ATLAS Tutorial: Data Sources - Procedure

OHDSI

23 May 201905:49

Summary

TLDRThis video explores the Procedure Report feature within Atlas, a data analysis tool. Users can select data sources and reports to analyze, visualized through a tree map and table. The script demonstrates how to drill down into specific concepts, like 'Radiologic exam chest two views,' to reveal prevalence, patient demographics, and seasonal patterns. It also shows how to filter and search for concepts, such as 'coronary artery bypass,' providing a comprehensive overview of data trends and insights.

Takeaways

🌐 The script is about exploring the 'Procedure Report' within the data sources capability of Atlas.
🔍 Users can start from the Atlas homepage, navigate to 'Data Sources', and select a specific data source and report to explore.
📊 The 'Procedure Report' initially presents a tree map representation showing the prevalence of all concepts in the procedure domain.
🔢 The size of each box in the tree map indicates the concept prevalence, while the color represents the intensity of the concept.
📝 A tabular display of the same information is available under the 'Table' tab, listing concept IDs, names, and prevalence data.
🔍 The table can be sorted, searched, and filtered to find specific information about the concepts.
🔎 By selecting a row in the table, users can drill down to get more detailed information about a particular concept.
📈 The report includes various graphs, such as concept prevalence stratified by year, age, gender, and a seasonal pattern of the concept occurrence.
🏥 The data source's provenance is identified, showing where the data for a given concept originates, such as inpatient or outpatient claims.
📊 The report also includes box plots showing the age at the first occurrence of a concept, stratified by gender.
📊 A cumulative frequency distribution graph is provided, showing the number of occurrences of a concept for given individuals.
🔎 Users can filter the report by searching for specific concepts, such as 'coronary artery bypass', to explore their prevalence in detail.

Q & A

What is the main feature of Atlas explored in the video script?
-The main feature explored in the video script is the 'procedure report' within the data sources capability of Atlas.
How does one access the procedure report in Atlas?
-To access the procedure report in Atlas, one must go to the data sources from the Atlas homepage, then select the source of data and the report they wish to explore.
What is represented by the size of the boxes in the tree map representation of the procedure report?
-The size of the boxes in the tree map representation corresponds to the concept prevalence within the data source.
How is the intensity of the concepts represented in the tree map?
-The intensity of the concepts is represented by the color of the boxes in the tree map.
What additional information is available under the 'table' tab in the procedure report?
-Under the 'table' tab, a line listing is available that represents each concept ID, its name, and the number of persons who have had that concept, along with the concept prevalence and records per person.
How many different concepts are shown in the table from the procedure report?
-The table shows 27,000 different concepts within the particular data source.
What actions can be performed on the table in the procedure report?
-The table in the procedure report can be sorted, searched, and filtered for any information.
What happens when a row in the table is selected?
-When a row in the table is selected, it allows the user to drill down and find further information about that particular concept.
Can you provide an example of the information obtained after drilling down into a concept?
-An example given is selecting the concept 'Radiologic exam chest two views frontal and lateral', which shows the number of patients, the prevalence of the concept within the data source, and the average number of times patients have that concept.
How is the concept prevalence information stratified in the first graph after drilling down into a concept?
-The concept prevalence information is stratified by year, age, and gender, with each graph showing index year on the x-axis, age deciles, and gender represented by line series.
What does the second graph after drilling down into a concept represent?
-The second graph represents the prevalence of the concept by month, showing a seasonal pattern of when chest radiologic exams occur.
What does the 'type concept ID' graph indicate?
-The 'type concept ID' graph identifies the provenance of the data for the given source, showing where the data records for radiologic exams occur, such as inpatient and outpatient claims.
How is the age at the first occurrence of a concept displayed?
-The age at the first occurrence of a concept is displayed in a box plot, stratified by gender, with age on the y-axis.
What does the cumulative frequency distribution graph show?
-The cumulative frequency distribution graph shows the number of occurrences of a particular concept for given individuals, indicating how many people had multiple occurrences of a chest x-ray.
How can a user search for a specific concept within the procedure report?
-A user can search for a specific concept, such as 'coronary artery bypass', by typing the term in the search bar, which filters the set of concepts to those that match the search string.
What additional information is provided when a specific concept is selected?
-When a specific concept is selected, the user can further explore the prevalence of that concept by year, age, gender, by month, by provenance of data, and by age.
Where can one find more information about Atlas and the Odyssey community?
-More information about Atlas and the Odyssey community can be found at Odyssey.org.

Outlines

00:00

📊 Exploring Procedure Reports in Atlas

The video introduces the procedure report feature within the data sources capability of Atlas. From the Atlas homepage, users can navigate to data sources, select the desired data source and report, and view a tree map representation of concept prevalence within the procedure domain of the OMOP Common Data Model. The tree map displays concept prevalence by box size and intensity by color. Additionally, a tabular view is available, showing a detailed listing of concept IDs, names, prevalence, and records per person. Users can sort, search, and filter this table, and drill down into specific concepts for further details. For example, selecting 'Radiologic exam chest two views frontal and lateral' reveals data on patient numbers, average occurrences, and prevalence over time. Various graphs illustrate concept prevalence by year, age, gender, month, data provenance, age at first occurrence, and cumulative frequency distribution, providing comprehensive insights into the data.

