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[bioontology-support] RELATED synonyms are not working

sridevi polavaram spolavar at gmail.com
Mon Apr 14 08:43:04 PDT 2014


Ray,
 I finally got this working! I have uploaded my new ontology file at
version 1.0 as NMOSP.

You can go ahead and delete this:
http://bioportal.bioontology.org/ontologies/NMOSP_1_6

One of the major confusions i have had is that the projects and ontology
upload forms and how they are being accessible. I still am not clear what
is a project and how is it being used. Please go ahead and remove all the
projects related to NeuroMorpho.Org, if they are independent of the newly
created NMOSP ontology, I am not using them. I hope, this is a helpful
feedback!

Thank you for your timely responses. I will be playing a lot more with your
system in the next six months and will keep you posted.

Best,
Sridevi


On Sat, Apr 12, 2014 at 2:16 PM, sridevi polavaram <spolavar at gmail.com>wrote:

> Hi Ray,
>  I was successfully able to rename my ontolody in one place:
> https://bioportal.bioontology.org/ontologies/NMOSP_1_6
>
> However, i still see there are at least two other project links, which i
> am unable to edit, and all of them still have the NMOSP acronym.
> 1. https://bioportal.bioontology.org/projects/NMOSP_1_6
> 2. https://bioportal.bioontology.org/projects/NMOSp
> 3. https://bioportal.bioontology.org/projects/NMOSP
>
> None of 1, 2, & 3 are edit-able.
>
> I am still unable to create a new project (it is throwing the same error
> message - we have been reported...) with the acronym NMOSP and name
> NeuroMorpho.Org species ontology.
>
>
> Thank you,
> Sridevi
>
>
> On Tue, Apr 8, 2014 at 7:25 PM, Ray Fergerson <ray.fergerson at stanford.edu>wrote:
>
>> OK, we have figured this out. It turns out that both the acronym and the
>> ontology name must be unique. Unfortunately if the name is not unique the
>> system would say that the acronym was not unique! We are fixing this. To
>> handle your specific problem now, change the old ontology name to something
>> else (“old x”) and then create the new ontology with the name you want and
>> transfer whatever submissions you want. Then we can delete the old one.
>>
>>
>>
>> Sorry about the confusion.
>>
>>
>>
>> Ray
>>
>>
>>
>> *From:* sridevi polavaram [mailto:spolavar at gmail.com]
>> *Sent:* Monday, April 7, 2014 9:42 AM
>>
>> *To:* Ray Fergerson
>> *Cc:* Samson Tu; BioPortal Curators;
>> bioontology-support at lists.stanford.edu
>> *Subject:* Re: RELATED synonyms are not working
>>
>>
>>
>> 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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>
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