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[bioontology-support] Help with expression (cutoff)

Mobed, Ketty Ketty.Mobed at ucsf.edu
Wed May 9 15:48:53 PDT 2012


Thanks Paul. That's great to know. I actually already uploaded a new version of HOM-ORTHO.owl. I'll check it again.

Ketty

________________________________
From: Paul R Alexander [palexander at stanford.edu]
Sent: Wednesday, May 09, 2012 3:41 PM
To: Wynden, Rob
Cc: Mobed, Ketty; support at bioontology.org Support
Subject: Re: [bioontology-support] Help with expression (cutoff)

This is fixed for all future uploads and no action is needed on your part. It was an issue with encoding our output that was causing the problem.

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


On 5/9/12 1:06 PM, Rob Wynden wrote:
Is this fixed for all future uploads also?
Thanks!
Rob


On 5/9/12 1:04 PM, Mobed, Ketty wrote:
Thanks Trish. Yes, I saw. This was fast!

There are several other expression like this, have they all now been fixed or should I send you the specific instances to be fixed internally?

Thanks again,
Ketty

________________________________
From: Trish Whetzel [whetzel at stanford.edu<mailto:whetzel at stanford.edu>]
Sent: Wednesday, May 09, 2012 1:01 PM
To: Wynden, Rob; Mobed, Ketty
Cc: support at bioontology.org<mailto:support at bioontology.org> Support
Subject: Re: Help with expression (cutoff)

The expression is now correctly displayed in the UI:
http://bioportal.bioontology.org/ontologies/47403/?p=terms&conceptid=MM_CLASS_101

Trish


On May 9, 2012, at 10:06 AM, Rob Wynden wrote:

We are supposed to engage Allen by Friday of this week.

Rob



On 5/9/12 10:02 AM, Trish Whetzel wrote:
Thanks for the additional information. I didn't realize these values need to be curated. To help prioritize the issue, is this a blocker for your work and when will you be working with Barry to review this values?

Trish


On May 9, 2012, at 9:53 AM, Rob Wynden wrote:

Hi,

Well we can't curate HOM Bool expressions on BioPortal if folks can't read them.  We are about to start working in with Barry Smith's team.  This could hold up the train.

Rob



On 5/9/12 9:50 AM, Trish Whetzel wrote:
Hi Rob and Ketty,

It looks like there is an issue rendering the expression in the Web interface since the "Get Term" web service call returns the expression [1] and also calling the "Get Term" web service from Excel GoogleDocs also returns the expression. I'll submit a bug report related to the rendering issue. Can you confirm this using this ontology is working properly in your application?

Trish

[1] http://rest.bioontology.org/bioportal/concepts/47403?conceptid=MM_CLASS_101&apikey=YourAPIKey


On May 9, 2012, at 9:22 AM, Rob Wynden wrote:

I think that we may be triggering an escape character on the page.  Is that correct?
Rob


On 5/9/12 8:57 AM, Mobed, Ketty wrote:
Hi Trish,

here is a problem that I have run into. I have attached the Protege generated .owl file for HOM-ORTHO (BP ID# 1697). When you open up the Protege owl file and click on the left to open OrthoSurgery -> Diagnoses -> Comorbidities -> Anemia, then on the right hand side the expression for HOM-BOOL1 reads (I9CM>I9CM.2799 AND I9CM<I9CM.2860), and this is correct. Now when I upload the HOM-ORTHO.owl file to BP, then when you expand the ontology to Anemia you see that Hom Bool1 was cut-off and only reads (I9CM>I9CM.2799 AND I9CM  .

Why is this? This is the SQLite syntax that we need to process our HOM translator. Any help will be appreciated.

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









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