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

Chen Yang Chen.Yang at UGent.be
Mon Aug 13 15:59:52 PDT 2018


Dear Jennifer and John,
I am really sorry for what I said before. Yes, BioPortal did mappings automatically.
Could you please inform me once you solve the issue? It is also possible that I uploaded an file with errors, but I am not able to detect by myself.
I would be more than happy to hear from you, it would be a good opportunity for me to improve my understanding of ontology.
Thank you in advance.
Best regards,
Chen

From: Jennifer Leigh Vendetti [mailto:vendetti at stanford.edu]
Sent: 13 August 2018 20:42
To: Chen Yang <Chen.Yang at UGent.be>
Cc: support at bioontology.org
Subject: Re: [bioontology-support] [BioPortal] Feedback from chen.yang at ugent.be

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:image001.png at 01D43368.E178E940]

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:image002.png at 01D43368.E178E940]


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:

https://github.com/ncbo/ontologies_api/issues/50

Apologies for this inconvenience.

Kind regards,
Jennifer




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

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

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

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.

John

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

Hi Jennifer,

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

I import NCIT class “Administration” (http://ncicb.nci.nih.gov/xml/owl/EVS/Thesaurus.owl#C25409) 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,
Chen


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

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,
Jennifer






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

Name: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Email: chen.yang at ugent.be<mailto:chen.yang at ugent.be>
Location: http%3A%2F%2Fbioportal.bioontology.org<http://2fbioportal.bioontology.org/>%2Fontologies%2FONE%3Fp%3Dclasses%26conceptid%3Droot

Feedback:
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
650-736-1632

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