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[bioontology-support] [BioPortal] HOM-UPENN_EPICMEDS Parsing Was Successful

Paul R Alexander palexander at stanford.edu
Thu Apr 5 16:48:35 PDT 2012


Ketty,

It looks like the ontology you indicate (3032) has actually been parsed 
now. Did you end up receiving the email? There have been a few large 
ontologies submitted recently, though I don't think they should delay 
parsing for other ontologies. Please let us know if you continue to see 
delays.

In addition, I've deleted the two ontologies you indicated.

Let me know if you need help with anything else.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 4/5/12 3:27 PM, Mobed, Ketty wrote:
> Hi Trish/BP Support,
>
> I uploaded a new ontology (HOM-UPENNMEDS, ID 3032) this morning around 9:30, but it still hasn't parsed by 3:30 pm. I have noticed slow parsing issues lately. Is there something going on with BP? Also I didn't get the confirmatory email about the new ontology in BP.
>
> Could you also please delete 2 ontologies with ID 3026 and 3027.
>
> Thanks,
> Ketty
>
> ________________________________
> From: Mobed, Ketty
> Sent: Wednesday, April 04, 2012 8:29 AM
> To: Trish Whetzel; support at bioontology.org
> Cc: support at bioontology.org
> Subject: RE: [BioPortal] HOM-UPENN_EPICMEDS Parsing Was Successful
>
> Hello,
>
> I need to upload the UPENN-MEDS ontology freshly. I think it is mixing up the names. So would you please delete ontologies 3026 and 3027.
>
> Thanks,
>
> Ketty
>
> ________________________________
> From: Mobed, Ketty
> Sent: Tuesday, April 03, 2012 7:01 AM
> To: Trish Whetzel
> Cc: support at bioontology.org
> Subject: RE: [BioPortal] HOM-UPENN_EPICMEDS Parsing Was Successful
>
> Hi Trish,
>
> yes I was logged into BP, since I do all my BP ontologies as private.
>
> I think I am using the most up-to-date Version, Protege 3.4.9. But as I am thinking about it, I may have saved 'the Project' incorrectly so I will try again to resolve the problem on my end.
>
> Thanks and am looking forward to see you in Baltimore.
> Ketty
>
> 'It's the little things that matter'
>
> ________________________________
> From: Trish Whetzel [whetzel at stanford.edu]
> Sent: Monday, April 02, 2012 8:49 PM
> To: Mobed, Ketty
> Cc: support at bioontology.org
> Subject: Re: [BioPortal] HOM-UPENN_EPICMEDS Parsing Was Successful
>
> Hi Ketty,
>
> When you were reviewing the Browse page, where you logged in with the same BioPortal account used to upload the Private ontology?
>
> For HOM-UPENN_EPICMEDS [1], is the display of the term "LISINOPRIL-HYDROCHLOROTHIAZIDE ORAL" at the root node incorrect? If so, what version of Protege did you use to save the file?
>
> Thanks,
> Trish
>
> [1] http://bioportal.bioontology.org/ontologies/3027
>
>
> On Apr 2, 2012, at 10:10 PM, Mobed, Ketty wrote:
>
> Sorry for all this communication, but I searched for the 2 below mentioned ontologies in BP again by name and this time the last parsed one was there. Very strange, this has never happened before.
>
> In any case could you please delete now only this ontology  http://purl.bioontology.org/ontology/HOM-UPENN-MEDS
>
> Thanks,
> Ketty
>
> ________________________________
> From: Mobed, Ketty
> Sent: Monday, April 02, 2012 7:01 PM
> To: support at bioontology.org<mailto:support at bioontology.org>; Trish Whetzel
> Subject: RE: [BioPortal] HOM-UPENN_EPICMEDS Parsing Was Successful
>
> Hi Trish,
>
> something quite strange has occurred the last 2 times I uploaded the same ontology.
> The first time I uploaded it the NCBO url was http://purl.bioontology.org/ontology/HOM-UPENN-MEDS . But after opening it up, I couldn't get to the summary page and get the ontology ID.
>
> I also saw an error in the ontology tree. So I created the ontology owl file in Protege again and made sure that it looked okay and then I uploaded it again to BP (as a new ontology), as I couldn't upload it as a revision to the first one, because I wasn't able to recover the first one by name (HOM-UPENN-MEDS).
>
> Again the second time I wasn't able to find it by ontology name (HOM-UPENN_EPICMEDS) and only found it with the url http://bioportal.bioontology.org/ontologies/3027 . But funny thing again also was that even though the owl file in Protege looked fine, the ontology in BP had this extra parent node LISINOPRIL-.... that I didn't see in the original owl file and is an error.
>
> So I am at a loss of why this happened. Do you think that the problem may be in the owl file creation in Protege? I will try one more time. In the meantime could you please delete the 2 above name ontologies in BP.
>
> Thanks,
>
> Ketty
>
> 'It's the little things that matter'
>
> Ketty Mobed, PhD
> UCSF-IHPS-Informatics Lab
> ketty.mobed at ucsf.edu<mailto:ketty.mobed at ucsf.edu>
> 415-352-8815
> ________________________________
> From: Mobed, Ketty
> Sent: Monday, April 02, 2012 4:18 PM
> To: support at bioontology.org
> Subject: RE: [BioPortal] HOM-UPENN_EPICMEDS Parsing Was Successful
>
> Hello,
>
> how come this ontology (HOM-UPENN_MEDS) ID 3027 does not appear when I look for it under the Browse tab?
>
> Thanks,
> Ketty
>
> 'It's the little things that matter'
>
> Ketty Mobed, PhD
> UCSF-IHPS-Informatics Lab
> ketty.mobed at ucsf.edu
> 415-352-8815
> ________________________________
> From: support at bioontology.org [support at bioontology.org]
> Sent: Monday, April 02, 2012 1:32 PM
> To: Mobed, Ketty
> Subject: [BioPortal] HOM-UPENN_EPICMEDS Parsing Was Successful
>
> HOM-UPENN_EPICMEDS parsing was successful.
>
> The parsed version of your ontology will display here within the next two hours:
> http://bioportal.bioontology.org/ontologies/3027
>
> Please contact support at bioontology.org if you have questions.
>
> Thank you,
> The BioPortal Team
>
>
> Trish Whetzel, PhD
> Outreach Coordinator
> The National Center for Biomedical Ontology
> Ph: 650-721-2378
> http://www.bioontology.org
>
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>
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>
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>
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