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[bioontology-support] [BioPortal] Feedback from chen.yang at

Jennifer Leigh Vendetti vendetti at
Mon Aug 13 11:42:10 PDT 2018

Hello Chen,

BioPortal did generate the mapping that John mentioned below. You can see that mapping by selecting the Administration class in the ONE ontology, then clicking the Class Mappings link on the right-hand side. I’ve included a screenshot below of the LOOM and SAME_URI mappings that were generated for that term in the NCIT ontology:

[cid:B5EDCB4A-DF35-4D9D-A636-96B947E36CFA at]

What’s not clear to me is why the ontology-level mappings pane is empty (i.e., the tab that you navigate to by clicking the top-level “Mappings” link):

[cid:A38B3AD5-2EA1-4265-8D65-01D60AEB71CC at]

The same issue was reported for another ontology in BioPortal a couple of weeks ago. We have an existing issue in our tracker for this, so I’ve added a comment indicating that it’s happening with the ONE ontology:

Apologies for this inconvenience.

Kind regards,

On Aug 13, 2018, at 12:12 AM, Chen Yang <chen.yang at<mailto:chen.yang at>> wrote:

Hi John, thanks. However, there is no mapping automatically created by BioPortal. Chen

From: John Graybeal [mailto:jgraybeal at]
Sent: 13 August 2018 07:06
To: Chen Yang <Chen.Yang at<mailto:Chen.Yang at>>
Cc: Jennifer Leigh Vendetti <vendetti at<mailto:vendetti at>>; support at<mailto:support at>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at<mailto:chen.yang at>

Chen, a quick note to consider. Because the identifiers are the same, the concepts are already considered the same, and BioPortal will automatically create a mapping between the two entries.

This does not respond directly to your question, or and it does not prevent you from creating your own mapping. I just wanted to explain how BioPortal treats this situation.


On Aug 11, 2018, at 2:45 AM, Chen Yang <Chen.Yang at<mailto:Chen.Yang at>> wrote:

Hi Jennifer,

Source class: Administration
Target ontology: NCIT
Target class: Administration

I import NCIT class “Administration” ( into ONE.
I want to indicate the “Administration” is the same as the “Administration” in NCIT.
In a word, those two “Administration” classes share the same identifier (NCIT identifier) but are in ONE and NCIT respectively.

Best regards,

From: Jennifer Leigh Vendetti [mailto:vendetti at]
Sent: 11 August 2018 03:09
To: support at<mailto:support at>
Cc: Chen Yang <Chen.Yang at<mailto:Chen.Yang at>>
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at<mailto:chen.yang at>

Hello Chen,

Could you please tell us which two classes you’re trying to create a mapping between? I assume you’re using ONE as the source ontology. What is the source class, target ontology, and target class?

Thank you,

On Aug 10, 2018, at 2:35 AM, support at<mailto:support at> wrote:

Name: chen.yang at<mailto:chen.yang at>
Email: chen.yang at<mailto:chen.yang at>

Dear Jennifer and John,
For class mappings, now I can choose the target class, however, when I click "create mapping" in the bottom of the page, an error was reported and 1 sentence appeared:
"There was a problem creating the mapping, please try again."
I modified url (from https to http), and used different browsers (IE, chrome, etc.). and tried again and again. The problem was still reported.
Greetings from Gent, Belgium, Chen

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John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research

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