ATLAS Tutorial: Data Sources - Drug Exposure

Summary

This video script demonstrates the drug exposure report feature in Atlas, showcasing how to visualize and analyze data from various sources. It explains the use of tree maps and drill-down reports to examine drug prevalence, patient records, and exposure patterns over time. The script also compares the drug exposure report with the drug error report, highlighting how they aggregate data differently to provide insights into patient medication use and errors.

Takeaways

• 🗺️ The script demonstrates how to use Atlas to generate a drug exposure report, showcasing data visualization capabilities.
• 📊 The tree map visualization in Atlas represents drug concepts, with box size indicating prevalence and color representing records per person.
• 🔍 Hovering over a box in the tree map reveals additional information about the drug concept, such as prevalence and average records for patients.
• 📈 Clicking on a box in the tree map leads to a drill-down report that provides more detailed characterization of the drug concept within the data source.
• 📉 The script shows how to analyze drug usage trends over time, with a focus on lisinopril 10 mg oral tablet, indicating increased use over the years.
• 👥 Gender stratification in the report reveals differences in drug usage patterns between males and females.
• 📅 A plot of concept prevalence by month allows for the assessment of the stability of drug usage over time.
• 🔑 The provenance of data is shown through a donut plot, indicating the proportion of records from different sources, such as pharmacy dispensed vs. mail-order.
• 📊 Age at first occurrence is visualized through box plots, stratified by gender, providing insights into the median age of first exposure to a drug.
• 📝 A frequency distribution plot shows the cumulative distribution of the number of records for a drug among exposed patients.
• 💊 The drug error report in Atlas provides information on continuous persistence exposure, aggregating drugs to the ingredient level and showing exposure duration.
• 📝 The script concludes by encouraging viewers to explore other reports, data sources, and capabilities within Atlas, as well as to engage with the Odyssey community.

Q & A

What is the purpose of the drug exposure report in Atlas?

The drug exposure report in Atlas is used to demonstrate and analyze data related to drug usage, including prevalence, records per person, and various visualizations to understand patterns and trends.

How does the tree map visualization in the drug exposure report represent data?

The tree map visualization represents data by showing different concepts within the drug exposure table. The size of each box indicates the prevalence of the concept, while the color represents the number of records per person.

What additional information can be seen when hovering over a box in the tree map?

When hovering over a box, additional information such as the prevalence of the drug, the number of patients, and the average number of records per patient for that specific drug is displayed.

What does the drill-down report provide after clicking on a box in the tree map?

The drill-down report provides further detailed information about the selected concept, including graphs and data that characterize the concept within the data source, such as prevalence over time, age deciles, and gender stratification.

How are the graphs in the drill-down report structured to show concept prevalence?

The graphs display concept prevalence with time on the x-axis, age deciles represented in a trellis, and concept prevalence per thousand persons on the y-axis. There are two lines representing gender stratification, with blue for males and pink for females.

What does the plot showing concept prevalence by month indicate?

The plot indicates the stability of the concept over time, allowing users to assess changes in prevalence from month to month, which can help identify patterns or anomalies in drug usage.

What is the significance of the provenance of the data represented by the type concept ID?

The provenance of the data shows the proportion of records that have come from different sources, which can be important for understanding the reliability and diversity of the data source for a particular drug.

How does the age at first occurrence plot help in understanding drug exposure?

The age at first occurrence plot, stratified by gender, provides a box plot that shows the age distribution of when patients were first exposed to a drug, offering insights into demographic trends.

What does the frequency distribution plot represent in the drug exposure report?

The frequency distribution plot shows the cumulative distribution of the number of records for a particular drug concept among the patients who were exposed, indicating the range of usage from single records to multiple records per patient.

How can users explore specific drug concepts in the drug exposure report?

Users can explore specific drug concepts by using the search function to find a particular drug name, which will then display all associated records. Selecting a record allows users to explore the concept's existence within the data source.

What additional insights does the drug error report provide compared to the drug exposure report?

The drug error report provides information about the ingredients used in continuous persistence exposure, aggregating drugs to the ingredient level and representing the span of time a person is exposed to a particular drug, rather than the number of records.

Outlines

00:00

📊 Drug Exposure Report in Atlas: Visualization and Analysis

The video script introduces the drug exposure report feature within Atlas, a data analysis tool. It explains how to access and utilize the data sources to generate a report on drug exposure. The script demonstrates the selection of a report, the tree map visualization that represents drug concepts, and how the size and color of the boxes in the map indicate prevalence and records per person. The example of 'lisinopril 10 milligram oral tablet' is used to illustrate how additional information can be obtained by hovering over a concept. The script then details the drill-down report, which includes various graphs and plots that provide insights into the prevalence of the drug over time, age and gender stratification, concept prevalence by month, data provenance, age at first occurrence, and frequency distribution of records. The report allows for a thorough exploration of drug exposure concepts in a data source.

