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[bioontology-support] Ongoing parsing error message problem

Mobed, Ketty Ketty.Mobed at
Wed Jun 20 19:01:17 PDT 2012

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
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 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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