OMOP Teva

The OMOP Teva module of eds-scikit supports data scientists working on OMOP data. OMOP Teva generates an interactive dashboard for each OMOP table, allowing timely visualization of the volumes associated with each combination of values. This provides a general overview of the possible values, their relative importance and allows to detect quickly possible bias.

This module is an eds-scikit transposition of EDS-Teva

EDS-Teva is a more complete library designed to handle temporal bias in EHR data. See Adjusting for the progressive digitization of health records for a better understanding about those bias.

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"care_site_short_name": "care site 3", "count": 6, "datetime": "2021-01-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 10, "datetime": "2021-01-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 12, "datetime": "2021-01-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 24, "datetime": "2021-02-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 21, "datetime": "2021-02-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 17, "datetime": "2021-02-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 4, "datetime": "2021-02-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 2, "datetime": "2021-02-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 8, "datetime": "2021-02-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 5, "datetime": "2021-02-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 8, "datetime": "2021-02-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 14, "datetime": "2021-03-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 13, "datetime": "2021-03-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 17, "datetime": "2021-03-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 6, "datetime": "2021-03-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 4, "datetime": "2021-03-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 9, "datetime": "2021-03-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 5, "datetime": "2021-03-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 6, "datetime": "2021-03-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 14, "datetime": "2021-04-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 15, "datetime": "2021-04-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 8, "datetime": "2021-04-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 5, "datetime": "2021-04-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 5, "datetime": "2021-04-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 2", "count": 2, "datetime": "2021-04-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 3", "count": 12, "datetime": "2021-04-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 9, "datetime": "2021-04-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 4, "datetime": "2021-04-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 25, "datetime": "2021-05-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 12, "datetime": "2021-05-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 15, "datetime": "2021-05-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 1, "datetime": "2021-05-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 2, "datetime": "2021-05-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 2", "count": 2, "datetime": "2021-05-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 3", "count": 10, "datetime": "2021-05-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 9, "datetime": "2021-05-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 8, "datetime": "2021-05-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 18, "datetime": "2021-06-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 13, "datetime": "2021-06-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 14, "datetime": "2021-06-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 1, "datetime": "2021-06-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 1, "datetime": "2021-06-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 2", "count": 4, "datetime": "2021-06-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 3", "count": 5, "datetime": "2021-06-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 10, "datetime": "2021-06-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 6, "datetime": "2021-06-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 23, "datetime": "2021-07-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 23, "datetime": "2021-07-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 11, "datetime": "2021-07-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 6, "datetime": "2021-07-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 2, "datetime": "2021-07-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 2", "count": 3, "datetime": "2021-07-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 3", "count": 13, "datetime": "2021-07-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 10, "datetime": "2021-07-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 5, "datetime": "2021-07-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 24, "datetime": "2021-08-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 22, "datetime": "2021-08-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 10, "datetime": "2021-08-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 1, "datetime": "2021-08-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 5, "datetime": "2021-08-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 2", "count": 3, "datetime": "2021-08-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 3", "count": 