05:02

🔍 Drug Error Report: Understanding Drug Exposure and Persistence

The second paragraph of the script shifts focus to the drug error report, which offers information on the ingredients used in continuous persistence exposure. It describes the aggregation of drugs to the ingredient level and the representation of exposure duration rather than the number of records. The script uses 'lisinopril' as an example to show how one can identify records for the active ingredient and understand the average exposure duration. It also explains how to access a drill-down report for further analysis, including patterns of drug use by age, gender, and year, as well as prevalence by month. The script concludes by emphasizing the value of the drug error report in summarizing information on drug occurrence, ingredient roll-up, and patient exposure duration, and invites viewers to explore other reports, data sources, and capabilities within Atlas or learn more about the Odyssey community.

Keywords

💡Drug Exposure Report

A 'Drug Exposure Report' is a detailed analysis that provides insights into the usage of specific drugs within a dataset. In the video, this report is demonstrated within the Atlas platform, showing how to visualize and analyze drug usage patterns. The report is crucial for understanding the prevalence and distribution of drug usage among patients, as illustrated by the example of 'lisinopril 10 milligram oral tablet'.

💡Atlas

Atlas, as mentioned in the script, is a platform that enables users to explore and analyze data sources, particularly focusing on health-related data in this context. It is the main tool demonstrated in the video, where various reports like the 'Drug Exposure Report' are generated and analyzed.

💡Data Sources

In the context of the video, 'Data Sources' refers to the various databases or collections of information configured within the Atlas platform. These sources are critical for generating reports, as they provide the raw data that is analyzed and visualized to understand drug exposure and other health-related metrics.

💡Tree Map Visualization

A 'Tree Map Visualization' is a method used in data presentation where hierarchical data is displayed as nested rectangles. In the video, this visualization technique is used to represent different drug concepts within the 'Drug Exposure Report', with the size of the boxes indicating prevalence and color indicating records per person.

💡Concept Prevalence

'Concept Prevalence' is a term used to describe the frequency or commonness of a particular concept or, in this case, a drug within the dataset. The script uses this term to discuss how often a drug like 'lisinopril 10 mg oral tablet' appears in the data, indicating its usage among patients.

💡Records per Person

'Records per Person' is a metric that indicates the average number of records associated with a specific drug for each patient in the dataset. The video script mentions this in relation to the color coding of the tree map visualization, providing a deeper understanding of individual drug exposure.

💡Drill-Down Report

A 'Drill-Down Report' is a detailed breakdown of data that provides more specific information about a selected concept. In the script, clicking on a box in the tree map leads to a drill-down report for 'lisinopril 10 mg oral tab', which offers additional insights into the drug's usage patterns and patient demographics.

💡Stratification by Gender

The term 'Stratification by Gender' refers to the process of dividing data into different groups based on gender to analyze patterns separately for males and females. The video script uses this concept to show how the use of 'lisinopril' varies between men and women over time.

💡Concept ID

'Concept ID' is a unique identifier for a specific concept or drug within a dataset. In the video, the script discusses how the provenance of data is represented by 'Concept ID', helping to understand the source of the records for a particular drug.

💡Drug Error Report

The 'Drug Error Report' is another type of report within the Atlas platform that focuses on the continuous persistence exposure to ingredients used in drugs. It aggregates drugs to the ingredient level and provides information on the duration of exposure, as demonstrated with 'lisinopril' in the script.

💡Odyssey Community

The 'Odyssey Community' is mentioned at the end of the script as a resource for those interested in learning more about the platform and its capabilities. It suggests a community of users or stakeholders who engage with the Odyssey platform, which is likely the overarching system that includes Atlas.

Highlights

Demonstration of drug exposure report within Atlas, a data analysis tool.

Function menu in Atlas allows selection of data sources and reports of interest.

Tree map visualization represents concepts within the drug exposure table, with size indicating prevalence and color representing records per person.

Additional information on drug concepts is available upon hovering over boxes in the tree map.

Example given: Lisinopril 10 milligram oral tablet's prevalence and average records per patient.

Drill-down report provides detailed characterization of a selected drug concept.

Graphs in the drill-down report show concept prevalence over time, stratified by age and gender.

Trend analysis of drug usage over time, with a focus on age and gender demographics.

Concept prevalence by month plot allows assessment of stability over time.

Data provenance represented through a donut plot, showing the proportion of records from different sources.

Age at first occurrence plot with box plots to understand the distribution across genders.

Frequency distribution plot shows the cumulative distribution of records for a drug concept.

Drug exposure report facilitates exploration of concepts in both tree map and tabular views.

Search functionality within the report to find specific drugs and their associated records.

Introduction of the drug error report, focusing on continuous persistence exposure of ingredients.

Drug error report aggregates drugs to the ingredient level, showing exposure duration instead of record count.

