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[bioontology-support] [BioPortal] Feedback from Srilatha

Michael Dorf mdorf at stanford.edu
Tue Oct 3 13:15:59 PDT 2017


Hi Srilatha,

Thank you for writing to us. The "Include mappings” parameter does appear to be ignored. The REST service that serves the request does work correctly if you include the mapping parameter (expand_mappings=true) in the call, but the UI appears to pass a wrong parameter back to the REST API. I’ve created a Github issue to address this:

https://github.com/ncbo/bioportal_web_ui/issues/64

For the input text match, the Annotator will only match on terms that are subsets of the specific sets, not supersets. We use a technology called mgrep, developed by the University of Michigan that offers an extremely efficient string matching. Here is a direct call to mgrep using a string “Tuberculosis” (with the “match partial words” flag enabled):

ANNTuberculosis
-1200485993827614964 1 12 Tuberculosis
3237340737824699829 1 5 Tuber
649292473459365890 1 4 Tube
-6266379875759954152 1 3 Tub
-5889667316735819648 3 5 ber
8592169718518568026 4 6 erc
57772911975681607 6 8 cul
6624293267424415909 8 12 losis
7195257168618568523 8 10 los
-6423689050844403126 9 11 osi
-5916953809627475528 10 12 sis

And here is a match on a string "Tuberculosis (A15-A19)”, also with the “match partial words” flag enabled:

ANNTuberculosis (A15-A19)
6141307851558787445 1 22 Tuberculosis (A15-A19)
-1200485993827614964 1 12 Tuberculosis
3237340737824699829 1 5 Tuber
649292473459365890 1 4 Tube
-6266379875759954152 1 3 Tub
-5889667316735819648 3 5 ber
8592169718518568026 4 6 erc
57772911975681607 6 8 cul
6624293267424415909 8 12 losis
7195257168618568523 8 10 los
-6423689050844403126 9 11 osi
-5916953809627475528 10 12 sis
4292924354407803072 15 17 A15
-7761967337688627578 19 21 A19

As you can see, Tuberculosis is matched on the Tuberculosis (A15-A19) annotation, but not the other way around. This behavior is by design. By comparison, if the string “Tuberculosis” would annotate the term "Tuberculosis (A15-A19)”, then a string “cell” would annotate on “white cell”, which isn’t exactly desirable.

The best remedy to this issue would be for the makers of the ICD10CM ontology to attach a synonym “Tuberculosis” to the term "Tuberculosis (A15-A19)”.

Unlike the Annotator, our Search will match "Tuberculosis (A15-A19)" when searching on “Tuberculosis” (be sure to expand a link “72 more from this ontology):

http://bioportal.bioontology.org/search?q=Tuberculosis&ontologies=ICD10CM&include_properties=false&include_views=false&includeObsolete=false&require_definition=false&exact_match=false

Thank you again for your inquiry; feel free to contact us if you have further questions.

Michael



On Sep 20, 2017, at 11:58 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Srilatha

Email: srilatha.bandari at ggktech.com<mailto:srilatha.bandari at ggktech.com>

Location: https%3A%2F%2Fbioportal.bioontology.org<http://2Fbioportal.bioontology.org>%2F500

Feedback:

There are certain functionalities that are missing/not working. The "Include Mapping" option does not show any effect on the result whether enable/disbaled. Also, annotator does not take into account the input text that has partial class names eg:- "Tuberculosis" in the input text is not matched with "Tuberculosis (A15-A19)" class of ICD10CM ontology

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