05:01

🔍 Filtering and Drilling Down Concepts in Atlas

The video continues by demonstrating the filtering and drilling down capabilities within the procedure report in Atlas. Users can search for specific concepts, such as 'coronary artery bypass,' and filter the results accordingly. Selecting a concept allows users to explore its prevalence by various dimensions such as year, age, gender, month, and data provenance. This section concludes with an invitation to visit Odyssey.org for more information about Atlas's data sources capability and the broader Odyssey community.

Mindmap

Keywords

💡Procedure Report

A 'Procedure Report' in the context of the video refers to a type of report that details the prevalence and distribution of medical procedures within a dataset. It is a key concept as it is the central focus of the video's demonstration, showing how to explore and analyze data related to medical procedures using Atlas. For example, the script describes how to select a procedure report to view a tree map representation of concept prevalence.

💡Atlas

Atlas is the platform being demonstrated in the video, which offers capabilities for exploring and analyzing healthcare data. It is integral to the video's theme as it provides the interface through which users can access data sources and generate reports. The script mentions navigating the Atlas homepage to access data sources and reports.

💡Data Sources

In the script, 'Data Sources' refers to the various datasets available within the Atlas platform. These sources are crucial for generating reports and are the foundation of the analysis presented in the video. The video script illustrates how to select a data source to explore specific reports, such as the 'Procedure Report'.

💡Tree Map

A 'Tree Map' is a visualization technique used in the video to represent the prevalence of concepts within the procedure domain. The size of each box in the tree map indicates the prevalence of a concept, and the color represents the intensity. This concept is central to understanding how data is visually presented in the video.

💡Concept Prevalence

'Concept Prevalence' is a measure of how common a particular concept is within the dataset. It is a fundamental aspect of the video's analysis, as it quantifies the occurrence of medical procedures. The script uses the example of a 'Radiologic exam chest two views' to illustrate how concept prevalence is displayed and analyzed.

💡Tabular Display

A 'Tabular Display' is another method of presenting data, as mentioned in the script when switching to the 'table tab'. It lists concepts in a table format, showing concept IDs, names, and prevalence data. This is an alternative way to view information that complements the tree map and is part of the video's exploration of data representation.

💡Drill Down

'Drill Down' refers to the process of selecting a specific piece of data to view more detailed information. In the video, this term is used to describe how users can click on a row in the table to explore further details about a concept, such as the prevalence of 'Radiologic exam chest two views' among patients.

💡Stratification

Stratification in the context of the video is the process of organizing data into groups based on certain characteristics, such as year, age, and gender. It is used to analyze concept prevalence across different demographics, as shown in the graphs that display data trellised by age deciles and separated by gender.

💡Seasonal Pattern

A 'Seasonal Pattern' is identified in the video's analysis of medical procedure data, indicating that certain procedures, like chest radiologic exams, occur more frequently during specific times of the year. The script mentions a pattern of increased exams in the winter months, providing insight into seasonal trends within the data.

💡Provenance of Data

'Provenance of Data' pertains to the origin or source of the data within the dataset. The video discusses how to identify where data comes from, such as inpatient and outpatient claims records, using a donut plot to show the distribution of a concept's occurrence in different record types.

💡Cumulative Frequency Distribution

A 'Cumulative Frequency Distribution' is a statistical representation shown in the video that illustrates the number of occurrences of a concept for given individuals. It helps to understand the frequency at which individuals experience a particular medical procedure, such as the varying numbers of chest x-rays received by patients.

💡Search Filter

'Search Filter' is a feature within Atlas that allows users to search for specific concepts within the dataset. The video demonstrates how to use the search filter to find concepts like 'coronary artery bypass', highlighting the platform's functionality for targeted data exploration.

Highlights

Exploration of the procedure report within the data sources capability of Atlas.

Access to the procedure report through the Atlas homepage and data sources list.

Tree map representation of the prevalence of all concepts in the procedure domain.

Concept prevalence indicated by the size of boxes and intensity by color in the tree map.

Availability of a tabular display of concept prevalence and details under the 'table' tab.

Line listing in the table includes concept ID, name, and number of persons with the concept.

Capability to sort, search, and filter the table for detailed information.

Drill-down feature to find further information about a selected concept.

Example given: Radiologic exam chest two views frontal and lateral with 13 million patients.

Statistical data on the average occurrence of the chest radiologic exam concept.

Graphs showing concept prevalence stratified by year, age, gender, and index year.

Identification of a seasonal pattern in chest radiologic exams occurring in winter.

Visualization of the provenance of data for radiologic exams in inpatient and outpatient claims.

Donut plot showing the proportion of record appearances in outpatient records.

Age at first occurrence of a concept stratified by gender and represented in box plots.

Cumulative frequency distribution graph representing the number of occurrences of a concept.

Drill-down information available for all concepts within the procedure domain.

Filter feature for searching specific concepts such as 'coronary artery bypass'.

Summary of the procedure report and information about Atlas and the Odyssey community.