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[bioontology-support] Ongoing parsing error message problem

Wynden, Rob Rob.Wynden at
Wed Jun 20 18:50:25 PDT 2012


I'll look at it.

Sent from my HTC

----- Reply message -----
From: "Trish Whetzel" <whetzel at>
To: "Mobed, Ketty" <Ketty.Mobed at>
Cc: "Ray Fergerson" <ray.fergerson at>, "Wynden, Rob" <Rob.Wynden at>, "Tony Martin" <xtmartin at>, "support at Support" <support at>
Subject: [bioontology-support] Ongoing parsing error message problem
Date: Wed, Jun 20, 2012 6:12 pm

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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