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[bioontology-support] [BioPortal] Feedback from mmandal

Mandal, Meisha mmandal at rti.org
Thu Sep 2 07:18:14 PDT 2021


Hi Clement,

Thank you very much for the very thorough and quick response! What you explained makes perfect sense and we should be able to work with it now that we have a better understanding of the tool. Thanks again and have a wonderful day!

Best,
Meisha

From: Clement Jonquet <jonquet at lirmm.fr>
Date: Thursday, September 2, 2021 at 6:01 AM
To: "Mandal, Meisha" <mmandal at rti.org>
Cc: "support at bioontology.org" <support at bioontology.org>
Subject: Re: [bioontology-support] [BioPortal] Feedback from mmandal

EXTERNAL:  This email originated from outside of the organization.  Do not click links or open attachments unless you recognize the sender and know the content is safe.

Hi Meisha,

Just to reply this maybe before my colleagues at Stanford ;)

In fact, the Annotator is behaving as expected:
The word « adult » is a synonym of « adult-A stage » in AMPHX and a synonym of « adult organism » in UBERON.
While it is not in the other ontologies
e.g. « adult » is not a synonym of "human adult stage » in HSAPVD

Therefore, there is no match in HSAPVD and MMUSDV because the simple concept of « adult" does not exist in those ontologies.  A simple class search with « exact match » will confirm this :
 [cid:image001.png at 01D79FE3.D6EDF2F0]

So to come back to your question :
Is there a way to get the annotator to return longer matches
No. Because the Annotator does not work like a search tool. It can’ return things that are not explicitly defined in the ontology. Simply because « a longer match » will not be a right/valid annotation. According to the original developers of the ontologies (in our case HSAPVD and MMUSDV) the concept of « adult » doe snot exist in their ontologies.

If you believe the « adult » should be a synonym  of some concepts in HSAPVD and MMUSDV, then the request should come up to the HSAPVD and MMUSDV ontology developper to consider if yes or not « adult » is a relevant synonym for the concepts they have defined in their ontologies.
BioPortal offers

Note the other way around would work :
The Annotator offers the « match longest only » option. This option is used for instance to get in AMPHX only the match with « adult-A stage » and not the second, less precise annotation with « adult » (i.e; a shorter one) ASSUMING the sentence given contains the expression « blabla adult-A stage blabla bla ».

I hope it helps.
Clement

-------------------------------------------------------------------------------------------
Dr. Clement JONQUET  –  PhD in Informatics
Associate Research Scientist – INRAE (MISTEA)
Associate Professor – University of Montpellier (LIRMM)
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Le 1 sept. 2021 à 17:11, support at bioontology.org<mailto:support at bioontology.org> a écrit :

Name: mmandal
Email: mmandal at rti.org<mailto:mmandal at rti.org>
Location: https%3A%2F%2Fbioportal.bioontology.org<https://nam04.safelinks.protection.outlook.com/?url=http%3A%2F%2F2fbioportal.bioontology.org%2F&data=04%7C01%7Cmmandal%40rti.org%7C2fd1f320a882493c97ed08d96df8712e%7C2ffc2ede4d4449948082487341fa43fb%7C0%7C0%7C637661737117699592%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C1000&sdata=bIW%2B2t4MHdLb6YzjJWMPYJZoqAceZ9PT3QWCNeUgaao%3D&reserved=0>%2F

Feedback:
Hi, I am using your annotator tool and am hoping to get some help with an issue I'm running into an issue with certain ontologies. I'm trying to annotate a list of terms and the annotator tool appears to have different behavior depending on the ontology. For example, I am trying to annotate the word "adult". The annotator will return matches with phrases such as "adult organism" or "adult-A- stage" in Uber and AMPHX where the search term is contained within the match which is longer. However, it doesn't return "Human Adult Stage" for HSAPDV or "aged adult stage", "late adult stage", or "early adult stage" for MMUSDV unless you search for the entire phrase. Is there a way to get the annotator to return longer matches as it does with Uber, for ontologies such as HSAPDV and MMUSDV? Thanks! Meisha Mandal (mmandal at rti.org<mailto:mmandal at rti.org>)

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