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[bioontology-support] bioportal server error

Ray Fergerson ray.fergerson at
Thu Apr 21 11:17:53 PDT 2011


Unfortunately there isn’t a paper describing the existing architecture. 
Apparently no one is excited about writing one since we are planning to 
replace it. Below is a short description of where we are and where we are 
going. The end-state diagram is attached.

Currently the lowest levels of storage for all information in BioPortal, 
other than mappings, are a number of MySQL databases. These are not 
publically queriable. On top of these for various features are LexEVS, 
Protégé, and some custom NCBO layers for annotation and resource index. 
These are all in Java. There is also a Java layer that conceals the 
distinctions between LexEVS and Protégé. Above this is the REST API layer. 
This is the only publically available layer. The UI calls this layer 
exclusively. This layer is available for external users to use 

Mappings are currently handled differently. Mappings have been ported to use 
a triple-store (as a sort of experiment) but this triple-store is not 
publically queriable (yet).  There is a public triple-store prototype for an 
old set of ontologies but this is not maintained and there is no assurance 
that the production triple store implementation of BioPortal will look like 
this triple-store.

Our long term plan is to replace many of the MySQL databases with a 
triple-store. This includes all of the ontology storage pieces. This 
triple-store will be publically queriable with SPARQL.  There will also be a 

I am unwilling to commit publically to a date for when this work will be 
complete. We will begin working on it though within the next few months. It 
is a big effort. When we gain more experience we will be better able to 
estimate the effort.


From: Nigam Shah [mailto:nigam at]
Sent: Thursday, April 21, 2011 7:28 AM
To: Dhaval, Rakesh
Cc: Ray Fergerson
Subject: Re: bioportal server error

Hi Rakesh,

Not right now. Currently it is all relational databases (except the where there is a triple store).

Ray fergerson, our project manager, can tell you more about the most current 
architecture of BioPortal.



On Apr 21, 2011, at 6:21 AM, "Dhaval, Rakesh" <Rakesh.Dhaval at> 

Hi Nigam,

>From what I have read, I understand that Bioportal uses an RDF store as 
backend. Do you have a paper describing the most current architecture of 




From: Dhaval, Rakesh
Sent: Friday, December 17, 2010 11:26 AM
To: Trish Whetzel
Cc: Nigam Shah; support at
Subject: Re: bioportal server error

Thanks Trish.

From: Trish Whetzel <whetzel at>
Date: Fri, 17 Dec 2010 11:25:18 -0500
To: Rakesh Dhaval <rakesh.dhaval at>
Cc: Nigam Shah <nigam at>, "support at" 
<support at>
Subject: Re: bioportal server error

Hi Rakesh,

Our sysadmin informs me that the problem is resolved. I've run a few test 
queries and they are working properly.


On Dec 17, 2010, at 8:12 AM, Dhaval, Rakesh wrote:

Hi Nigam/Trish,

Is the bioportal instance down at this time.  It displays internal server 
error at this time.

Can you please let me know when will it up?



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