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[bioontology-support] RELATED synonyms are not working

sridevi polavaram spolavar at gmail.com
Wed Mar 19 03:10:06 PDT 2014


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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