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[bioontology-support] Ongoing parsing error message problem

Mobed, Ketty Ketty.Mobed at
Thu Jun 21 14:45:16 PDT 2012

No, version 1.1 of BP ID 3086 is not viewable via the Terms button. That is the hot problem on our end. I have cleared cache and reloaded.


From: Trish Whetzel [whetzel at]
Sent: Thursday, June 21, 2012 2:39 PM
To: Mobed, Ketty
Cc: palexander at; support at Support; Ray Fergerson; Wynden, Rob; Tony Martin; marc at
Subject: Re: [bioontology-support] Ongoing parsing error message problem

Hi Ketty,

In what step are you stuck? The ontology can be viewed by using the "Terms" select menu item, which resolves to: If this is an issue, perhaps you can clear your browser cache.

I've alerted Ray that the tracker item regarding the search issue needs attention.


On Jun 21, 2012, at 2:30 PM, Mobed, Ketty wrote:


could you please let us know where the below problem lies. We are really stuck now.


From: Mobed, Ketty
Sent: Wednesday, June 20, 2012 7:01 PM
To: Trish Whetzel
Cc: Ray Fergerson; Wynden, Rob; Tony Martin; support at<mailto:support at> Support; marc at<mailto:marc at>
Subject: RE: [bioontology-support] Ongoing parsing error message problem

Thanks Trish.

I can think of several issues that come to mind. One is that the first version of this ontology was automatically generated and uploaded to BP, using the Biostorm pathway by our TIIED developer Marc (this might be something that he can address). So when this is parsed in BP it gives a 'Parsing Error' message, but the ontology itself is still visible when the Terms tab is selected. We have done that ok.

But I had to reprocess this ontology, so I downloaded it again (although the download did not work for me on this one, I don't know because of the parsing error message maybe?), so I actually worked on Marc's delivered owl file. I then uploaded the 2nd version of this ontology back to BP. This is when we see the parsing error again, but this time I can't open the ontology from the Terms button either.

So is BP balking at the mixed messages it is getting?


'It's the little things that matter'

Ketty Mobed, PhD
UCSF-IHPS-Informatics Lab
ketty.mobed at<mailto:ketty.mobed at>
From: Trish Whetzel [whetzel at]
Sent: Wednesday, June 20, 2012 6:11 PM
To: Mobed, Ketty
Cc: Ray Fergerson; Wynden, Rob; Tony Martin; support at<mailto:support at> Support
Subject: Re: [bioontology-support] Ongoing parsing error message problem

Hi Ketty,

There are a couple of issues here. The ontology did parse and can at least be viewed. In order to view the ontology, use the "Terms" option from the select menu (attached screenshot).

Currently the "parsing error" status message is also displayed when there is an issue with the Metrics calculation or processing obsolete terms, therefore the link to view each version is not displayed. I've put in a tracker request to have the parsing error status displayed only when there is a parsing error.

There also appears to be an issue adding the ontology to the Search index. There is also a tracker item on this. Therefore, the "Jump To" will not work and the autocomplete in the Mappings window will not work. Mappings should be able to be created, however you will have to navigate to each term and then click on the "Term Mappings" tab.

Also, your term URIs are very strange as they reference a former Stanford project called Biostorm and also have other odd characters such as the "@" sign and another set of "//". Is this a result of using the DataMaster plugin?


On Jun 20, 2012, at 3:49 PM, Trish Whetzel wrote:

Hi Ketty,

I'll check a few things, but may need to hand this over to Paul.


On Jun 20, 2012, at 3:43 PM, Mobed, Ketty wrote:

Sorry to be so bothersome today, but the following ontology (3086) sends a parsing error message (attached), even though for version 1.0 we were able to view the terms,  but in this new version I cannot pull up the terms anymore.

We did receive the BP parsing failed message too.


<profectus.test.installation - Terms | NCBO BioPortal 2012-06-20 15-38-16.png>

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