Re: Question about 'ontologizing' a survey?

Hi,

Many thanks for this detailed response. I'm going to break it down to see
if I understand it or not ;-)

I am not sure you want markup:

   1. rich description of the questionnaire or
   2. semantic annotations (named entity recognition of some chunks of
   text) or
   3. semantic association (assigning tags/annotations to a question).


For 1, I guess it means some statements like, *this is a questionnaire*, *this
is a medical questionnaire*, *this relates to covid risk*, etc.? I can see
why this would be useful (and probably close to what BioSchemas is for),
but it isn't what I'm trying to do here. I should think about it though!
I'll look at the profiles here
<https://bioschemas.org/tutorials/howto/howto_right_profile> and look
at annotations
here <https://bioschemas.org/tutorials/howto/howto_add_markup>.

As you said, "questionnaire markup could be of interest for others", I've
kicked off a discussion here:
https://github.com/BioSchemas/specifications/issues/635


For 2, I think that's what I want. I've looked at putting the question
strings here:
https://bioportal.bioontology.org/annotator

but my 'issue' is that I don't know which ontologies to pick... The idea is
to use the annotation to find all questions related to 'heart health'
broadly, while the specific terms used in the question may be very specific
or apparently unrelated. e.g. "What is your blood pressure?", "How many
times a week do you exercise?"... Which ontology relates these two back to
'heart health'?

For 3, how is this different from 2? The linked profile looks good, but
seems like a way to implement something that I don't have a grasp of yet...

Many thanks again for your detailed reply. Sorry for the (continued!) basic
questions!


Dan.

On Sun, 5 Feb 2023 at 10:07, LJ.Garcia <lj.garcia.co@gmail.com> wrote:

> Dear Dan,
>
> Please be aware that I did not look into the questionnaire.
>
> I am not sure you want markup (e.g., rich description of the
> questionnaire) or semantic annotations (named entity recognition of some
> chunks of text) or some semantic association (assigning tags/annotations to
> a question). If (i), then please have a look at tutorials on how to add
> Bioschemas markup, there is though no profile for questionnaires but you
> could find some inspiration, questionnaire markup could be of interest for
> others. If (ii), have a look at named entity recognition approaches, which
> vocabulary to use depends on what you want to recognize and possibly on
> what you want to do later with those annotations. If (iii) again, you would
> need to find a named entity recognition and tagging approach on whole
> sentences. If you want to express the annotations with Bioschemas for (ii)
> or (iii), you could use the SemanticTextAnnotation profile (
> https://bioschemas.org/profiles/SemanticTextAnnotation).
>
> Kind regards,
>
> On Thu, Feb 2, 2023 at 4:26 PM Dan Bolser <dan.bolser@gmail.com> wrote:
>
>> Hi all,
>>
>> Random question really...
>>
>> If I were to ask you to 'mark up' this questionnaire with ontology terms,
>> how would you do it:
>> https://alama.org.uk/covid-19-medical-risk-assessment/
>>
>> I'm guessing the questions could be 'tagged' with a disease ontology and
>> the answers with a phenotype ontology that includes either numerical values
>> and units or categorical answers.
>>
>> Which ontologies would you choose to annotate these questions and answers?
>>
>> This is for a student project.
>>
>>
>> Many thanks,
>> Dan.
>>
>