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How to model "Fronto-insular L" into a schema model? #11

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andrawaag opened this issue Sep 8, 2022 · 1 comment
Open

How to model "Fronto-insular L" into a schema model? #11

andrawaag opened this issue Sep 8, 2022 · 1 comment
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GBM-1 Schema modelling issues related to the first mockup data set on GBM question Further information is requested Schema modelling

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@andrawaag
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andrawaag commented Sep 8, 2022

The GBM-1 dataset has a column "Localization". One of the values in that column is "Fronto-insular L". I am already assumed that this resolves to the concept "Left side of the Fronto-insular cortex" (#10). However, with this assumption, there are multiple possibilities.
Currently, the schema modellings pattern applied for two other lobes applied is as follows:

if row["Localization"] == "frontal R":
        localization = BNode()
        g.add((pathology, WD.P927, localization))
        g.add((localization, RDF.type, OBO.NCIT_C12352))
        g.add((OBO.NCIT_C25228, OBO.NCIT_A4, localization))

ie. Pathology has a localization (WD.P927) on one of the lobes. That localization is specified with an RDF.type predicate where the specific location (here frontal lobe) is identified by the identifier from NCIT (OBO.NCIT_C12352). That class does not contain qualifiers (i.e. R in this example). That is solved by using the Qualifier_Applies_To (OBO.NCIT_A4). and the class OBO.NCIT_C25228 (Right).

When trying to apply the same design pattern on the value fronto insular L I am facing the following challenges.

  1. Is it correct that that token reads as "Left side of the Fronto-insular cortex"
  2. When searching for Fronto-insular cortex on the Ontology Lookup Service, different candidate classes surface. In some, the localisation is part of the class, e.g. Cortex of left insula. If this term is to be selected, should the qualifier be frontal?
  3. Or do we stick to the design pattern to not include qualifiers in the ontology terms?
@andrawaag andrawaag added question Further information is requested Schema modelling GBM-1 Schema modelling issues related to the first mockup data set on GBM labels Sep 8, 2022
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Labels
GBM-1 Schema modelling issues related to the first mockup data set on GBM question Further information is requested Schema modelling
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