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[bioontology-support] RELATED synonyms are not working

Ray Fergerson ray.fergerson at
Wed Mar 19 15:48:52 PDT 2014

I think that I may have misunderstood your request. The
"include_properties" parameter is on the search REST call. It looks like
instead you are using the widgets to do autocomplete. We can't really add
"include_properties" to a widget based dropdown list and have it do
anything reasonable. Include properties would do matches on definitions,
for example, and we have no easy way to display such a thing.


Can you provide a use case where matches on "related synonyms" are useful
but where you do not want matches on the real (exact) synonyms for the
term. This would seem to be me to an uncommon situation.




From: sridevi polavaram [mailto:spolavar at] 
Sent: Wednesday, March 19, 2014 12:48 PM
To: Ray Fergerson
Cc: Samson Tu; BioPortal Curators; bioontology-support at
Subject: Re: RELATED synonyms are not working


Hi Ray, 
That's great! But i am not sure where exactly the include_properties
parameter goes. Is there any example available? 

I initiate the search using this:

<input type="text" name="str" id="str" size="50" onfocus=""
class="bp_form_complete-NMOSP_1_6" size="100"> 

Thank you,





On Wed, Mar 19, 2014 at 3:18 PM, Ray Fergerson
<ray.fergerson at> wrote:



You can search on all property values (including "related synonyms") by
using the include_properties=true switch on the search command.




From: sridevi polavaram [mailto:spolavar at] 
Sent: Wednesday, March 19, 2014 3:10 AM
To: Ray Fergerson
Cc: Samson Tu; BioPortal Curators; bioontology-support at
Subject: Re: RELATED synonyms are not working


Hi Ray, 

 I have checked back into my test cases that i ran before. I was using
this: bp_form_complete-2072-name to search for synonyms, and to my
surprise, i realized that I may very well be under the wrong impression
that Bioportal allows RELATED synonym searches. I have to fix my ontology
file and re-upload it.

But can i ask what is the rationale behind allowing only EXACT synonyms
and eliminating the RELATED? and why can't the user make that choice
whether he wants to use one or the other or both? 




On Mon, Mar 17, 2014 at 7:02 PM, Ray Fergerson
<ray.fergerson at> wrote:

It is true that we only recognize OBO exact synonyms as "bioportal
synonyms". The other things are not synonyms in normal English usage, even
though the word synonym is in the label. This has always been the case
though. You indicate below that you think that this was not always the
case. Can you explain when this behaved differently?




From: sridevi polavaram [mailto:spolavar at] 
Sent: Monday, March 17, 2014 4:17 AM
To: Samson Tu; Ray Fergerson; BioPortal Curators;
bioontology-support at
Subject: RELATED synonyms are not working


I have noticed something different in the newly upgraded web services in
bioportal. My newly created project is now accessible via the following

i was browsing:

and i was testing out the autocomplete widget (especially Example 3 which
gets the preferred name for a class), but i see that synonyms tagged as
'RELATED' are not being recognized. Previously, i remember this was not
the case. 

hasRelatedSynonym terms are not being picked up in the auto completion.
e.g., birds, WIP KO, roundworms, 

only hasExactSynonym are working

e.g., sheep, carnivores, etc.

The OBO ontology that i have uploaded mostly has RELATED synonyms with
very important information. Is there a way to include them in my
auto-complete searches?

Thank you




On Sat, Mar 15, 2014 at 2:53 PM, Samson Tu <swt at> wrote:

Submitting an ontology

Go to the "Browse" page (on Bioportal web site) and press the "Submit
Ontology" button near the top of the page.


On Mar 15, 2014, at 11:34 AM, sridevi polavaram <spolavar at>


Hi Samson, 

 Finally it worked! thanks for your suggestion. But now, how do i upload
my ontology? i don't see any link  that allows me to upload! 




Samson Tu                                                     email:
swt at

Senior Research Scientist                               web:

Center for Biomedical Informatics Research  phone: 1-650-725-3391

Stanford University                                          fax:








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