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The Ontology for Biomedical Investigations
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interpreting data, performing diagnosis and related terms #623

Open obi-bot opened 12 years ago

obi-bot commented 12 years ago

interpreting data (suggest change to drawing conclusion during OBI/ECO discussion) (planned process) http://purl.obolibrary.org/obo/OBI\_0000338 Definition: the process of evaluating the data gathered in an investigation in the context of literature knowledge with the objective to generate more general conclusions or to identify what additional data is necessary to draw conclusions has_specified_output some conclusion textual entity planned process

performing a clinical assessment (assay) http://purl.obolibrary.org/obo/OBI\_0600003 definition: a protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition. has_specified_input some (organism and (has role some patient role)) has_specified_output some diagnosis textual entity achieves_planned_objective some assay objective has part some performing a diagnosis assay

performing a diagnosis (data transformation) http://purl.obolibrary.org/obo/OBI\_0000988 definition: The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis has_specified_output some diagnosis textual entity data transformation

By looking at the details of these terms, is 'performing diagnosis'/'performing a clinical assessment' a kind of 'interpreting data'? Besides, I feel 'performing diagnosis' and 'performing a clinical assessment' are same if ignoring their type and their labels are kind of confused.

'diagnosis textual entity' http://purl.obolibrary.org/obo/OBI\_0000075 definition: diagnosis is an assessment of a disease or injury, its likely prognosis and treatment. textual entity

'conclusion textual entity' http://purl.obolibrary.org/obo/IAO\_0000144 definition: A textual entity that expresses the results of reasoning about a problem, for instance as typically found towards the end of scientific papers. is_supported_by_data some data item is_specified_output_of some interpreting data textual entity

Is 'diagnosis textual entity' a kind of 'conclusion textual entity'?

Also I suggest to change 'data item' to 'information content entity' in 'conclusion textual entity' restriction (refer to OBI/ECO discussion).

Reported by: zhengj2007

Original Ticket: obi/obi-terms/637

zhengj2007 commented 3 years ago

Some changes have been made in the OBI.

  1. http://purl.obolibrary.org/obo/OBI_0000338 Label and definition have been updated and reviewed during OBI core terms review process.

    • Label: 'interpreting data' -> 'drawing a conclusion based on data'
    • Definition: A planned process in which data gathered in an investigation is evaluated in the context of existing knowledge with the objective to generate more general conclusions or to conclude that the data does not allow one to draw general conclusion
    • Logical axioms:
    • planned process
    • has_specified_input some data item
    • has_specified_output some conclusion based on data

  2. http://purl.obolibrary.org/obo/OBI_0600003

    • Label: performing a clinical assessment
    • Definition: A protocol application during which a series of tests are made of a patient leading to determination of disease state, or condition.
    • Logical axioms:
    • planned process
    • has part some performing a diagnosis
    • has_specified_input some (organism and (has role some patient role))
    • has_specified_output some 'diagnosis textual entity'

Is it an assay or 'drawing a conclusion based on data'?

  1. http://purl.obolibrary.org/obo/OBI_0000988

    • Label: performing a diagnosis
    • Definition: The interpretation of the information available about bodily features (clinical picture) of a patient resulting in a diagnosis
    • Logical axioms:
    • data transformation
    • has_specified_output some 'diagnosis textual entity'

Is it 'data transformation' which output is some/only 'data item'? How is it different from OGMS: 'diagnostic process' (http://purl.obolibrary.org/obo/OGMS_0000104)?

  1. http://purl.obolibrary.org/obo/OBI_0000075

    • Label: diagnosis textual entity
    • Definition: Diagnosis is an assessment of a disease or injury, its likely prognosis and treatment.
    • Logical axioms:
    • textual entity
    • Notes: output of 'performing a clinical assessment' and 'performing a diagnosis'

Can it be replaced with OGMS:diagnosis (http://purl.obolibrary.org/obo/OGMS_0000073)?

Or keep it like, IAO: 'conclusion textual entity' (http://purl.obolibrary.org/obo/IAO_0000144) and OBI: 'conclusion based on data' (http://purl.obolibrary.org/obo/OBI_0001909)?

zhengj2007 commented 3 years ago

Discussed on OBI call 2021-10-11. Need more time to discuss and will revisit in future call.

johnwjudkins commented 3 years ago

2021-10-18: Will discuss in proposed workshop (need more time).

zhengj2007 commented 2 years ago

Discussed on 2022 OBI workshop (Feb 1st, 2022). Decided to deprecate terms: http://purl.obolibrary.org/obo/OBI_0000988 performing a diagnosis http://purl.obolibrary.org/obo/OBI_0600003 performing a clinical assessment