ATLAS Tutorial: Search Example #1 (Hypertension)
Summary
TLDRThis video tutorial explores the search functionality within the Atlas platform, focusing on how to utilize the standardized vocabularies to identify relevant concepts and codes for analysis. It demonstrates searching for 'hypertension', filtering results by vocabulary, class, and domain, and navigating concept hierarchies to understand relationships between terms. The tutorial highlights the platform's ability to filter and sort concepts based on record counts, making it easier to select appropriate terms for Odyssey analyses.
Takeaways
- 🔍 The script introduces the search capability within the Atlas platform, which is used to explore standardized vocabularies and identify concepts and codes for analysis.
- 📚 The search tool can be accessed by clicking on the 'search' option on the left-hand side of the platform, leading to a screen for concept-based searches.
- 🔑 Users can search for concepts using keywords, identifiers, or concept sets, with the example given of searching for 'hypertension' to find related concepts.
- 📊 The search results are displayed in a tabular format, providing information such as concept ID, code, name, class, record counts, and domain within a vocabulary.
- 🌐 The search results can be filtered using facets on the right-hand side, allowing users to narrow down the concepts by vocabulary, class, domain, standard concept status, validity, and record counts.
- 📈 The table is sorted by record counts by default, showing the most prevalent concepts in the data source, with an example of 'essential hypertension' having millions of records.
- 🔎 Clicking on a concept, such as 'essential hypertension', brings up a detailed view with information about the concept's domain, vocabulary, and identifiers.
- 👉 The 'related concepts' tab allows users to explore relationships between concepts, with filtering options to find broader or more specific terms.
- 📝 The 'hierarchy' tab provides a visual representation of parent and child concepts, helping users understand the relationships and hierarchy within the vocabulary.
- 🔗 The script demonstrates how to navigate from a non-standard code to a standard concept using the 'related concepts' feature, emphasizing the importance of using standard codes for community-wide analysis.
- 📚 The platform's search experience is concluded with a summary of how to explore concepts like 'hypertension' in the vocabulary, and an invitation to learn more about Atlas and the Odyssey community.
Q & A
What is the primary function of the search capability within the Atlas platform?
-The primary function of the search capability within the Atlas platform is to explore the OHM standardized vocabularies and identify sets of concepts and codes for use in analysis.
How can users initiate a search for a specific concept in the Atlas platform?
-Users can initiate a search by clicking on the 'search' option on the left-hand side of the platform and then typing in the concept of interest in the search bar.
What type of information is displayed in the tabular view after a search is performed?
-The tabular view displays information associated with the concept ID, concept code, concept name, class, record count, descendant record count, domain, and vocabulary.
How many different concepts were found when searching for 'hypertension' in the script?
-When searching for 'hypertension', 1278 different concepts were found across various vocabularies and domains.
What are the facets on the left-hand side of the screen used for?
-The facets on the left-hand side of the screen are used to filter and narrow down the search results by vocabulary, class, domain, standard concept status, validity, record presence, and descendant counts.
What does the term 'standard condition concept' refer to in the context of the script?
-In the context of the script, 'standard condition concept' refers to a concept that is considered standard and valid for use in Odyssey analyses.
How can users explore a particular concept further within the Atlas platform?
-Users can explore a particular concept further by clicking on it, which brings them to a detailed view describing the concept, its domain, vocabulary, and other relevant identifiers.
What is the purpose of the 'related concepts' tab in the Atlas platform?
-The 'related concepts' tab allows users to navigate the OMA standardized vocabularies to explore relationships between the concept of interest and other related concepts.
How does the 'hierarchy' tab help users in exploring concepts?
-The 'hierarchy' tab provides a representation that shows the parent and child concepts, allowing users to understand the broader and more specific terms related to the concept of interest.
What can users do if they know a specific code they are interested in searching for?
-If users know a specific code, they can type it into the search bar, and the platform will explore all vocabularies to determine if there are any codes containing that string.
How does the script demonstrate the process of navigating from a non-standard code to a standard concept?
-The script demonstrates this by showing how a non-standard ICD-9 code for malignant essential hypertension can be related to a standard SNOMED concept, allowing users to navigate back to the parent concept of essential hypertension.
