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[bioontology-support] RELATED synonyms are not working

sridevi polavaram spolavar at gmail.com
Wed Mar 19 12:47:41 PDT 2014


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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