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[bioontology-support] Ontology identifiers, API key

Pradnya Gawade pgawade at openclinica.com
Fri Jan 27 09:20:07 PST 2012


Paul,

 

By Acronym were you referring to the ontology abbreviation like MDR in
case of MEDDRA? If yes, I guess it is not editable. Meaning probably we
cannot generate it on my web application side and replace it on
BioPortal. Also not sure if it can be used with web services.

 

Thank you,

Pradnya

 

________________________________

From: Pradnya Gawade 
Sent: Thursday, January 26, 2012 11:57 AM
To: 'Paul R Alexander'
Cc: bioontology-support at lists.stanford.edu
Subject: RE: [bioontology-support] Ontology identifiers, API key

 

Hi Paul,

 

Thank you for your reply.

 

About the identifiers, where do I see the acronym for an ontology? Can I
use it with REST web services in place of ontology id and ontology
version id? From your answer it seems is should be editable, is that
correct?

 

About the API key enabling, I do not know which version of BioPortal we
are using on VM appliance? How can I know the version? I tried to
explore the software for it but did not get the answer. I had downloaded
it from
http://www.bioontology.org/ncbo-appliance/ncbo-appliance-v0.2.ova on
7/13/11
<http://www.bioontology.org/ncbo-appliance/ncbo-appliance-v0.2.ova%20on%
207/13/11> . Should this version have API key protection enabled on it?
If not, is there any newer version of VM appliance released which has
API key protection enabled?

 

Thank you,

Pradnya

 

________________________________

From: Paul R Alexander [mailto:palexander at stanford.edu] 
Sent: Wednesday, January 25, 2012 7:09 PM
To: Pradnya Gawade
Cc: bioontology-support at lists.stanford.edu
Subject: Re: [bioontology-support] Ontology identifiers, API key

 

Pradnya,

1.	I see that some of the bioportal REST web services need ontology
id and some need ontology version id as parameter depending on what they
serve. I am using my own instance of bioportal  and as far as I
understand when we upload a new ontology, both these identifiers are
generated by bioportal and we cannot edit them.

Correct, these identifiers are generated. However, you can use the
acronym as a consistent identifier.



2.	How to enable API key on bioportal VM image? With the VM image
we have presently, I can access the REST web services without providing
any API key, so I believe I will have to enable the API key protection
explicitly. 

These cannot be enabled or disabled as it is a fundamental change to the
NCBO codebase. If you're running an older NCBO Virtual Appliance image
then you will not have them while the newer ones do.

Paul R Alexander
Web / UI Developer
NCBO BioPortal
Stanford Center for Biomedical Informatics Research


On 1/24/12 11:13 AM, Pradnya Gawade wrote: 

Hi Trish,

 

Few questions for you or any body else on the list to answer. Thanks in
advance.



1.	I see that some of the bioportal REST web services need ontology
id and some need ontology version id as parameter depending on what they
serve. I am using my own instance of bioportal  and as far as I
understand when we upload a new ontology, both these identifiers are
generated by bioportal and we cannot edit them.

For the integration of my web application with bioportal, we wanted to
maintain the generation of dictionary identifier (we call them as
dictionary oid) on my web application side. Is it possible to accomplish
this with bioportal? 

Just FYI here that we are going to maintain every individual dictionary
version as its own separate dictionary for bioportal (called "private"
ontology supported in bioportal 3.4).

 

2.	How to enable API key on bioportal VM image? With the VM image
we have presently, I can access the REST web services without providing
any API key, so I believe I will have to enable the API key protection
explicitly. 

 

Thank you,

Pradnya








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