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[bioontology-support] Problem retrieving classes - Help

Jennifer Leigh Vendetti vendetti at stanford.edu
Thu Dec 6 15:03:47 PST 2018


Hi Mohamed,

BioPortal has a background process that runs every 15 minutes to begin the parsing process for new ontology submissions in the parsing queue. There are also front and back-end caches to facilitate application performance. There is generally a time window between 30 minutes and a few hours before new ontology data becomes available in the system.

I went ahead and manually flushed the caches so that you can see your version 3_4 now.

On a related note, I’m wondering if there’s a particular reason you’re overwriting the file for the existing submission instead of creating new submissions for new versions?

Kind regards,
Jennifer



On Dec 6, 2018, at 1:48 PM, Mohamed Keshk <mohamed.keshk at gmail.com<mailto:mohamed.keshk at gmail.com>> wrote:

Hi Jennifer,
  Thanks for your reply.
I'm still experiencing the same issue of not syncing the class tree/structure with latest uploaded ontology.
I just uploaded a new version of pcl ontology (pcl_3_4.owl), but still showing the old class structure view.
Is there a way to solve this issue?

Thanks,
Mohamed

On Thu, Dec 6, 2018 at 12:37 PM Jennifer Leigh Vendetti <vendetti at stanford.edu<mailto:vendetti at stanford.edu>> wrote:
Hello Mohamed,

Are you still experiencing an issue?

I looked at the data folder for your ontology on our production server and it appears that quite a number of ontology files were uploaded, including:

IFW.owl
jcvi.owl
jcvi2.owl
nsf2_full_mtg_class.owl
pcell.owl
pcl.owl
pcl_3_2.owl
Provisional_Cell_Ontology.ttl
test.owl
test2.owl

I assume that pcl.owl is the preferred / latest ontology?

Jennifer




On Nov 29, 2018, at 8:34 AM, John Graybeal <jgraybeal at stanford.edu<mailto:jgraybeal at stanford.edu>> wrote:

Forwarding to support list…

________________________________
From: Mohamed Keshk <mohamed.keshk at gmail.com<mailto:mohamed.keshk at gmail.com>>
Sent: Thursday, November 29, 2018 07:48
To: John Graybeal
Subject: Re: [bioontology-support] Problem retrieving classes - Help

Hi John,
  I'm experiencing an issue of not updating the ontology after uploading a new one.
The browser still shows the old ontology hierarchy instead.
Is there anything I'm missing to solve this problem?

Here's my URL:
http://bioportal.bioontology.org/ontologies/PCL

Thanks,
Mohamed

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