ATLAS Tutorial: Search Example #1 (Hypertension)

Summary

This 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

00:00

🔎 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.

05:03

🌐 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.

Keywords

💡Atlas platform

The Atlas platform is the central focus of the video, serving as a tool for exploring standardized vocabularies within a database. It is integral to the video's theme as it is the medium through which the search capabilities are demonstrated and explained. The script mentions the platform's search feature, which allows users to identify concepts and codes for analysis.

💡Search capability

The search capability is a key function of the Atlas platform, enabling users to look up and explore concepts and codes. It is crucial to the video's content as the tutorial walks through how to use this feature to find relevant concepts, such as 'hypertension', and is demonstrated through the process of typing a search term and filtering results.

💡Concept identifier

A concept identifier is a unique code used to represent a specific concept within a standardized vocabulary. In the context of the video, it is used to search for and identify specific concepts, such as 'hypertension', and is highlighted when discussing the search results and their details.

💡Vocabulary

Vocabulary in this context refers to a collection of standardized terms and codes used in a particular domain, such as healthcare. The video explains how the Atlas platform allows users to search across different vocabularies like SNOMED, MedDRA, and ICD codes, to find relevant concepts.

💡Concept set

A concept set is a group of related concepts that are used together for analysis. The video mentions the ability to import and search based on concept sets, which is important for conducting comprehensive studies within the platform.

💡Tabular view

The tabular view is the format in which search results are presented on the Atlas platform. It includes various details about the concepts, such as ID, code, name, and record counts. The video script describes how this view is used to filter and sort through the search results.

💡Facet

In the context of the video, a facet refers to a filter that can be applied to the search results to narrow down the information. Facets allow users to refine their search by criteria such as vocabulary, class, domain, and validity of the concept.

💡Record count

Record count is a metric that indicates the frequency of a concept's occurrence in the data. The video uses the example of 'essential hypertension' to illustrate how record counts can reflect the prevalence of a concept within the data set.

💡Descendant record count

Descendant record count refers to the number of records that are related to a more specific concept derived from the original concept. The video explains this in relation to 'essential hypertension', showing how it has a large descendant record count, indicating its extensive use in the data.

💡Standard concept

A standard concept is a term that adheres to a standardized vocabulary and is recognized for use in analyses. The video emphasizes the importance of identifying standard concepts, such as 'essential hypertension', for Odyssey analyses.

💡Odyssey community

The Odyssey community is a group of users who utilize the Atlas platform and its standardized vocabularies for analysis. The video mentions this community in the context of using standard and valid concepts for analyses, indicating a collaborative environment for data exploration.

💡Hierarchy view

The hierarchy view is a feature within the Atlas platform that displays the relationships between concepts in a parent-child structure. The video uses this view to demonstrate how users can explore the connections between a concept like 'essential hypertension' and its broader and more specific terms.

💡Related concepts

Related concepts are terms that are associated with the main concept of interest. The video script explains how the Atlas platform allows users to navigate and explore these related concepts to understand the broader context and implications of a specific concept.

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