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[bioontology-support] How to handle imported ontologies on bioportal

sridevi polavaram spolavar at gmail.com
Mon Oct 12 09:53:23 PDT 2015


Hi Ray,
 Thank you for the update. It will take me until Oct 25th to upload a new
set of ontologies. Do you think this can be fixed by then?

-Sridevi

On Fri, Oct 9, 2015 at 8:58 PM, Ray Fergerson <rayferg at stanford.edu> wrote:

> We are continuing to look into this problem. It is more difficult than we
> originally guessed.
>
>
>
> Ray
>
>
>
> *From:* sridevi polavaram [mailto:spolavar at gmail.com]
> *Sent:* Thursday, September 24, 2015 2:48 PM
>
> *To:* Ray Fergerson
> *Cc:* Jennifer Leigh Vendetti; bioontology-support at lists.stanford.edu
> *Subject:* Re: [bioontology-support] How to handle imported ontologies on
> bioportal
>
>
>
> Yep, it's still there.
>
> I go to: http://bioportal.bioontology.org/ontologies/NMOBR?p=classes
>
> and search for 'Cerebellum', and it takes for ever. its' past 3 minutes
> and i don't see any change.
>
> Thank you
>
> Sridevi
>
>
>
> On Thu, Sep 24, 2015 at 5:27 PM, Ray Fergerson <rayferg at stanford.edu>
> wrote:
>
> I cannot see the problem with search delays. Is this still happening for
> you?
>
>
>
> We should be handling all obo synonym types correctly when you retrieve a
> single term. When you search though, or if you retrieve pages of classes,
> we have a known bug that results in only a single synonym/class being
> loaded into the “Synonym” property. We are looking into this now and hope
> to have it fixed by next week. The problem is buried deep in our backend
> software.
>
>
>
> Ray
>
>
>
> *From:* sridevi polavaram [mailto:spolavar at gmail.com]
> *Sent:* Thursday, September 24, 2015 7:05 AM
> *To:* Ray Fergerson
> *Cc:* Jennifer Leigh Vendetti; bioontology-support at lists.stanford.edu
>
>
> *Subject:* Re: [bioontology-support] How to handle imported ontologies on
> bioportal
>
>
>
> Hi Ray,
>  Thanks for the update. But I notice two things:
>
> 1. The search is way too slow (takes more than 2 mins for NMOBR). Is it
> because of a larger index size? because NMOSP (which is smaller size) seem
> to be working fine.
>
> 2. The synonym (hasExactSynonym) is not being read. Is this something that
> can be fixed?
>
> I have at least 10 more ontologies lined up to be uploaded, and eventually
> I plan to make a mother ontology of all to take advantage of the auto
> complete search. Therefore, I want to understand the system to make this
> smooth and maybe even fine tune the pipeline at my end accordingly.
>
> Thank you
>
> Sridevi
>
>
>
>
>
> On Wed, Sep 23, 2015 at 7:20 PM, Ray Fergerson <rayferg at stanford.edu>
> wrote:
>
> Search won’t be faster. We load the file from wherever and then create a
> local index. Searches always go against the index.
>
>
>
> Ray
>
>
>
> *From:* bioontology-support [mailto:
> bioontology-support-bounces at lists.stanford.edu] *On Behalf Of *sridevi
> polavaram
> *Sent:* Monday, September 21, 2015 2:03 PM
> *To:* Jennifer Leigh Vendetti
> *Cc:* bioontology-support at lists.stanford.edu
> *Subject:* Re: [bioontology-support] How to handle imported ontologies on
> bioportal
>
>
>
> Got it! Would locally imported ontologies make auto complete search faster
> than Web imported ones?
> Thank you
> Sridevi
>
> On Sep 21, 2015 1:59 PM, "Jennifer Leigh Vendetti" <vendetti at stanford.edu>
> wrote:
>
> Hello Sridevi,
>
>
>
> If you want to upload an ontology with local imports, you need to create a
> ZIP file that contains your main ontology file, along with all of the
> imported ontology files.  In addition, your ZIP file must have the same
> name as the main ontology file so that BioPortal knows which ontology is
> the one you’re trying to upload.  For example:
>
>
>
> my_ontology.zip (the ZIP file you create with the same name as your main
> ontology file)
>
> - my_ontology.owl (the main ontology file)
>
> - imported_ontology_1.owl
>
> - imported_ontology_2.owl
>
> - imported_ontology_3.owl
>
>
>
> … etc.
>
>
>
> Jennifer
>
>
>
>
>
>
>
> On Sep 17, 2015, at 11:57 AM, sridevi polavaram <spolavar at gmail.com>
> wrote:
>
>
>
> Hi All,
>
>  I need some guidance on how to upload ontologies that import from local
> files. Because, I believe my recent upload (
> http://bioportal.bioontology.org/ontologies/NMOBR) didn't work due to
> imported ontologies.
>
>  Should i upload all local ontologies together? Instead of referring to
> local files i even tried importing directly from bioportal (e.g.,  http://purl.bioontology.org/ontology/NMOSP
> ) <http://purl.bioontology.org/ontology/NMOSP> but got an error!
>
> I would appreciate if you can provide some examples in this regard.
>
> Thank you
>
> Sridevi
>
> On Wed, Sep 16, 2015 at 3:53 PM, sridevi polavaram <spolavar at gmail.com>
> wrote:
>
> Hi Ray,
>
>  I have uploaded a new ontology of brain regions to bioportal at
> http://bioportal.bioontology.org/ontologies/NMOBR
>
> But the parsing didn't go through. Can you please help me figure out what
> is going on here? I am able to open this file and test in protege 4.3.
>
> Thank you
>
> Sridevi
>
>
>
>
>
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>
>
>
>
>
>
>
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