Hello Scott,
That is exactly what I did. Oops, maybe I dragged the wrong file into the
imports, because I just did it again and it worked as originally expected.
Many apologies. Yes, this does speed things up. The access to items in the
TDB is faster though the search for items in the class navigator is still
taking several seconds. Thanks Scott, Irene, and Holger.
Jack
On Sunday, June 8, 2014 2:40:03 AM UTC-7, Scott Henninger wrote:
>
> Jack; I haven't been following this too closely, but I assume you now
> have a .tdb connector file for your data. If you want to import that data
> into any other model use the owl:imports, just like any other model. The
> easiest is to drag/drop the .tdb file connector into the Imports view for
> the target model.
>
> To do this manually, specify the base URI (the graph name) of the .tdb
> connector for import into the target files.
>
> There are a few sections in Composer Help that you will find useful:
> TopBraid Composer > Importing Data Sources > Working with imported
> ontologies
> TopBraid Composer > User Interface Overview > Imports View
> TopBraid Composer > Importing Data Sources > Import external information
> > Add or Import External Triples
>
> -- Scott
>
> On 6/8/2014, 7:03 AM, Jack Hodges wrote:
>
> I am a bit unsure of Holger's comment about the size of the FMA
> repository. When I did the export as you suggested, Irene, it says about
> 1.7 million triples. This is what I also heard from someone else. Anyway,
> the export seems to have worked.
>
> Now the question is how to use this TDB of the FMA model/repository with
> my models. I can open the database, but cannot import it into my model. Do
> you have more documentation on how to use repositories in TBC? I dislike
> having to ask questions when I can answer them in documentation.
>
> Jack
>
> On Friday, June 6, 2014 12:10:35 PM UTC-7, Irene Polikoff wrote:
>>
>> Just open your model then do File -> Export -> Export/Merge RDF Graphs
>> and pick TDB as the format.
>>
>>
>>
>> *From:* topbrai...@googlegroups.com [mailto:topbrai...@googlegroups.com] *On
>> Behalf Of *Jack Hodges
>> *Sent:* Friday, June 06, 2014 1:38 PM
>> *To:* topbrai...@googlegroups.com
>> *Subject:* Re: [topbraid-users] Model loading...taking forever
>>
>>
>>
>> Creating a TDB seems like a good idea but I cannot find the 'Add Files'
>> button referenced in the help blurb. Unless it is called something else in
>> the UI.
>>
>> On Thursday, June 5, 2014 7:49:53 PM UTC-7, Holger Knublauch wrote:
>>
>> 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
