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[bioontology-support] new ontology abbreviations- broke purls

Trish Whetzel whetzel at stanford.edu
Tue Jul 17 23:39:54 PDT 2012


Hi Laurel, 

The PURLs are now updated.

Trish 


On Jul 15, 2012, at 4:26 AM, Laurel Cooper wrote:

> HI Trish, 
> I went ahead and changed the abbreviations on the files below when I was updating the PO_PAE (Plant Anatomy) and PO_PSDS (Plant Development stage) files on Bioportal.  I did not realize that I could do that, but now I see the purl links are now broken:
> 
> http://purl.bioontology.org/ontology/PO_PSDS
> 
> http://purl.bioontology.org/ontology/PO_PAE
> 
> http://purl.bioontology.org/ontology/GRO_CPD
> 
> http://purl.bioontology.org/ontology/GRO_CPGA
> 
> Can you see about getting those fixed on your end? Otherwise, let me know and I will change them back.
> 
> Thanks, Laurel
> 
> 
> On 7/13/12 12:08 AM, Laurel Cooper wrote:
>> Any resolution on these?  I see the link on GRO_CPG is still going to Gene Regulation Ontology
>> Laurel
>> 
>> On 6/20/12 2:24 PM, Laurel Cooper wrote:
>>> Yes,
>>> I see that we had a conversation about these a while back, but it was never followed up on from our end.
>>> you had suggested: 
>>> Cereal plant gross anatomy: GRO --> GRO-CPGAO
>>> Cereal Plant Development GRO --> GRO-CPDO
>>> 
>>> I would suggest: 
>>> Cereal plant gross anatomy: GRO --> GRO_CPG
>>> Cereal Plant Development GRO --> GRO_CPD
>>> 
>>> For the PO ontologies, I would suggest using PO_PAE (Plant Anatomy) and PO_PSDS (Plant Development stage) and keeping PO for the main Plant Ontology file.  (Since Jan 2011, the PO was combined into one file, but for the time being we are still offering the two aspects of the main ontology as separate files by request of some of our users.)  
>>> 
>>> Would these changes affect any other features, such as how the searches work?  Or is it strictly on the backend?
>>> 
>>> 
>>> Thanks!
>>> Laurel
>>> 
>>> 
>>> On 6/20/12 2:03 PM, Trish Whetzel wrote:
>>>> 
>>>> Yes, that is another case of duplicated ontology abbreviations that needs to be resolved. Do you manage (or can suggest) an alternative display abbreviation for the Cereal plant development ontology?
>>>> 
>>>> Trish 
>>>> 
>>>> 
>>>> On Jun 20, 2012, at 1:49 PM, Laurel Cooper wrote:
>>>> 
>>>>> Hi Trish, noticed something weird today:
>>>>> the link: http://purl.bioontology.org/ontology/GRO
>>>>> 
>>>>> from this page: Cereal plant development: http://bioportal.bioontology.org/ontologies/1047  (this is a retired ontology, legacy data)
>>>>> 
>>>>> Takes you to: Gene Regulation Ontology : http://bioportal.bioontology.org/ontologies/44629?p=terms
>>>>> 
>>>>> Thanks, Laurel
>>>>> 
>>>>> On 6/19/12 5:43 PM, Trish Whetzel wrote:
>>>>>> 
>>>>>> We are pleased to announce the release of BioPortal 3.9. The major new features in this release are:
>>>>>>  
>>>>>> ·         We have revised the search interface, both for specifying a search and in the format of the returned results. The new “advanced search” capability allows users to specify more clearly exactly what terms they would like to find. This capability also allows us to choose better (more commonly desired) defaults for the “basic search”. The returned search results are now grouped by ontology and the results are ranked so that terms from “better”  ontologies are returned first. We also show definitions for terms that have them. In general this response format was inspired by the Google search response interface so we hope that it looks familiar. We are specifically soliciting feedback from users on this revision. Please send any comments to support at bioontology.org.  *
>>>>>>  
>>>>>> ·         We include the first version of the BioMixer visualization software (available through the “Visualize” links). This software replaces the older FlexViz system. There are a number of technology improvements (i.e. the removal of Flash technology) over the older system and the newer system is more powerful as well (i.e. you can now navigate mappings from the basic interface). More complete versions of BioMixer will be introduced in subsequent releases. Please provide any feedback you can on this new system. *
>>>>>>  
>>>>>> ·         We have regenerated all automatically generated mappings in the system. These include lexical mappings, UMLS CUI mappings, identical identifier mappings, and OBO-xref mappings. We have also loaded mappings between selected UMLS ontologies as specified in the UMLS database (MRMAP).
>>>>>>  
>>>>>> *  This item was requested via the User Support mailing list. Thank you for your comments and suggestions!
>>>>>> 
>>>>>> 
>>>>>> Trish Whetzel, PhD
>>>>>> Outreach Coordinator
>>>>>> The National Center for Biomedical Ontology
>>>>>> Ph: 650-721-2378
>>>>>> http://www.bioontology.org
>>>>>> 
>>>>>> "Like" NCBO on Facebook: http://on.fb.me/bioontology
>>>>>> 
>>>>>> Follow NCBO on Twitter: http://twitter.com/#!/bioontology
>>>>>> 
>>>>>> Join in Discussions on LinkedIn: http://linkd.in/ncbo-group
>>>>>> 
>>>>>> 
>>>>>> 
>>>>>> _______________________________________________
>>>>>> bioportal-announce mailing list
>>>>>> bioportal-announce at lists.stanford.edu
>>>>>> https://mailman.stanford.edu/mailman/listinfo/bioportal-announce
>>>>> 
>>>>> -- 
>>>>> **********************************************************
>>>>> Laurel (Lol) Cooper, PhD
>>>>> Coordinator, Plant Ontology Consortium
>>>>> Dept. of Botany and Plant Pathology
>>>>> Rm 3086, Cordley Hall
>>>>> Oregon State University
>>>>> Corvallis, OR 97331
>>>>> Web: www.plantontology.org
>>>>> 
>>>>> Phone: 541-737-5272
>>>>> Fax: 541-737-3573
>>>>> Skype: cooperlol910
>>>>> ***********************************************************
>>>> 
>>>> 
>>> 
>>> -- 
>>> **********************************************************
>>> Laurel (Lol) Cooper, PhD
>>> Coordinator, Plant Ontology Consortium
>>> Dept. of Botany and Plant Pathology
>>> Rm 3086, Cordley Hall
>>> Oregon State University
>>> Corvallis, OR 97331
>>> Web: www.plantontology.org
>>> 
>>> Phone: 541-737-5272
>>> Fax: 541-737-3573
>>> Skype: cooperlol910
>>> ***********************************************************
>> 
>> -- 
>> **********************************************************
>> Laurel (Lol) Cooper, PhD
>> Coordinator, Plant Ontology Consortium
>> Dept. of Botany and Plant Pathology
>> Rm 3086, Cordley Hall
>> Oregon State University
>> Corvallis, OR 97331
>> Web: www.plantontology.org
>> 
>> Phone: 541-737-5272
>> Fax: 541-737-3573
>> Skype: cooperlol910
>> ***********************************************************
>> 
>> 
> 
> -- 
> **********************************************************
> Laurel (Lol) Cooper, PhD
> Coordinator, Plant Ontology Consortium
> Dept. of Botany and Plant Pathology
> Rm 3086, Cordley Hall
> Oregon State University
> Corvallis, OR 97331
> Web: www.plantontology.org
> 
> Phone: 541-737-5272
> Fax: 541-737-3573
> Skype: cooperlol910
> ***********************************************************
> 
> 

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