Search Mailing List Archives


Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] Cannot access 1649

Paul R Alexander palexander at stanford.edu
Thu Aug 9 14:44:00 PDT 2012


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 
> [bioontology-support-bounces at lists.stanford.edu] on behalf of Mobed, 
> Ketty [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
> *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]
> *Sent:* Thursday, August 09, 2012 12:56 PM
> *To:* Mobed, Ketty
> *Cc:* Trish Whetzel; Wynden, Rob; Lakshminarayanan, Prakash; 
> 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]
>> *Sent:* Thursday, August 09, 2012 11:58 AM
>> *To:* Mobed, Ketty
>> *Cc:* Trish Whetzel; Wynden, Rob; Lakshminarayanan, Prakash; 
>> 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 
>>> [bioontology-support-bounces at lists.stanford.edu] on behalf of Mobed, 
>>> Ketty [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
>>> *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]
>>> *Sent:* Thursday, August 09, 2012 9:58 AM
>>> *To:* Mobed, Ketty
>>> *Cc:* 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
>>>>
>>>
>>>
>>>
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>
>

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://mailman.stanford.edu/pipermail/bioontology-support/attachments/20120809/41704b83/attachment-0001.html>


More information about the bioontology-support mailing list