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[bioontology-support] Help with Submission

Pan, Huaqin (Helen) hpan at
Wed Jan 24 18:05:51 PST 2018

OK. Thank you for your advice. Jennifer!

Best regards,

From: Jennifer Leigh Vendetti [mailto:vendetti at]
Sent: Wednesday, January 24, 2018 8:19 PM
To: Pan, Huaqin (Helen) <hpan at>
Cc: NCBO User Support <support at>
Subject: Re: [bioontology-support] Help with Submission

Hi Helen,

On Jan 22, 2018, at 1:59 PM, Pan, Huaqin (Helen) <hpan at<mailto:hpan at>> wrote:

Hi Jennifer,

I am working on another project that developed an ontology that I will submit soon. It’s currently available at our project site,

Here is my questions. Due to the fact that owl/Protégé display the hierarchical relation only for “subclass-of”, not “part-of”, I have developed 2 versions of the ontology in .owl for each ontology, and I need your guidance on which version to submit. I have seen both on BioPortal.

My expertise is on the software development side of things with regard to BioPortal. It’s difficult for me to comment on which version of your ontology the biomedical community might find more useful.

  *   Version 1 with exclusive “subclass_of” – Pros: display the hierarchical relationships among the classes, Cons: lacks the biological distinction of “part-of” and “subclass_of”
  *   Version 2 with mix of “part-of” and “subclass_of” – Cons: lacks the display of hierarchical relationships among the classes, Pros: captures the biological distinction of “part-of” and “subclass_of”

We used version 2 (part-of and subclass-of) for the project site, with some rules to enable the display properly for “part-of”.

One option I can suggest would be for you to create two separate ontology entries in BioPortal for your versions 1 and 2 above. You could initially make the viewing restriction “private”, which would give you the opportunity to view them and decide which seems better for your needs / use cases. After you’ve made your decision, we could remove whichever one you decide not to publish, and change the viewing restriction of your preferred ontology to “public”.

Kind regards,

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