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[bioontology-support] [BioPortal] Feedback from Baker

Sam Rathnayake Sam.Rathnayake at
Wed Mar 21 18:59:17 PDT 2018

Hi John,

Thank you very much for the response and my apologies for late reply to you.

We appreciate your willingness to lead the process yourself.

Still we currently in the process of finding ontology data provider for Australian standards.

Do you have any idea whether we can upload Ontology list (ex: MIMS under their approval) in to Bioportal as one go and we can review the list timely based say once every quarter and re-upload the list?

I'll let you know the outcome.


From: John Graybeal [mailto:jgraybeal at]
Sent: Thursday, 15 March 2018 1:04 PM
To: support at
Cc: Sam Rathnayake <Sam.Rathnayake at>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Baker

Hello Sam,

Thank you for your interest.  I'm going to give a general answer for the benefit of the list, our team can follow up according to your preferences.

BioPortal is a community ontology repository, and anyone can add any ontologies for which they have permission to do so.  So you could either encourage them to add it, get their permission to add it for them, or get us the contact information of the responsible party so that we can contact them. The advantage of the first option is that they will be able to maintain the BioPortal distribution as part of their operational workflow, and ensure that any changes are updated and represented correctly as they occur.

While in the last case we are willing to lead the research process ourselves, you can speed up the process by doing any of the following parts of the process: finding a URL that presents the ontology in OWL (.ttl or other variants will work) or OBO formats, determining who the responsible manager is, and getting their permission for putting the ontology in BioPortal.

As a side note, it is often the case that if it is difficult to find the ontology served in a standard way, the authors may not want it published elsewhere. If that is the case, of course we would not be able to help.


On Mar 14, 2018, at 5:14 PM, support at<mailto:support at> wrote:

Name: Baker
Email: sam.rathnayake at<mailto:sam.rathnayake at>

Email: sam.rathnayake at<mailto:sam.rathnayake at>
Organisation: Baker Heart & Diabetes Institute, Australia
Currently we use RedCap web based survey application internally. We use your APIkey for biomedical ontology. But we can't find MIMS in your list which is the standard for Australia.
Just wandering whether there is an standard procedure to request adding new antology in to your list?

bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

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

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