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

Ray Fergerson rayferg at stanford.edu
Wed Sep 23 16:20:12 PDT 2015


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<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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