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[bioontology-support] Ontology identifiers, API key

Paul R Alexander palexander at stanford.edu
Fri Jan 27 11:47:54 PST 2012


Pradnya,

> 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?
>
It is editable if you are the one that submitted the ontology (or if you 
are an administrator of an NCBO Virtual Appliance). We're looking at 
implementing lookups using the abbreviation in a future version.

> 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.
>
Yes, acronym == abbreviation in this case. It is not editable unless the 
conditions above are met. However, if you administer an ontology or a 
Virtual Appliance then you can edit it. When we enable lookups using the 
abbreviation, we likely won't allow you to easily change the 
abbreviation once an ontology has been created in the system.

> 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?
Version .2 does not have API Key protection enabled, this started in 
version .3. We'll be releasing a new NCBO Virtual Appliance version in 
the coming weeks, I would recommend waiting until that is out before you 
decide to upgrade.

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


On 1/26/12 8:56 AM, Pradnya Gawade wrote:
>
> 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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