is an instance of itself but is not even
declared as a class! My previous speculations about the class tree were
irrelevant, but I assumed you were using some kind of flat class
structure used by many other bio ontologies.
Anyway, I have loaded that file (took two minutes on my 8 GB Windows 7
machine) and exported it to TDB. Loading the TDB into TBC takes about 2
seconds. A SPARQL query such as
SELECT ?type COUNT(?type)
WHERE {
?subject rdf:type ?type .
} GROUP BY ?type
also responded within a second or two. Auto-complete in the main search
box in the tool bar is also responding very quickly for me (e.g. try
dl:Liq + CTRL-Space) which takes one second on my machine.
The model has about 215k triples, which is not very large but certainly
a challenge for a machine with little memory (unless a database such as
TDB is used).
I am not really sure what else to do next, as I am not able to reproduce
the severe slowness you report.
Thanks,
Holger
On 6/6/2014 12:12, Jack Hodges wrote:
Holger,
Here is the link to the major player in this exercise (the
Foundational Model of Anatomy):
http://www.bioontology.org/wiki/index.php/FMAInOwl
I downloaded and load the owl file:
http://bioontology.org/projects/ontologies/fma/fmaOwlFullComponent_2_0.owl
but they say it can be referenced:
http://bioontology.org/projects/ontologies/fma
Jack
On Thursday, June 5, 2014 2:57:02 PM UTC-7, Holger Knublauch wrote:
On 6/6/2014 5:06, Jack Hodges wrote:
> My apology, I meant class name searches in the navigator.
>
> On my new Windows 7 laptop these searches take less than a
minute, but
> are still noticeable.
Ok, auto-complete is indeed not optimized in TBC and the system
may need
to walk through all 70k classes. I will record this as an enhancement
request.
> I tried many configurations of memory and they have no impact on
load
> times for my models on this new machine. They remain at 11
minutes. I
> am not sure why it was faster on the iMac but will time it again
when
> I am home again (where the iMac is).
Is the load time still 11 minutes if you have switched to TDB?
Also, I would like to drill down into your scenario a bit: could you
point me at the RDF files that you are playing with?
Thanks
Holger
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