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[bioontology-support] Cannot access 1649

Mobed, Ketty Ketty.Mobed at ucsf.edu
Thu Aug 9 14:52:23 PDT 2012


Thanks Paul.

I'll check it out then.

Ketty

________________________________
From: Paul R Alexander [palexander at stanford.edu]
Sent: Thursday, August 09, 2012 2:44 PM
To: Mobed, Ketty
Cc: Lakshminarayanan, Prakash; Wynden, Rob; support at bioontology.org
Subject: Re: [bioontology-support] Cannot access 1649

The only import I removed was an ontology located at this URL:
http://purl.bioontology.org/ontology/HOM-OSHPD/

There is no OWL file there, so the import was just failing. I don't think this has affected the ontology classes at all. Imports that are available at the appropriate URL would have gotten pulled in already.

Paul


On 8/9/12 2:42 PM, Mobed, Ketty wrote:
Paul, I actually did want the extraneous imports included. I am testing out the Protege BP import plugin and have imported the ICD9 ontology (ID 1101) (2x).

On our end we will be mapping between ontologies directed at ICD9 nodes, so thiose imports are necessary. It would have been more difficult to import them otherwise. But we are still testing out different methods to get the ontologies and mappings in place.

Thanks,
Ketty

________________________________
From: bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu> [bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>] on behalf of Mobed, Ketty [Ketty.Mobed at ucsf.edu<mailto:Ketty.Mobed at ucsf.edu>]
Sent: Thursday, August 09, 2012 2:36 PM
To: Paul R Alexander
Cc: Lakshminarayanan, Prakash; Wynden, Rob; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Cannot access 1649

Thanks Paul.

Just fyi, the 1649 contains 2x the full ICD9 (ID 1101) ontology.

Ketty

________________________________
From: Paul R Alexander [palexander at stanford.edu<mailto:palexander at stanford.edu>]
Sent: Thursday, August 09, 2012 12:56 PM
To: Mobed, Ketty
Cc: Trish Whetzel; Wynden, Rob; Lakshminarayanan, Prakash; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Cannot access 1649

The size of the ontology should not have a bearing on speed, except for two things (which I don't think apply here):
1. There is a parent node with thousands of child nodes.
2. There is a node with thousands of properties or property values.

However, I have found a problem with the HOM-OSHPD ontology. When it is first loaded by any one of our Protege back-end systems (there are three that respond to requests), it takes 230+ seconds. We then cache the loaded ontology for some time. When it is dropped from the cache on any of the systems, it will then take another 230+ seconds to load. I think the issue might be a missing import (http://purl.bioontology.org/ontology/HOM-OSHPD/). There's a chance we can fix this on our end. I'll keep investigating.

Paul


On 8/9/12 12:07 PM, Mobed, Ketty wrote:
Hi Paul,

I am experiencing fewer problems since switching the mapping target. Before I tried mapping individuals nodes from ID 3125 (profectus.oshpd.installation) to ID 1649 (HOM-OSHPD) and wasn't able to pull up the terms to create the mappings. Now I have switched and am mapping from 1649 to 3125. This seems to be working okay, with slowing down on occasion which I remedy with reloading the page and continuing on mapping. So this now works for me. Can you inspect and see if 1649 may have a size issue related to the inability to map?

Thanks very much,
Ketty

________________________________
From: Paul R Alexander [palexander at stanford.edu<mailto:palexander at stanford.edu>]
Sent: Thursday, August 09, 2012 11:58 AM
To: Mobed, Ketty
Cc: Trish Whetzel; Wynden, Rob; Lakshminarayanan, Prakash; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Cannot access 1649

Ketty,

Are you still experiencing issues? Can you give me a basic idea of what you are doing? My guess is that you are on the HOM-OSHPD page where it shows terms. You navigate to a particular term, select the mapping tab, and then try to create a mapping. It sounds like the part that is slow is after you have searched for and selected a term from the target ontology it can take a while for the term information to appear.

Is this correct? If so, which ontologies are you using as targets?

Thanks,
Paul


On 8/9/12 10:55 AM, Mobed, Ketty wrote:
...just fyi, but I can do otherway around mapping more quickly (which i am doing now)

Ketty


________________________________
From: bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu> [bioontology-support-bounces at lists.stanford.edu<mailto:bioontology-support-bounces at lists.stanford.edu>] on behalf of Mobed, Ketty [Ketty.Mobed at ucsf.edu<mailto:Ketty.Mobed at ucsf.edu>]
Sent: Thursday, August 09, 2012 10:47 AM
To: Trish Whetzel
Cc: Lakshminarayanan, Prakash; Wynden, Rob; support at bioontology.org<mailto:support at bioontology.org>
Subject: Re: [bioontology-support] Cannot access 1649

Thanks Trish.

I am now able to pull up the 1649 ontology and pull up mapping terms, but it is very! slow to pull up the details and finish the mapping.

Ketty

________________________________
From: Trish Whetzel [whetzel at stanford.edu<mailto:whetzel at stanford.edu>]
Sent: Thursday, August 09, 2012 9:58 AM
To: Mobed, Ketty
Cc: support at bioontology.org<mailto:support at bioontology.org>; Wynden, Rob; Lakshminarayanan, Prakash
Subject: Re: Cannot access 1649

Hi Ketty,

I am able to view the ontology. Although I am seeing slowness in loading some terms and am checking with the sysadmin/developers about this. Can you re-start your browser and clear the cache to see if that helps?

Trish


On Aug 9, 2012, at 12:37 PM, Mobed, Ketty wrote:

Hi Trish,

Help, high priority! I uploaded a new version of ontology ID 1649 (HOM-OSHPD) which is substantially larger than the previous version. I need this new version to map to, but I cannot even access the terms. It keeps churning and after a while I see the 'We're sorry something has gone wrong' message. I have tried this both using Safari and Firefox with the same result. Could it be the size of the ontology?

Thanks,
Ketty





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