Explanation on ERD

[anuradhawick]

Greetings,

In my understanding, we should be able to have cohorts defined under different criteria such as study, described in beacon or user-defined (I guess this is done using ontology terms).

In these scenarios, having a particular individual referenced across several cohorts is inevitable. However, from the ETD diagram, it seems the cohort-individual relationship has cardinality 1 -<> n or one to many. Could you kindly elaborate on this design aspect? I have attached the ERD for reference.

Thanks

[mbaudis]

@anuradhawick I'd say this is just ill defined. datasets and cohorts are 2 types of "collections"; datasets are "physical" groups (e.g. with common access, DAC, storage ... based on the variants) while cohorts can be flexible collections related to groupings of e.g. phenotype, diseases, studies...

We do not model all entity relationships for such parameters. E.g. a cohort may be assembled from members of multiple datasets - though such definitions are pushed out to cohort definitions beyond the Beacon model.

I'll adjust the cohorts<-->individuals to many-to-many:

classDiagram

    analyses <-- genomicVariations : 1..n
    runs <-- analyses : 1..n
    biosamples <-- runs : 1..n
    individuals <-- biosamples : 1..n

    runs <.. genomicVariations : 1..n
    biosamples <.. genomicVariations : 1..n
    individuals <.. genomicVariations : 1..n
    biosamples <.. analyses : 1..n
    individuals <.. analyses : 1..n
    individuals <.. runs : 1..n

    cohorts o-- individuals : m..n
    datasets o-- genomicVariations : 1..n

    class genomicVariations{
        analysisId
        runId
        biosampleId
        individualId
        variation
        clinicalInterpretations
        caseLevelData
        ...
    }
    class analyses{
        id
        runId
        biosampleId
        individualId
        analysisDate
        pipelineName
        aligner
        ...
    }
    class biosamples{
        id
        individualId
        biosampleStatus
        sampleOriginType
        histologicalDiagnosis
        collectionDate
        ...
    }
    class individuals{
        id
        sex
        diseases
        phenotypicFeatures
        ethnicity
        pedigrees
        ...
    }
    class runs{
        id
        biosampleId
        individualId
        runDate
        librarySource
        libraryStrategy
        platform
        ...
        }
    class datasets{
        id
        name
        description
        dataUseCondition
        info
        updateDateTime
        ...
    }
    class cohorts{
        id
        name
        cohortType
        cohortSize
        cohortDataTypes
        cohortDesign
        ...
    }

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[anuradhawick]

Thanks for the prompt response and explanation. I will close this issue now.