Re: Question about 'ontologizing' a survey?

Dear Dan,

The difference between 2 and 3. In 2 you annotate a chunk of text in the
question, e.g., "Has anyone in your family been diagnosed with Diabetes?"
Only "Diabetes" is annotated and associated with the term
http://purl.obolibrary.org/obo/DOID_9351 in the Disease Ontology. In 3 you
annotated the whole question with the term from the ontology (so the
annotation would come from a NER but would be applied to the whole question
rather than only the recognized bit in the text).

Kind regards,

On Mon, Feb 6, 2023 at 1:05 PM Dan Bolser <dan.bolser@gmail.com> wrote:

> 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.
>>>
>>