Outlines
🔎 Exploring Search Functionality in Atlas Platform
This paragraph introduces the search capability within the Atlas platform, which is designed to explore standardized vocabularies and identify concepts and codes for analysis. The process begins by accessing the search function and can involve searching for a concept, such as hypertension, or importing based on identifiers or concept sets. The search results are displayed in a tabular format, providing detailed information about each concept, including the concept ID, code, name, class, record counts, and domain. Facets on the left allow for filtering by vocabulary, class, and other attributes. The paragraph also explains how to navigate through the concept details, related concepts, and hierarchy, which helps in understanding the relationships between different concepts and identifying the most relevant terms for analysis.
🌐 Navigating Concept Hierarchies and Relationships
The second paragraph delves deeper into navigating concept hierarchies and relationships within the Atlas platform. It explains how to use the 'hierarchy' tab to view the parent and child concepts of a selected term, such as 'essential hypertension'. This view provides a clear representation of how concepts are organized within the standardized vocabulary. The paragraph also addresses searching by specific codes, such as an ICD-9 code, and how to identify and navigate non-standard codes to their corresponding standard concepts. The process of using related concepts and hierarchy tabs to explore and identify the clinical terms for analysis is emphasized, concluding with a summary of how to explore hypertension within the vocabulary and an invitation to learn more about the Odyssey community.
Mindmap
Keywords
💡Atlas platform
💡Search capability
💡Concept identifier
💡Vocabulary
💡Concept set
💡Tabular view
💡Facet
💡Record count
💡Descendant record count
💡Standard concept
💡Odyssey community
💡Hierarchy view
💡Related concepts
Highlights
Review of the search capability within the Atlas platform, a tool for exploring standardized vocabularies and identifying concepts and codes for analysis.
Introduction of the search function accessible by clicking on the search tab on the left-hand side.
Explanation of searching by concept, identifier, source codes, or concept set within the search bar.
Demonstration of searching for the term 'hypertension' and the resulting display of associated concepts.
Overview of the tabular view showing concept ID, code, name, class, record counts, and domain in a vocabulary.
Discussion on the variety of terms returned for 'hypertension' across different vocabularies and domains.
Description of facets on the right-hand side for filtering information by vocabulary, class, domain, and other criteria.
Example of narrowing down search results by applying filters for standard concepts used in Odyssey analyses.
Illustration of sorting the table by record counts to identify the concept of essential hypertension.
Explanation of the details view for the concept of essential hypertension, including its domain and vocabulary.
Identification of essential hypertension as a standard and valid concept suitable for Odyssey analyses.
Navigation through the 'Related Concepts' tab to explore relationships between essential hypertension and related terms.
Use of the 'Hierarchy' tab to visualize the parent-child relationships of concepts within the standardized vocabulary.
Guidance on how to explore and identify clinical terms for analysis using the hierarchy and related concepts views.
Alternative method of searching using a known code, such as an ICD-9 code, to explore vocabularies.
Identification of non-standard codes and their mapping to standard concepts within the platform.
Concluding remarks summarizing the search experience for exploring hypertension within the vocabulary.
Invitation for further exploration of Atlas and the Odyssey community for additional details and resources.
