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[bioontology-support] About the issue of annotating

John Graybeal jgraybeal at
Wed Mar 17 17:24:55 PDT 2021

hello Erica,

I am not 100% sure of the source of the problem, but I have written up the ticket about it.

As the ticket suggests, I suspect this is a function of BioPortal not indexing words shorter than 3 characters, including numbers. (If this is true, then Segment 6 works only by accident, it's the first term beginning with 'segment' *and* it matches.) BioPortal won't index those shorter words because they are so likely to be matched elsewhere. Though certainly the full label should be indexed, that's something we could verify if we had resources.

Unfortunately we are unlikely to be able to fix it right now, as we have extraordinarily limited staff time. I am sorry I can't provide a more helpful answer at this point.


On Mar 16, 2021, at 5:00 PM, Zhou, Shuxin <sz23 at<mailto:sz23 at>> wrote:

Dear BioPortal Technical Team,
This is Erica Zhou, and I met some problems with using the BioPortal annotator page.
I uploaded a private ontology RCIT_A1 a few days ago, and some concepts(classes) were not successfully referred to when I tried to annotate certain text.

For example, I have a text containing "segment 7", "segment 6", and "segment 4A", and they are all included in RCIT_A1.
<Screen Shot 2021-03-16 at 7.52.28 PM.png>

But only "segment 6" is recognized as below, but "segment 7" and "segment 4A" are not correctly annotated out, instead, they are annotated partially to "Segment".
<Screen Shot 2021-03-16 at 7.55.42 PM.png>

So, could you help me fix this issue? I would appreciate it very much!

Best regards
Shuxin(Erica) Zhou

[NJIT logo]<>      Shuxin Zhou
Phd Student of SABOC Lab

sz23 at<mailto:sz23 at>
bioontology-support mailing list
bioontology-support at<mailto:bioontology-support at>

John Graybeal
Technical Program Manager
Center for Expanded Data Annotation and Retrieval /+/ NCBO BioPortal
Stanford Center for Biomedical Informatics Research
650-736-1632  | ORCID  0000-0001-6875-5360

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