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[bioontology-support] A Bug Report and Two Questions

Anders Riutta anders.riutta at gladstone.ucsf.edu
Tue Oct 28 16:04:14 PDT 2014


That solved it. Thanks!
Anders

----- 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: Tuesday, October 28, 2014 3:56:00 PM
> Subject: Re: [bioontology-support] A Bug Report and Two Questions
> 
> 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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