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[bioontology-support] Bioportal Annotator

Sarantis, Demetrios demetrios.sarantis at
Mon Oct 13 10:45:07 PDT 2014


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

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


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.


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

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

Thank you



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