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[bioontology-support] A Bug Report and Two Questions

Paul R Alexander palexander at stanford.edu
Tue Oct 28 15:56:00 PDT 2014


Sorry, that's not a very informative error message. Could you try capitalizing the whole thing? So you would use WIKIPATHWAYS instead of wikipathways.

Paul


> On Oct 28, 2014, at 3:07 PM, Anders Riutta <anders.riutta at gladstone.ucsf.edu> wrote:
> 
> Another issue: I am trying to submit a new ontology for the WikiPathways vocabulary [3], but when I choose the acronym "wikipathways", I get the following error:
> 
> Errors On Form
> acronym_value_validator : The acronym value wikipathways is invalid
> 
> Thanks.
> Anders
> 
> [3] http://vocabularies.wikipathways.org/wp
> 
> 
> ----- Original Message -----
>> From: "Anders Riutta" <anders.riutta at gladstone.ucsf.edu>
>> To: "Paul R Alexander" <palexander at stanford.edu>
>> Cc: support at bioontology.org
>> Sent: Tuesday, October 28, 2014 2:20:40 PM
>> Subject: Re: [bioontology-support] A Bug Report and Two Questions
>> 
>> Hi Paul,
>> 
>> Thanks for the response. I went to the URL at [1], but it took me to a page
>> with the message "The page you are looking for wasn't found. Please try
>> again." Changing "&t=mappings" to  "#mappings" as in [2] gave me a list of
>> mappings, but I don't see an option for deleting. There is just a button to
>> "Create New Mapping".
>> 
>> Anders
>> 
>> [2]
>> https://bioportal.bioontology.org/ontologies/BP?p=classes&conceptid=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Control#mappings
>> 
>> 
>> ----- Original Message -----
>>> From: "Paul R Alexander" <palexander at stanford.edu>
>>> To: "Anders Riutta" <anders.riutta at gladstone.ucsf.edu>
>>> Cc: support at bioontology.org
>>> Sent: Monday, October 27, 2014 4:14:03 PM
>>> Subject: Re: [bioontology-support] A Bug Report and Two Questions
>>> 
>>> Thanks for reporting the problems with projects. These have now been fixed.
>>> 
>>> To delete the mapping, you can go to the class page for the class you have
>>> mapped [1] and there should be a checkbox and button for deleting.
>>> 
>>> We do not have data available in SKOS, but you can get the mapping data per
>>> ontology using our REST API and convert as needed. For example,
>>> http://data.bioontology.org/ontologies/BRO/mappings
>>> <http://data.bioontology.org/ontologies/BRO/mappings>. Documentation on
>>> using the REST API is here: http://data.bioontology.org/documentation
>>> <http://data.bioontology.org/documentation>
>>> 
>>> Please let me know if you have other questions.
>>> 
>>> Paul
>>> 
>>> [1]
>>> https://bioportal.bioontology.org/ontologies/BP?p=classes&conceptid=http%3A%2F%2Fwww.biopax.org%2Frelease%2Fbiopax-level3.owl%23Control&t=mappings
>>> <https://bioportal.bioontology.org/ontologies/BP?p=classes&conceptid=http://www.biopax.org/release/biopax-level3.owl#Control&t=mappings>
>>> 
>>> 
>>>> On Oct 22, 2014, at 12:04 PM, Anders Riutta
>>>> <anders.riutta at gladstone.ucsf.edu> wrote:
>>>> 
>>>> Hello,
>>>> 
>>>> Thanks for making the BioPortal available. It's a great resource. I have
>>>> one bug report and two questions.
>>>> 
>>>> Bug Report: When I try to access projects, I get the following error:
>>>> 
>>>> "We're sorry but something has gone wrong. We have been notified of this
>>>> error."
>>>> 
>>>> This happens both when I'm logged in
>>>> <https://bioportal.bioontology.org/projects?user=http%3A%2F%2Fdata.bioontology.org%2Fusers%2Fariutta>
>>>> and when I'm not <http://bioportal.bioontology.org/projects>.
>>>> 
>>>> Question 1: How do I delete a mapping I created? I added the following
>>>> mapping, but it's not exactly correct, so I would like to delete it.
>>>> Also,
>>>> it appears to be duplicated
>>>> Control (BP) <=> stimulation (SBO)
>>>> REST Mapping 08/17/2014 by ariutta
>>>> 
>>>> Question 2: Can I bulk download the mapping data in SKOS format?
>>>> 
>>>> Thanks.
>>>> Anders Riutta
>>>> Gladstone Institutes
>>>> _______________________________________________
>>>> bioontology-support mailing list
>>>> bioontology-support at lists.stanford.edu
>>>> https://mailman.stanford.edu/mailman/listinfo/bioontology-support
>>> 
>>> 
>> 




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