ATLAS Tutorial: Data Sources - Procedure
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
📊 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.
🔍 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
💡Atlas
💡Data Sources
💡Tree Map
💡Concept Prevalence
💡Tabular Display
💡Drill Down
💡Stratification
💡Seasonal Pattern
💡Provenance of Data
💡Cumulative Frequency Distribution
💡Search Filter
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.
Transcripts
[Music]
today we're going to explore the
procedure report within the data sources
capability of Atlas from the Atlas
homepage we can go to data sources and
from the data sources list we can select
the source of data that we want to
explore as well as the report that we
would like to explore here we're
selecting the procedure report once we
select the procedure report we are
brought to a tree map representation of
the prevalence of all concepts in the
procedure domain with inside the OU mop
common data model each of these boxes
represents the concept prevalence the
size of the box is the concept
prevalence and the color of the box
represents the intensity of those
particular concepts a tabular display of
this information is also available under
the table tab if I select that tab we
see a line listing that represents each
concept ID its name and then the number
of persons who have had that concept
that concept prevalence and the records
per person this shows 27,000 different
concepts within this particular source
this table can be sorted or searched and
filtered for any information if I select
any row in this table we can drill down
to find further information about that
concept here for example if I select the
concept of Radiologic exam chest two
views frontal and lateral we can see
that there are 13 over 13 million
patients and 16 percent of this data
source that have that particular concept
and on average those that have a
radiologic exam of the chest have that
concept 2.3 times if I scroll down we
can gain additional information about
how this concept plays out in this data
source the first graph shows the concept
prevalence this information is
stratified by year age NJ
so each graph shows in index year on the
x axis it is trellis by age deciles and
the gender is represented by the line
series with blue indicating males and
pink indicating females the y axis of
each of these plots shows the concept
prevalence per thousand persons so here
we can see for the concept of Radiologic
exam of the chest we can see that this
concept appears in the data from the
years 2000 through 2017
it appears that chest radiologic exams
occur more in older individuals than
younger individuals occurs slightly more
in women were relative to men and seemed
to have had a slight increase in the
year 2009 the next graph down shows the
prevalence of this concept by month here
the x-axis represents the calendar month
and the y-axis represents the concept
prevalence per thousand persons here we
can see a seasonal pattern in when chest
radiologic exams occurring in the winter
of each year the next graph shown is the
type concept ID this identifies where
the provenance of the data is for this
given source and here we can see that
radiologic exams are occurring in both
inpatient and outpatient claims records
for this particular data source and if
we hover over any element within this
donut plot we can see the proportion of
where this record appears in this
particular source we can see that the
prevalence of this concept appears most
commonly in the outpatient record in the
fourth position representing 89% of the
data records the next graph shows you
the age at the first occurrence of one
of these concepts it is stratified by
gender and we show age as on the y axis
so here if I hover over any of these box
plots we can see a distribution of the
values here indicating that the median
age of people at the first time that
they've had
chest x-ray is 50 and then finally the
graph below shows us a cumulative
frequency distribution representing the
number of occurrences of a particular
concept for given individuals so here
whereas 16 percent of the people had at
least one occurrence of a chest x-ray we
can see that 8 percent of these people
had 2 or more all the way down to some
individuals having 7 or 8 chest x-rays
within the data this drill down
information is available for all
particular concepts within the procedure
domain in the top right filter if I'm
interested in searching for any
particular concept such as coronary
artery bypass I can type in that word
and the set of concepts will be filtered
to those that meet that string search
here I can see coronary artery bypass
has occurred in 140,000 individuals in
this database selecting that concept
allows me to drill down to information
to further explore the prevalence of
that concept by year age gender by month
by provenance of data in by age this
includes our summary of the procedure
report for more information about the
data sources capability atlas as a whole
or anything about the entire odyssey
community check us out at Odyssey org
5.0 / 5 (0 votes)