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

Ray Fergerson rayferg at stanford.edu
Fri Oct 9 17:58:07 PDT 2015


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<mailto: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<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<mailto: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<mailto: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<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<mailto: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<mailto: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<mailto: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<mailto: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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