8, "datetime": "2021-08-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 11, "datetime": "2021-08-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 9, "datetime": "2021-08-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 20, "datetime": "2021-09-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 17, "datetime": "2021-09-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 21, "datetime": "2021-09-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 3, "datetime": "2021-09-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 2, "datetime": "2021-09-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 2", "count": 2, "datetime": "2021-09-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 3", "count": 12, "datetime": "2021-09-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 9, "datetime": "2021-09-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 6, "datetime": "2021-09-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 23, "datetime": "2021-10-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 21, "datetime": "2021-10-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 19, "datetime": "2021-10-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 4, "datetime": "2021-10-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 3, "datetime": "2021-10-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 2", "count": 3, "datetime": "2021-10-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 3", "count": 7, "datetime": "2021-10-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 8, "datetime": "2021-10-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 8, "datetime": "2021-10-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 27, "datetime": "2021-11-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 1", "count": 14, "datetime": "2021-11-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 10, "datetime": "2021-11-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 2", "count": 3, "datetime": "2021-11-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 2", "count": 4, "datetime": "2021-11-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 2", "count": 1, "datetime": "2021-11-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 3", "count": 8, "datetime": "2021-11-01T00:00:00", "stay_source_value": "MCO" }, { "care_site_short_name": "care site 3", "count": 6, "datetime": "2021-11-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 3", "count": 4, "datetime": "2021-11-01T00:00:00", "stay_source_value": "PSY" }, { "care_site_short_name": "care site 1", "count": 1, "datetime": "2021-12-01T00:00:00", "stay_source_value": "Other" }, { "care_site_short_name": "care site 1", "count": 1, "datetime": "2021-12-01T00:00:00", "stay_source_value": "PSY" } ] }, "params": [ { "bind": "legend", "name": "param_7", "select": { "clear": "dblclick", "fields": [ "care_site_short_name" ], "on": "click", "type": "point" }, "views": [ "view_7" ] }, { "bind": "legend", "name": "param_8", "select": { "clear": "dblclick", "fields": [ "stay_source_value" ], "on": "click", "type": "point" }, "views": [ "view_8" ] } ], "resolve": { "scale": { "color": "independent" } }, "vconcat": [ { "hconcat": [ { "encoding": { "color": { "field": "care_site_short_name", "scale": { "domain": [ "care site 1", "care site 2", "care site 3" ], "range": [ "#1f77b4", "#ff7f0e", "#2ca02c" ] }, "type": "nominal" }, "opacity": { "condition": { "param": "param_7", "value": 1 }, "value": 0.3 }, "tooltip": [ { "field": "care_site_short_name", "type": "nominal" } ], "x": { "aggregate": "sum", "field": "count", "type": "quantitative" } }, "mark": { "type": "bar" }, "name": "view_7", "transform": [ { "filter": { "param": "param_8" } } ] }, { "encoding": { "color": { "field": "care_site_short_name", "scale": { "domain": [ "care site 1", "care site 2", "care site 3" ], "range": [ "#1f77b4", "#ff7f0e", "#2ca02c" ] }, "type": "nominal" }, "opacity": { "condition": { "param": "param_7", "value": 1 }, "value": 0.3 }, "x": { "field": "datetime", "timeUnit": "yearmonth", "type": "temporal" }, "y": { "aggregate": "sum", "axis": { "format": "s" }, "field": "count", "type": "quantitative" } }, "height": 50, "mark": { "type": "line" }, "transform": [ { "filter": { "param": "param_8" } } ], "width": 300 } ], "title": "care_site_short_name" }, { "hconcat": [ { "encoding": { "color": { "field": "stay_source_value", "scale": { "domain": [ "MCO", "Other", "PSY" ], "range": [ "#1f77b4", "#ff7f0e", "#2ca02c" ] }, "type": "nominal" }, "opacity": { "condition": { "param": "param_8", "value": 1 }, "value": 0.3 }, "tooltip": [ { "field": "stay_source_value", "type": "nominal" } ], "x": { "aggregate": "sum", "field": "count", "type": "quantitative" } }, "mark": { "type": "bar" }, "name": "view_8", "transform": [ { "filter": { "param": "param_7" } } ] }, { "encoding": { "color": { "field": "stay_source_value", "scale": { "domain": [ "MCO", "Other", "PSY" ], "range": [ "#1f77b4", "#ff7f0e", "#2ca02c" ] }, "type": "nominal" }, "opacity": { "condition": { "param": "param_8", "value": 1 }, "value": 0.3 }, "x": { "field": "datetime", "timeUnit": "yearmonth", "type": "temporal" }, "y": { "aggregate": "sum", "axis": { "format": "s" }, "field": "count", "type": "quantitative" } }, "height": 50, "mark": { "type": "line" }, "transform": [ { "filter": { "param": "param_7" } } ], "width": 300 } ], "title": "stay_source_value" } ] }

OMOP Teva - Quick use

Quick use for OMOP dataset exploration.

OMOP Teva - Config

See how your can configurate your own OMOP dashboards .

Custom Teva

For any dataframe exploration.

OMOP Teva - Example

A toy example of what can be obtained with this module.