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[bioontology-support] [BioPortal] Feedback from Jay Franklin

John Graybeal jgraybeal at stanford.edu
Wed Jun 3 14:12:54 PDT 2020


Hello Jay,

Thank you for your query. You are correct that 1- and 2-character strings are not annotated, due to the problem with spurious matches for typical short words and abbreviations.

So I would call this intentional rather than an error. Conceivably it could be partially fixed through stop words for common English words like 'a', 'no', 'in', and so on—even then you would lose annotations of many chemicals. I can't speak authoritatively about the difficulties posed by the remaining 1- and 2-character strings that have important meaning, but the fact I almost never see search support 1- and 2-letter strings makes me think it is a non-trivial problem to solve.

John

On Jun 3, 2020, at 12:53 PM, support at bioontology.org<mailto:support at bioontology.org> wrote:


Name: Jay Franklin

Email: frankj7 at rpi.edu<mailto:frankj7 at rpi.edu>

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

Feedback:

Hi,

I was using the Annotator and noticed the following behavior, and was wondering if it was intentional.
When annotating text such as "Meter," or synonyms for meter like "Metre," the units ontology concept for Meter is correctly matched to the text. However, the 'm' abbreviation for meter, which is listed as a synonym for meter in the units ontology, is not annotated with the meter concept.
This seems to hold true with any abbreviation of one or two characters, so "kg" will not be annotated with "kilogram," but "mol" will be annotated with "mole."
Is not annotating words of length two or one character(s) intentional behavior? Or is this an error in the annotator that could be fixed?

Thanks very much,
Jay Franklin
Rensselaer Polytechnic Institute

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========================
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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