- From: LJ.Garcia <lj.garcia.co@gmail.com>
- Date: Tue, 7 Feb 2023 19:46:35 +0100
- To: Dan Bolser <dan.bolser@gmail.com>
- Cc: public-bioschemas@w3.org
- Message-ID: <CAPZUG=D+1p2o7Pp8V3ZnxeAT9O+yTrEKeemcPV3thaSA781aJA@mail.gmail.com>
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. >>> >>
Received on Tuesday, 7 February 2023 18:46:59 UTC