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[bioontology-support] RELATED synonyms are not working

sridevi polavaram spolavar at gmail.com
Thu Mar 27 08:13:32 PDT 2014


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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