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[bioontology-support] [BioPortal] Feedback from Olivier Rossel

Ray Fergerson ray.fergerson at
Wed Jul 31 16:58:08 PDT 2013


Our entire system is available as either a VMware VM or Amazon EC2 instance 
and people can and have set it up with content outside of biomedicine. There 
is an "earth portal" for example that is based on BioPortal. There is also a 
"marine biology portal". We are happy at this point in having outside users 
set up non-biomedical ontology portals. We prefer that others not compete 
with us, using our own software, in the biomedical space...

BTW, the software is open source under a very non-restrictive license (BSD 

If you are interested in exploring this then please send me email off-list 
and I will set you up with a VM.


-----Original Message-----
From: Olivier Rossel [mailto:olivier.rossel at]
Sent: Wednesday, July 31, 2013 3:10 PM
To: Ray Fergerson
Cc: <support at>
Subject: Re: [bioontology-support] [BioPortal] Feedback from Olivier Rossel

Hi Ray.

First let me tell you that I am a huge fan of your work on Protege. And i am 
happy to have the opportunity to talk with you.

Next, i will tell you my opinion about the concept search in the portal.
I think it is a great tool for ontology engineers. Valuable to many 
communities. And with virtually no alternative (concept search is a wreck in 
the Semantic Web).

I presume most of your funding comes from the field of biomedical, so I 
understand you focus on services for that community.
But I really would love to have such a service available for the whole SW 

Are there any hope the concept search can be made available as a deployable 
service, or as hackable open source code, so a generic service can be 
deployed (for example) on

Envoyé de mon iPad

Le 31 juil. 2013 à 22:08, "Ray Fergerson" <ray.fergerson at> a 
écrit :

> Olivier,
> Let me address the easy questions first. You must first register and
> create a bioportal account. You can then submit an ontology from the
> top of the "Browse" page. It will show up within a day, automatically.
> It will be indexed for search when it shows up in the UI. It will be
> indexed for use by the annotator in a few weeks. This is all fairly 
> automatic.
> As for content, we are a bit flexible. We accept ontologies that are
> either in the biomedical domain and which we feel might be of interest
> to someone in biomedicine. Thus we allow generic "top level"
> ontologies and we have an ontology of places (GAZ). Neither of these
> has biomedical content be we could imagine a biomedical researcher
> might find them valuable. On the other end we have recently removed a
> generic ontology of books for being off topic. The slope is slippery
> though and it is difficult to be crisp. Curation of this sort happens
> after submission though.
> Ray
> -----Original Message-----
> From: bioontology-support-bounces at
> [mailto:bioontology-support-bounces at] On Behalf Of
> support at
> Sent: Wednesday, July 31, 2013 7:55 AM
> To: support at; olivier.rossel at
> Subject: [bioontology-support] [BioPortal] Feedback from Olivier
> Rossel
> Name: Olivier Rossel
> Email: olivier.rossel at
> Location:
> Comment:
> Hi guys,
> First, I think you have the best infrastructure to search for concepts
> in ontologies.
> My question is:
> Do you accept to reference and index ontologies that are not biomedic
> related.
> (cf for example the NASA "sweet.owl" that is already in bioportal)
> And then:
> what is the process to add an ontology to the set you are already
> indexing ?
> Can (motivated) people do that job by themselves?
> Or is there an approval to ask to your team?
> _______________________________________________
> bioontology-support mailing list
> bioontology-support at

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