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[bioontology-support] Latest version of NIFSTD failed parsing in BioPortal

Paul R Alexander palexander at stanford.edu
Fri Aug 16 15:10:47 PDT 2013


We just finished re-parsing the ontology this morning. The parse failure data was cached, but it shows appropriately now. We're still indexing the ontology for use with search and calculating the metrics. These should be ready later today or tomorrow.

Paul


On Aug 16, 2013, at 2:58 PM, Trish Whetzel <plwhetzel at gmail.com> wrote:

> Hi Ray, 
> 
> Just checking back on the failed parsing of NIFSTD. Is there anything on our side we can do to help resolve this?
> 
> Trish 
> 
> 
> On Wed, Aug 14, 2013 at 10:42 AM, Trish Whetzel <whetzel at ucsd.edu> wrote:
> Great, we'll check back at the end of the week.
> Trish 
> 
> 
> 
> 
> On Aug 14, 2013, at 10:39 AM, "Ray Fergerson" <ray.fergerson at stanford.edu> wrote:
> 
>> Yes, we have confirmed that this was due to an out of memory issue on the parsing server. We are going to parse it manually. Should be up in a few days.
>>  
>> Ray
>>  
>> From: Trish Whetzel [mailto:plwhetzel at gmail.com] 
>> Sent: Tuesday, August 13, 2013 6:37 PM
>> To: Fahim Imam
>> Cc: Ray Fergerson; Maryann Martone; BioPortal User Support; Trish Whetzel
>> Subject: Re: [bioontology-support] Latest version of NIFSTD failed parsing in BioPortal
>>  
>> Ray, 
>> 
>> Do you have any updates on the issue related to the failed parsing status of NIFSTD [1]?
>> 
>> Trish 
>> 
>> [1] http://bioportal.bioontology.org/ontologies/1084
>>  
>> 
>> On Thu, Aug 8, 2013 at 9:33 PM, Fahim Imam <smtifahim at gmail.com> wrote:
>> Yes. The ontology is relatively bigger than the previous version.
>>  
>> Thanks,
>> Fahim
>>  
>> 
>> On Thu, Aug 8, 2013 at 7:39 PM, Ray Fergerson <ray.fergerson at stanford.edu> wrote:
>> Trish,
>> 
>> My guess after a small be of investigation is that this problem appears to
>> be related to the size of the ontology. Has it gotten a lot bigger
>> recently? Our expert will be back next week. A solution will probably have
>> to wait until then.
>> 
>> Ray
>> 
>> -----Original Message-----
>> From: bioontology-support-bounces at lists.stanford.edu
>> [mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of Trish
>> Whetzel
>> Sent: Thursday, August 08, 2013 11:36 AM
>> To: BioPortal User Support; Fahim Imam
>> Cc: Maryann Martone
>> Subject: [bioontology-support] Latest version of NIFSTD failed parsing in
>> BioPortal
>> 
>> Hello Support,
>> 
>> I noticed that the latest version of NIFSTD failed parsing. Do you know
>> how we can resolve this issue?
>> 
>> Thanks,
>> Trish
>> 
>> 
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>> bioontology-support at lists.stanford.edu
>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>  
>> 
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>> 
>>  
> 
> 
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