Transcripts
[Music]
today we're going to review the search
capability within the Atlas platform
search is a tool that allows us to
explore the Oh mop standardized
vocabularies and to identify the sets of
concepts and codes that we are going to
be able to use in any of our analysis to
use search we just click on search on
the left hand side where we are brought
to a screen where we can either search
for per some particular concept we might
be interested in or we can import our
ability to search based on concept
identifier source codes or a concept set
today we'll talk about how to search in
this search bar we can type in any word
or code that we might be interested in
exploring say that we are interested in
doing a study of hypertension we can
simply type in the word hypertension and
search for available concepts once the
search returns are displayed
we're brought into this tabular view
that I'll explain now over on the right
hand side you see a table that provides
information associated with the concept
ID the concept code the concept name the
class a record count and a descendant
record count a domain in a vocabulary
what we can see is by searching for the
string hypertension that we've gotten a
variety of different terms to show up in
fact twelve hundred and seventy eight
different concepts that contain the
string hypertension from across a
variety of different vocabularies and
and domains on the left hand side of the
screen you can see facets that allow you
to filter and narrow down this
information you can filter this
information by vocabulary here you can
see that hypertension appears in
vocabularies including sno-med Medra
icd-9 icd-10 etc we can also filter by
class by domain
whether or not the concept is a standard
concept to be used in Odyssey analyses
whether or not it is valid whether it
has records and whether it has
descendants counts so when I typed
hypertension if I was interested in a
standard condition concept I can click
on any of these filters on the left hand
side and we can see that the information
to the right is then filtered
accordingly here we now are left with
238 different concepts this table as the
default is sorted by the number of
record counts in your source data so
here we can see that the concept of
essential hypertension it has a direct
record count of over 177 million in this
particular source and a descendant
record count of 240 million indicating
that this concept or more specific
concepts are actively persistent in our
data if I'm interested in exploring this
particular concept further I can click
on the concept essential hypertension to
explore and navigate it within the
vocabularies when I click on essential
hypertension we're brought to a details
view that describes this particular
concept essential hypertension belongs
to the condition domain and it is a
clinical finding within the vocabulary
of sno-med the standard OMA vocabulary
identifier is three two zero one eight
zero but if you are interested in the
identifier used within the sno-med
vocabulary that's provided here as a
concept code and we can see that this is
a standard and valid concept meaning
that it can be used for any Odyssey
analyses the next tab is the related
concepts and this is allows us to
navigate the OMA standardized
vocabularies to explore relationships
between essential hypertension and
things that it may be related to the
same navigation applies you have a
tabular display showing you related
concepts with facets on the left-hand
side to allow you to navigate and
explore this this list and filter down
to information that you might be
interested in for example if we are
interested in standard concepts
we may be interested specifically in
whether or not there are broader terms
than essential hypertension that might
be interested I can select has ancestor
of and we can actually see that
essential hypertension has an ancestor
of hypertensive disorder which happens
to be a disorder of the cardiovascular
system which happens to be a
cardiovascular finding which ultimately
is a disease and rolls up to clinical
finding navigating these set of
relationships can allow us to explore
and identify the clinical terms that
were interested in using for our
analysis an additional way to explore
these relationships is through this tab
called hierarchy by selecting the
hierarchy tab we specifically get a
representation that shows us the parents
of the concept of interest and the
children here in the middle of the
screen we can see we are still focused
on essential hypertension as the concept
but its parents within the OMA p--
standardized vocabulary include multiple
terms from the meddra vocabulary and one
parent in the sno-med vocabulary called
hypertensive disorder we can also see
that there are multiple ways of
specifying essential hypertension with
additional granularity represented by
the children concept here we can see
that there's concepts for benign
essential hypertension malignant
essential hypertension etc between the
hierarchy view and the related concepts
view we have the ability to explore and
navigate any particular concepts that we
may be interested in we started this
search on the search page by typing the
word hypertension sometimes you may know
a particular code that you are
interested in for example if I was
particularly interested in icd-9 code
for 0 1 dot I can type in that code in
my search and the search is going to
explore all of the vocabularies and to
determine if there are any codes that
contain that string here we can see that
there are 3 vocabularies that have 4 0 1
. including the icd-9 vocabulary which
has codes for benign
essential hypertension by looking at
these codes we can actually select a
particular source code we can then learn
more about it in this particular case
seeing that this is an icd-9 code for
malignant essential hypertension but
also highlighting that it is a non
standard code we know this is not the
common representation to be used to
explore the condition across the odyssey
community but by clicking related
concepts we can actually identify what
concepts are related to this
non-standard code and here we can see
that the non-standard icd-9 code for
bullying and essential hypertension maps
to a standard sno-med concept of
malignant essential hypertension and by
selecting that malignant essential
hypertension we can use the related
concepts or the hierarchy to navigate
our way back to find that a parent of
malignant essential hypertension is
essential hypertension and by clicking
on there we're back to where we started
identify an essential hypertension as a
disease which is a hypertensive disorder
and has multiple children concepts this
concludes our summary of how to explore
hypertension in the vocabulary if you
are interested in additional details
about how to use Atlas in the search
experience for other concepts or you'd
like to learn more about the Odyssey
community please check us out at Odyssey
org
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