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[FIX] Add validators for BIDS-Neurobagel categorical column levels al…
…ignment (#160) * add example with json missing BIDS 'Levels' attr * add new example12 to e2e bagel pheno test * add basic util + smoke test for checking presence of BIDS levels * expand warning for missing bids levels * add example with BIDS-Neurobagel mismatched levels * add validator util + test that BIDS/Neurobagel categorical levels mismatch raises warning --------- Co-authored-by: Alyssa Dai <[email protected]> Co-authored-by: Sebastian Urchs <[email protected]>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,75 @@ | ||
| { | ||
| "participant_id": { | ||
| "Description": "A participant ID", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:ParticipantID", | ||
| "Label": "Unique participant identifier" | ||
| } | ||
| } | ||
| }, | ||
| "session_id": { | ||
| "Description": "A session ID", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:SessionID", | ||
| "Label": "Unique session identifier" | ||
| } | ||
| } | ||
| }, | ||
| "group": { | ||
| "Description": "Group variable", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:Diagnosis", | ||
| "Label": "Diagnosis" | ||
| }, | ||
| "Levels": { | ||
| "PAT": { | ||
| "TermURL": "snomed:49049000", | ||
| "Label": "Parkinson's disease" | ||
| }, | ||
| "CTRL": { | ||
| "TermURL": "purl:NCIT_C94342", | ||
| "Label": "Healthy Control" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "sex": { | ||
| "Description": "Sex variable", | ||
| "Levels": { | ||
| "M": "Male", | ||
| "F": "Female" | ||
| }, | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:Sex", | ||
| "Label": "Sex" | ||
| }, | ||
| "Levels": { | ||
| "M": { | ||
| "TermURL": "snomed:248153007", | ||
| "Label": "Male" | ||
| }, | ||
| "F": { | ||
| "TermURL": "snomed:248152002", | ||
| "Label": "Female" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "participant_age": { | ||
| "Description": "Age of the participant", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:Age", | ||
| "Label": "Chronological age" | ||
| }, | ||
| "Transformation": { | ||
| "TermURL": "nb:iso8601", | ||
| "Label": "A period of time defined according to the ISO8601 standard" | ||
| } | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,5 @@ | ||
| participant_id session_id group sex participant_age | ||
| sub-01 ses-01 PAT M "P20Y6M" | ||
| sub-01 ses-02 PAT M "P20Y8M" | ||
| sub-02 ses-01 CTRL F "P25Y8M" | ||
| sub-02 ses-02 CTRL F "P26Y4M" |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,128 @@ | ||
| { | ||
| "participant_id": { | ||
| "Description": "A participant ID", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:ParticipantID", | ||
| "Label": "Unique participant identifier" | ||
| } | ||
| } | ||
| }, | ||
| "session_id": { | ||
| "Description": "A session ID", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:SessionID", | ||
| "Label": "Unique session identifier" | ||
| } | ||
| } | ||
| }, | ||
| "pheno_age": { | ||
| "Description": "Age of the participant", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:Age", | ||
| "Label": "Chronological age" | ||
| }, | ||
| "Transformation": { | ||
| "TermURL": "nb:euro", | ||
| "Label": "writing the time with a comma - why not" | ||
| }, | ||
| "MissingValues": ["NA"] | ||
| } | ||
| }, | ||
| "pheno_sex": { | ||
| "Description": "Sex variable", | ||
| "Levels": { | ||
| "M": "Male", | ||
| "F": "Female", | ||
| "missing": "Missing sex", | ||
| "O": "Other unimportant level" | ||
| }, | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:Sex", | ||
| "Label": "Sex" | ||
| }, | ||
| "Levels": { | ||
| "M": { | ||
| "TermURL": "snomed:248153007", | ||
| "Label": "Male" | ||
| }, | ||
| "F": { | ||
| "TermURL": "snomed:248152002", | ||
| "Label": "Female" | ||
| } | ||
| }, | ||
| "MissingValues": ["missing"] | ||
| } | ||
| }, | ||
|
|
||
| "pheno_group": { | ||
| "Description": "Group variable", | ||
| "Levels": { | ||
| "PAT": "Patient", | ||
| "CTRL": "Control subject", | ||
| "NA": "Missing group" | ||
| }, | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:Diagnosis", | ||
| "Label": "Diagnosis" | ||
| }, | ||
| "Levels": { | ||
| "PAT": { | ||
| "TermURL": "snomed:49049000", | ||
| "Label": "Parkinson's disease" | ||
| }, | ||
| "CTRL": { | ||
| "TermURL": "purl:NCIT_C94342", | ||
| "Label": "Healthy Control" | ||
| } | ||
| }, | ||
| "MissingValues": ["NA"] | ||
| } | ||
| }, | ||
| "tool1_item1": { | ||
| "Description": "item 1 scores for tool1", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:Assessment", | ||
| "Label": "Assessment tool" | ||
| }, | ||
| "IsPartOf": { | ||
| "TermURL": "cogatlas:1234", | ||
| "Label": "Imaginary tool" | ||
| }, | ||
| "MissingValues": ["missing"] | ||
| } | ||
| }, | ||
| "tool1_item2": { | ||
| "Description": "item 2 scores for tool1", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:Assessment", | ||
| "Label": "Assessment tool" | ||
| }, | ||
| "IsPartOf": { | ||
| "TermURL": "cogatlas:1234", | ||
| "Label": "Imaginary tool" | ||
| }, | ||
| "MissingValues": ["missing"] | ||
| } | ||
| }, | ||
| "tool2_item1": { | ||
| "Description": "item 1 scores for tool2", | ||
| "Annotations": { | ||
| "IsAbout": { | ||
| "TermURL": "nb:Assessment", | ||
| "Label": "Assessment tool" | ||
| }, | ||
| "IsPartOf": { | ||
| "TermURL": "cogatlas:4321", | ||
| "Label": "A different imaginary tool" | ||
| }, | ||
| "MissingValues": ["not completed"] | ||
| } | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,11 @@ | ||
| participant_id session_id pheno_age pheno_sex pheno_group tool1_item1 tool1_item2 tool2_item1 | ||
| sub-01 ses-01 34,1 F CTRL good far hello | ||
| sub-01 ses-02 35,3 F CTRL bad near world | ||
| sub-02 ses-01 NA M PAT ok missing hello | ||
| sub-02 ses-02 39,0 M PAT good middle friends | ||
| sub-03 ses-01 22,1 missing NA bad near not completed | ||
| sub-03 ses-02 23,2 missing PAT ok far hello | ||
| sub-04 ses-01 21,1 F CTRL missing missing hello | ||
| sub-04 ses-02 22,3 F CTRL good middle friends | ||
| sub-05 ses-01 42,5 M PAT bad near friends | ||
| sub-05 ses-02 43,2 M PAT good far world |
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