Search Mailing List Archives

Limit search to: Subject & Body Subject Author
Sort by: Reverse Sort
Limit to: All This Week Last Week This Month Last Month
Select Date Range     through    

[bioontology-support] About the issue of annotating

Zhou, Shuxin sz23 at
Wed Mar 17 18:42:08 PDT 2021

Hi Mr.Graybeal,

Thank you for the quick response! I do appreciate it very much!
In addition to the issue, we tried some other concepts which are included
in the RCIT_A1 ontology as well.
The problem is:
(1). For the classes ending with "L/min", 3 out of 6 are annotated out. Why
half of them can be annotated, but the rest cannot?
(2). For concepts like: "3 days ago", "3 days later", "three days ago" (
which is the synonym of "3 days ago") are not successfully recognized, but
wrongly annotated by another class "3 days".
      Since they are 3-character concepts, they should meet with the
indexing rule you mentioned.

I apologize for disturbing you again, but our team needs to know the reason
for such annotation results, then we can continue our research on the basis
of that.
Again, thank you very much for the help!
[image: Screen Shot 2021-03-17 at 9.14.18 PM.png]
[image: Screen Shot 2021-03-17 at 9.18.30 PM.png]

On Wed, Mar 17, 2021 at 8:25 PM John Graybeal <jgraybeal at>

> 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.
> John
> On Mar 16, 2021, at 5:00 PM, Zhou, Shuxin <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
> --
> [image: NJIT logo] <> *Shuxin Zhou*
> Phd Student of SABOC Lab
> sz23 at
> _______________________________________________
> bioontology-support mailing list
> 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
-------------- next part --------------
An HTML attachment was scrubbed...
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2021-03-17 at 9.14.18 PM.png
Type: image/png
Size: 33904 bytes
Desc: not available
URL: <>
-------------- next part --------------
A non-text attachment was scrubbed...
Name: Screen Shot 2021-03-17 at 9.18.30 PM.png
Type: image/png
Size: 164725 bytes
Desc: not available
URL: <>

More information about the bioontology-support mailing list