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[bioontology-support] Bioportal Annotator

Ray Fergerson ray.fergerson at stanford.edu
Mon Oct 13 13:49:09 PDT 2014


I believe that this is fixed now, including he previously indicated
problem with "CD4". Now the matched terms for the text in the items below
all have synonyms that match the terms.

 

Let me know if you see other problematic cases.

 

Ray

 

From: bioontology-support
[mailto:bioontology-support-bounces at lists.stanford.edu] On Behalf Of
Sarantis, Demetrios
Sent: Monday, October 13, 2014 10:45 AM
To: NCBO User Support
Subject: Re: [bioontology-support] Bioportal Annotator

 

Hi

 

Are there any results/news for the annotation problem?

Some more examples:

text to be annotated    select ontologies              class(result)

INTERLEUKIN                     CYTO
INTERFERON BETA-1A

LIGHT                                    CYTO
C-X-C MOTIF CHEMOKINE 11

INTERLEUKIN                     CYTO
MACROPHAGE COLONY-STIMULATING FACTOR 1

CYTOKINES                         CYTO
PLATELET-DERIVED GROWTH FACTOR

 

The result classes are not correct. The text to be annotated does not
exist in classes' metadata.

 

Thank you

Dimitris

 

 

From: Paul R Alexander [mailto:palexander at stanford.edu] 
Sent: Friday, September 26, 2014 6:31 PM
To: Sarantis, Demetrios
Cc: NCBO User Support
Subject: Re: Bioportal Annotator

 

Dimitris,

 

I've CCed the NCBO Support email list here. It's always a good idea to
email that list with questions as there is a higher chance someone on the
list will provide an answer.

 

As for your problem, it appears as though this is a bug on our end. I've
submitted a ticket so that we can investigate the problem and we'll get
back to you.

 

Paul

 

 

On Sep 25, 2014, at 9:39 AM, Sarantis, Demetrios
<demetrios.sarantis at yale.edu> wrote:

 

Hi Paul

 

Could you please check this issue for me with the Annotator?

It produces results which seem not have any relation with the inserted
text.

Another example is CD4 (see picture). It produces three results that do
not contain CD4 in their metadata.

 

Thank you

Dimitris

 

From: Sarantis, Demetrios 
Sent: Monday, September 22, 2014 12:39 PM
To: 'Paul R Alexander'
Subject: Bioportal Annotator

 

Hi Paul

 

I would like to ask you a basic question regarding the operation of
bioportal annotator.

I insert in the text box IL-17, I select CYTO ontology and I press the
button 'Get Annotations'.

The results are 2 classes:

INTERLEUKIN-26 BINDING

DENILEUKIN DIFTITOX

None of them has IL-17 in its metadata (synonym etc.) Why has annotator
produced those results? What is the annotation rationale?

 

 

Thank you

 

Dimitris

 

 

 

<Annotator.JPG>

 

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