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[bioontology-support] RELATED synonyms are not working

Ray Fergerson ray.fergerson at stanford.edu
Fri Apr 4 14:49:00 PDT 2014


We will look into this. It is unclear why the system says that you can't
use these acronyms. From what I can see they do not appear to be taken.

 

For clarity though, from your screenshot you are attempting to create an
Ontology in BioPortal and not a Project. A "Project" is a team that uses
BioPortal one or more ontologies.

 

Ray

 

From: sridevi polavaram [mailto:spolavar at gmail.com] 
Sent: Wednesday, April 2, 2014 9:38 AM
To: Ray Fergerson
Cc: Samson Tu; BioPortal Curators; bioontology-support at lists.stanford.edu
Subject: Re: RELATED synonyms are not working

 

Ray, 

 I am trying to create a new project like you suggested, but i am
consistently getting an error saying acronym already exists. the choices i
am making are NMOSPTAXON, NMOTAXON_SP, etc. i don't believe these are
taken!

Thank you, 
Sridevi

 

 

On Fri, Mar 28, 2014 at 5:22 PM, Ray Fergerson
<ray.fergerson at stanford.edu> wrote:

Sridevi,

 

We will try to get the "synonym" business cleaned up with the OBO Foundry
folks. For now though only "exact synonyms" count as synonyms in
BioPortal. You can search all other properties, including the other
synonym types, by using the "include_properties parameter on search.

 

We use the ontology acronym to index lots of information about an
ontology. Thus we do not allow it to be changed. Admittedly we should
advertise this 'feature' more clearly. Thus to do what you want, create a
new ontology with the acronym that you want and submit the versions of the
ontology that you want to keep. Then send us email to have us delete the
original ontology. Sorry that this is so painful.

 

Ray

 

From: sridevi polavaram [mailto:spolavar at gmail.com] 
Sent: Thursday, March 27, 2014 8:14 AM


To: Ray Fergerson
Cc: Samson Tu; BioPortal Curators; bioontology-support at lists.stanford.edu
Subject: Re: RELATED synonyms are not working

 

Hi Ray, 
 Sorry, i got off track with other things, but i do have some
clarifications to make. To answer your question, i use *both* related and
exact synonyms for searching the species taxonomy, which is layered on top
of NeuroMorpho.Org. Since the data is heterogeneous the search keywords
vary from lay man terms to gene specific terms. The semantics between the
related and exact synonyms is not well-defined. I integrate multiple
ontologies, and i have noticed various ontologies using them very loosely.
But, from an informatics perspective these annotations still help augment
data visibility. 

One simple example is reptiles vs. testudines. It would be nice if the
bioportal auto completion can point to the preferred name 'testudines'
when keyword 'reptiles' is entered. I don't understand why definitions and
synonyms should be mixed together in the 'related synonyms', if anything,
it makes more sense to allow various types of synonyms to be searched
together.

Given that OBO allows for adding custom synonym types, i can imagine by
choosing to allow one or more synonym types (in this case related and
exact) one can make their searches more specific vs. general. 

Lastly, i have couple of questions. 

- Can i change the acronym of my ontology? if so, i would like to drop
_1_6 from NMOSP_1_6. I tried by editing the ontology but i get an error.

- I notice discrepancy in metrics. I know that my recent upload v1.8 has
1420 terms, but the metrics show only 1342. 

Thank you
Sridevi

 

 

 

 

On Wed, Mar 19, 2014 at 6:48 PM, Ray Fergerson
<ray.fergerson at stanford.edu> wrote:

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.

 

Ray

 

From: sridevi polavaram [mailto:spolavar at gmail.com] 
Sent: Wednesday, March 19, 2014 12:48 PM


To: Ray Fergerson
Cc: Samson Tu; BioPortal Curators; bioontology-support at lists.stanford.edu
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,

Sridevi

 


 


 

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

Sridevi,

 

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

 

Ray

 

From: sridevi polavaram [mailto:spolavar at gmail.com] 
Sent: Wednesday, March 19, 2014 3:10 AM
To: Ray Fergerson
Cc: Samson Tu; BioPortal Curators; bioontology-support at lists.stanford.edu
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? 

Thanks

Sridevi

 

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

 

Ray

 

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

 

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

i was browsing:
http://bioportal.bioontology.org/ontologies/NMOSP_1_6?p=classes

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

Sridevi

 

 

On Sat, Mar 15, 2014 at 2:53 PM, Samson Tu <swt at stanford.edu> 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 gmail.com>
wrote:

 

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! 

Thanks
Sridevi

 

-- 

Samson Tu                                                     email:
swt at stanford.edu

Senior Research Scientist                               web:
www.stanford.edu/~swt/

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

Stanford University                                          fax:
1-650-725-7944

 

 

 

 

 

 

 

 

 

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