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[bioontology-support] RELATED synonyms are not working

sridevi polavaram spolavar at gmail.com
Mon Apr 7 09:42:23 PDT 2014


Hi Ray,
 Thanks for bringing the project and ontology difference to my attention. I
have already created the project for NeuroMorpho.Org, which is pointing to
https://bioportal.bioontology.org/projects/NMOSp. But the problem i am not
able to edit it. It throws an error message.

I want to keep the acronym NMOSP and delete everything else, I see a bunch
of NeuroMorpho.Org projects including the NMOSP_1_6. If editing error is
something you have to look into, then i would request to delete everything,
so that i can create a new project and then upload a new ontology version.

FYI. We are introducing a new search feature, which uses bioportal to our
upcoming release of NeuroMorpho.Org, for that reason, i am trying to clean
up and make sure the information is up-to-date on our project. I really
appreciate your cooperation in this regard!

Sincerely,
Sridevi


On Fri, Apr 4, 2014 at 5:49 PM, Ray Fergerson <ray.fergerson at stanford.edu>wrote:

> 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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