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[bioontology-support] Ongoing parsing error message problem

Trish Whetzel whetzel at stanford.edu
Thu Jun 21 17:21:31 PDT 2012


The "Terms" link should resolve to the latest version, i.e.version 1.1. The 1.1. version specific URL is:
http://bioportal.bioontology.org/ontologies/47718/?p=terms

You can get the ontology version identifier a few ways, one way in the browser is to hover over the "Ontology" link in the Downloads column in the "Versions" table. Another is to click on the link and open in a new tab (at least with Firefox) and the ontology version identifier will be in the browser URL. There are also ways using the Web service if you don't mind reading XML. The "List latest version of an ontology id" [1] will return the latest ontology version identifier in the XML attribute <id> along with other information. In this case the call is:
http://rest.bioontology.org/bioportal/virtual/ontology/3086?apikey=YourAPIKey  and this call can be put directly in the browser URL to get the information. 

Trish 

[1] http://www.bioontology.org/wiki/index.php/NCBO_REST_services#Get_latest_version_of_an_ontology_id


On Jun 21, 2012, at 2:50 PM, Mobed, Ketty wrote:

> I actually can see the terms, but can't tell if it is from version 1.0 or 1.1 
> 
> Ketty
> 
> From: Trish Whetzel [whetzel at stanford.edu]
> Sent: Thursday, June 21, 2012 2:39 PM
> To: Mobed, Ketty
> Cc: palexander at stanford.edu; support at bioontology.org Support; Ray Fergerson; Wynden, Rob; Tony Martin; marc at cybre.net
> 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: http://bioportal.bioontology.org/ontologies/3086/?p=terms 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.
> 
> Trish 
> 
> 
> On Jun 21, 2012, at 2:30 PM, Mobed, Ketty wrote:
> 
>> Hi,
>> 
>> could you please let us know where the below problem lies. We are really stuck now.
>> 
>> Thanks,
>> Ketty
>> 
>> From: Mobed, Ketty
>> Sent: Wednesday, June 20, 2012 7:01 PM
>> To: Trish Whetzel
>> Cc: Ray Fergerson; Wynden, Rob; Tony Martin; support at bioontology.org Support; marc at cybre.net
>> 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?
>> 
>> Ketty
>> 
>> 'It's the little things that matter'
>> 
>> Ketty Mobed, PhD
>> UCSF-IHPS-Informatics Lab
>> ketty.mobed at ucsf.edu
>> 415-352-8815
>> From: Trish Whetzel [whetzel at stanford.edu]
>> Sent: Wednesday, June 20, 2012 6:11 PM
>> To: Mobed, Ketty
>> Cc: Ray Fergerson; Wynden, Rob; Tony Martin; support at bioontology.org 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? 
>> 
>> Trish 
>> 
>> 
>> 
>> 
>> 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.
>>> 
>>> Trish 
>>> 
>>> 
>>> 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.
>>>> 
>>>> Ketty
>>>> 
>>>> 
>>>> <profectus.test.installation - Terms | NCBO BioPortal 2012-06-20 15-38-16.png>
>>> 
>>> 
>>> _______________________________________________
>>> bioontology-support mailing list
>>> bioontology-support at lists.stanford.edu
>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>> 
>> 
> 
> 


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