Drill-down reporting in the drug error report provides additional insights into drug usage patterns.

Summary of information from both reports helps understand drug occurrence, ingredient roll-up, and exposure duration.

Invitation to explore other reports, data sources, and capabilities within Atlas or join the Odyssey community.

Transcripts

[Music]

today we're going to demonstrate the

drug exposure report on the data sources

capability within Atlas in the top left

hand side you can see the function menu

within Atlas and we'll click on data

sources when we click on data sources

you first are able to select any of

these sources of data that have been

configured within Atlas and then you can

select your report of interest here

we're selecting drug exposure once you

select the drug exposure report you will

see a tree map visualization which shows

you all of the concepts within the drug

exposure table the size of the box

represents the prevalence of that

concept and the color of the box

represents the number of Records per

person that concept represents if we

hover over any particular box we can see

additional information here for example

I have hovered over lisinopril

10 milligram oral tablet it has a

prevalence of 2.5 6 percent meaning 2.2

million patients in this data set have

lisinopril 10 mg oral tablet in the drug

exposure data domain and for those

people on average they have 8.8 records

of lisinopril 10 mg or old tablet if I

click on any of these boxes we will

identify a drill-down report which will

provide additional information to

characterize this particular concept

within the data source now that I've

clicked on lisinopril 10 mg oral tab we

can see the drill down report provided

below the first graph displays the

concept prevalence of this concept on

the x-axis we see time in in years so in

this particular data source going from

2002 to 2007 teen we have a trellis

representing age deciles going from 0 to

9 to 90 to 99 and on the x-axis we have

concept prevalence per thousand persons

within each graph you see two lines here

representing stratification by gender

the line in blue represents males in the

line in pink represents females so this

graph can show us for example that

amongst patients who are having exposure

to less interval 10 mg oral tablet it

appears that the use of this drug has

increased over time we see that it is

used more in an older population than a

younger population and is used more in

men than women if I scroll down further

we have a plot that shows the concept

prevalence by month here the x-axis

represents calendar month the y-axis

represents per thousand persons if I

hover over any particular month I can

identify information such as here June

2012 the prevalence was 8 per thousand

persons this allows you to assess the

stability of the concept over time the

next plot shows us the provenance of the

data represented by the type concept ID

here we can see in the donut plot the

proportion of records that have come

from different sources here this record

for this source 94 93.6%

of the records come from a prescription

dispensed in a pharmacy while the

additional 6.4% seemed to be

prescriptions dispensed through

mail-order the graph to the right here

represents the age at first occurrence

here we see this is stratified by gender

and for each of the genders we have a

box plot the box plot then allows us to

know a patient's age at the first

occurrence of the lisinopril 10 mg oral

tab so here we can see amongst women the

median age was 60 at the time of first

exposure finally there is a plot of

frequency distribution showing you the

cumulative distribution of the number of

Records for this particular concept

amongst the patients who were exposed so

here we can see that everybody has at

least one record but we can see that

many individuals have 2 3 4 all the way

out to 13 are records of lisinopril

within their medic

record the drug exposure report allows

us to explore any particular concept in

the drug exposure table both by

selecting any concept in this tree map

view but also by being able to explore

the information in this tabular view so

if we were interested in a particular

job like hydrochlorothiazide we could

search for that drug name and we would

see all associated records and simply

selecting a record from the table would

allow you to determine the and explore

the concepts existence in this

particular data source so for example

here by selecting on hydrochlorothiazide

50mg or all tab we can see the use of

hydrochlorothiazide in the databases

buying those same graphs

um now going to select a different

report the drug error report the drug

error report provides information about

the ingredients used in continuous

persistence exposure here we are rep the

same representation with a treemap

visualization in a tabular display what

is different with the drug error report

however is that drugs have been

aggregated to the ingredient level and

rather than representing the number of

records we can now represent the span of

time that a person is exposed to a

particular drug so if I search for

lisinopril we can now see that there is

one record for the active ingredient

lisinopril we can see that there are six

million patients in this particular data

source represented a prevalence of 7%

and that on average patients on

lisinopril were exposed for about 300

days I can click on any record in this

table to be able to get to a drill down

reporting which will provide us

additional information so here I can see

the same plot of concept prevalence by

age gender and year to see the pattern

of lisinopril use I can see a pattern of

the prevalence by month

here we see

Spike's in the data at January

indicating that that's a moment in time

when we see continuous use and we

further see a graph broken down by age

at first exposure between the drug

exposure report in the drug error report

it provides you a summary of information

that allows you to understand both which

concepts are occurring how those

concepts roll up to an ingredient and

how long patients are exposed for

periods of time that's all for our drug

reporting in the data sources if you

have additional interest in other

reports and data sources or other

capabilities in Atlas or just want to

learn more about the Odyssey community

check us out at Odyssey org