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[bioontology-support] [ncbo-annotator-users] Sample OBA Java client code

Clement Jonquet jonquet at lirmm.fr
Wed Apr 25 00:44:00 PDT 2012


Hi Sanson, 

 

We recommended to use « virtual ontology id » (i.e. an id that do not change
across versions) when using the Annotator writing an application that do not
care about a specific version. This will free you of going back to your code
each time a new version is added to the Annotator backend DB and previous
version removed.

 

The important thing is to let the Annotator know that your ontology ids are
“virtual ontology id” by activating having the parameter
isVirtualOntologyId=true.

 

Concerning the views, as far as I know the ontology views are not grabbed in
the backend DB.

In order to avoid having to many annotations generated by the Annotator
workflow (also used for the NCBO Resource Index) we have decided in the past
to make available only the latest version of ontologies and not views,
although it is technically possible. Trish and Ray will confirm if this
stamen is still true today.

I am actually building a version of the Annotator using only views. I can
update you on this next week if you want (I will be in Stanford for 2
weeks).

 

Clement

 

 

 

 

De : annotator-discuss at googlegroups.com
[mailto:annotator-discuss at googlegroups.com] De la part de Samson Tu
Envoyé : mardi 24 avril 2012 20:45
À : annotator-discuss at googlegroups.com
Objet : Re: [ncbo-annotator-users] Sample OBA Java client code

 

Thanks. I was able to get the archived software for the OBA client.

 

The OBA documentation emphasizes the need to use the "virtual ontology id."
Is the "ontology id" displayed in the Bioportal browser for each ontology a
virtual ontology id? (For example, for ICF, the "ontology id" displayed in
the ontology browser is 1411. Is that the virtual ID? It would be good if
the labeling of ontologies can be made consistent with the documentation on
how to use them.

 

Can one use views of an ontology instead of the ontology as the source of
concepts? The OBA interface for annotating short fragments does not allow
one to enter views as sources of annotation concepts. The html OBA client
returned an empty set of annotations when I used the "ontology id" of an ICF
view.

 

Thank you.

 

With best regards,

Samson 

On Thu, Apr 19, 2012 at 11:52 PM, Trish Whetzel <plwhetzel at gmail.com> wrote:

It looks like the httpclient 3.1 can be downloaded from:
http://archive.apache.org/dist/httpcomponents/commons-httpclient/binary/

This is in the directory from the "archives" link on:
http://hc.apache.org/downloads.cgi  .. this link is mentioned in Java sample
code section on:
http://www.bioontology.org/wiki/index.php/Annotator_Client_Examples#Java_cli
ent_example

Trish 

 

On Thu, Apr 19, 2012 at 11:15 PM, Samson Tu <samsontu at gmail.com> wrote:

I don't see any place to download the older modules.

 

Samson

 

On Thu, Apr 19, 2012 at 11:01 PM, Trish Whetzel <plwhetzel at gmail.com> wrote:

Hi Samson, 

Thanks for the information. I'll submit a tracker item on this.  Are you
able to get the Java code running using the older modules or is this a
blocker?

Trish 

 

On Thu, Apr 19, 2012 at 10:00 AM, Samson Tu <samsontu at gmail.com> wrote:

The Commons HttpClient project  is now end of life and is being replaced by
the  <http://hc.apache.org/> Apache HttpComponentsproject in its
<http://hc.apache.org/httpcomponents-client-ga> HttpClient and
<http://hc.apache.org/httpcomponents-core-ga/> HttpCore modules. Is there
any plan to update the sample Java code for OBA client?

 

Thank you.

 

With best regards,

Samson 

 

 

 

 

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