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[bioontology-support] FW: NCBO bioportal - SO

Natasha Noy noy at stanford.edu
Wed Mar 24 09:45:53 PDT 2010


Hi Colin,

You are right -- there is a problem. We've reported it as a bug with  
High priority. Hopefully, will be able to fix it quickly.

Natasha


On Mar 24, 2010, at 7:47 AM, Colin Batchelor wrote:

> Hello Natasha,
>
> Yes, please take down the first one.
>
> Something has gone very wrong with the Explore option, though.   
> sequence_feature should be one of the root terms and I can't see it.
>
> Best wishes,
> Colin.
>
> -- 
> Dr Colin Batchelor MChem MRSC, Senior Informatics Analyst,  
> Informatics R&D
> Informatics Department,
> Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4 0WF
> batchelorc at rsc.org t: +44 1223 432280
>
>> -----Original Message-----
>> From: Natasha Noy [mailto:noy at stanford.edu]
>> Sent: 23 March 2010 20:01
>> To: Colin Batchelor
>> Cc: 'support at bioontology.org'; 'Michel Dumontier'; Trish Whetzel
>> Subject: Re: [bioontology-support] FW: NCBO bioportal - SO
>>
>> Colin,
>>
>> Just to clarify: you are referring to the Sequence Ontology being
>> listed twice on this page:
>> http://bioportal.bioontology.org/ontologies
>>
>> Right?
>>
>> I  think the first one (http://bioportal.bioontology.org/ontologies/36782
>> ) was pulled from OBO Foundry a while ago, but then something  
>> probably
>> changed in its metadata and it got migrated into the second one
>> (http://bioportal.bioontology.org/ontologies/42321
>> ).
>>
>> The second one seems to be the correct and the active one. According
>> to out logs,  both were uploaded automatically through our OBO Pull
>> process.
>>
>> Should we just  take down the first one
>> (http://bioportal.bioontology.org/ontologies/36782
>> ) entirely?
>>
>> Natasha
>>
>>
>> On Mar 23, 2010, at 2:21 AM, Colin Batchelor wrote:
>>
>>> Hello support!
>>>
>>> Do you know why the Sequence Ontology is in twice?
>>>
>>> http://bioportal.bioontology.org/visualize/42321/
>>>
>>> Which URL are you taking as the source?
>>>
>>> best wishes,
>>> Colin.
>>>
>>>
>>> --
>>> Dr Colin Batchelor MChem MRSC, Senior Informatics Analyst,
>>> Informatics R&D
>>> Informatics Department,
>>> Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4  
>>> 0WF
>>> batchelorc at rsc.org t: +44 1223 432280
>>>
>>> ________________________________________
>>> From: Trish Whetzel [mailto:plwhetzel at gmail.com]
>>> Sent: 22 March 2010 18:05
>>> To: Colin Batchelor
>>> Cc: Michel Dumontier
>>> Subject: Re: NCBO bioportal - SO
>>>
>>> I'm at a meeting today. Would you mind sending to
>> support at bioontology.org
>>> ?
>>>
>>> Thanks!
>>> Trish
>>>
>>> On Mon, Mar 22, 2010 at 9:24 AM, Colin Batchelor
>>> <BatchelorC at rsc.org> wrote:
>>> Hello,
>>>
>>> Yes---we haven't had the top-level term SO:0000000 in ages and ages,
>>> so #1 should go go go.
>>>
>>> Odd about #2.  Trish: are you working from so.obo or so-xp.obo?  The
>>> latter is the canonical one with the formal definitions, the former
>>> is the "toy" one.
>>>
>>> There are disjoint_from relations between the high-level classes---
>>> could that be causing trouble?
>>>
>>> Colin.
>>>
>>> --
>>> Dr Colin Batchelor MChem MRSC, Senior Informatics Analyst,
>>> Informatics R&D
>>> Informatics Department,
>>> Royal Society of Chemistry, Thomas Graham House, Cambridge UK CB4  
>>> 0WF
>>> batchelorc at rsc.org t: +44 1223 432280
>>>
>>> ________________________________________
>>> From: Michel Dumontier [mailto:michel.dumontier at gmail.com]
>>> Sent: 22 March 2010 16:15
>>> To: Trish Whetzel; Colin Batchelor
>>> Subject: NCBO bioportal - SO
>>>
>>> Hello,
>>>  I'm trying to figure out what's going on with the NCBO bioportal
>>> rendering of SO.
>>>
>>> First, I see two entries:
>>>
>>> 1. Sequence Ontology (SO)
>>> 2. Sequence types and features (SO)
>>>
>>> looks like the second is newer, so should the first one disappear?
>>>
>>> Second, the rendering of 2. appears incomplete, even though i can
>>> search and find terms:
>>>
>>> http://bioportal.bioontology.org/visualize/42321/
>>>
>>>
>>> m.
>>>
>>> --
>>> Michel Dumontier
>>> Associate Professor of Bioinformatics
>>> Carleton University
>>> http://dumontierlab.com
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>
>
> DISCLAIMER:
>
> This communication (including any attachments) is intended for the  
> use of the addressee only and may contain confidential, privileged  
> or copyright material. It may not be relied upon or disclosed to any  
> other person without the consent of the RSC. If you have received it  
> in error, please contact us immediately. Any advice given by the RSC  
> has been carefully formulated but is necessarily based on the  
> information available, and the RSC cannot be held responsible for  
> accuracy or completeness. In this respect, the RSC owes no duty of  
> care and shall not be liable for any resulting damage or loss. The  
> RSC acknowledges that a disclaimer cannot restrict liability at law  
> for personal injury or death arising through a finding of  
> negligence. The RSC does not warrant that its emails or attachments  
> are Virus-free: Please rely on your own screening.




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