ohdsi / atlas

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data

ATLAS

ATLAS is an open source software tool for researchers to conduct scientific analyses on standardized observational data converted to the OMOP Common Data Model V5. Researchers can create cohorts by defining groups of people based on an exposure to a drug or diagnosis of a particular condition using healthcare claims data. ATLAS has vocabulary searching of medical concepts to identify people with specific conditions, drug exposures etc. Patient profiles can be viewed within a specific cohort allowing visualization of a particular subject's health care records. Population effect level estimation analyses allows for comparison of two different cohorts and leverages R packages.

Resources

• Atlas (ohdsi.org) Please note: Google Chrome is the recommended browser for ATLAS.
• Documentation
• Releases

Technology

ATLAS is built using HTML, CSS and Knockout JavaScript. For more information on using Atlas, please refer to the setup guide.

Dependencies

• WebAPI

Getting Involved

• Developer questions/comments/feedback: OHDSI Forum
• We use the GitHub issue tracker for all bugs/issues/enhancements

License

ATLAS is licensed under Apache License 2.

atlas's Issues

confirm method issue

the confirm method is used in a few places to prompt the user and ensure they don't unintentionally navigate away and lose unsaved changes. If the user has checked the 'no longer allow this window to pop up messages' checkbox then the message is never displayed and call to confirm defaults to true.

A different approach to the confirmation messages may need to be considered.

active job count display

display the number of active jobs on the side menu with polling to update every 90 seconds.

feasibility attrition table editor

using existing bit string based rule results

Confirm R Services hidden for this release

Let's make sure that we hide any in-progress features before we finalize the release.

Add commas to number formatting for record counts

Show which concepts are descendants in included concepts tab

After adding a concept and checking its descendants in a concept set, it would be nice to see which descendants belong to which concept. Thanks!

Export feature in ATLAS does not let you copy concept

I am unable to copy a long concept list from the export tab because of the new scrolling feature. It is very slow in letting me select the list

treemap disappears on conditions by index report

to recreate view a conditions by index report, switch to table view and click a row to load the drill down report. then click back to treemap.

only request vocabulary version for sources with vocabulary daimons

this is an issue specifically on the configuration tab

Job Cleanup Routine

When WebAPI starts, mark any jobs still listed as active as Unknown status as it seems that the WebAPI was terminiated while the job was still in progress

Has Data - filter bugged by not recognizing the RC and DRC column update

negative control tab on concept manager

feedback on report generation

from the cohort definition screens provide feedback when a user clicks the generate button to inform them that the process has started and perhaps a link to a job monitor page to see when it has completed.

Refreshing ATLAS causes concept sets to disappear

Not sure if its a bug or intentional (but not very user friendly)...refreshing ATLAS at anytime throws away any unsaved concept sets.

report builder

allow selection of cohort definitions and various results to be compiled into a single web document.

If you click on 'vocabulary search', have to reset to blank, not re-run past search

Currenty, if you've done a prior search, and you click on 'vocabulary search' on lefthand menu, it re-runs the last search, including the API calls to get RC/DRC. But if I'm clicking 'vocabulary search' I'm generally wanting to search for something new, and would prefer not to wait for the past search to come back (particluarly when sometimes that past search migth be a big one that's time consuming),.

Integrate clipboard.js

Based on issue #39, incorporate the use of clipboard.js to make it easier to copy values from different text boxes.

https://clipboardjs.com/

column meaning?

Atlas is a great tool
simple question:

What RC and DRC mean? (and how are they computed) and what sites contdibuted to the calculation

Add exclude button to 'included concepts' tab

For concepts in 'included concepts' tab add a dropdown in cart to allow for exclusion, instead of heading back to 'concept set' to exclude

Thank you!

Cannot clear out concept set

Once a new concept set is created I cannot clear out the set to import a new one or start on a new defintion

Importing source codes, they do not get added to cart

When importing a list of source codes, they don't get added to the cart, and need to be manually added.

New Cohort - Concept Set properties not set

Scenario: create a new cohort, add concept sets. These new concept sets' concepts do not contain all of the attributes required by the concept set editor which then throws errors.

loading multiple concept sets in succession does not reset active list of concepts

Can't select visit type filters

This could be a icon/image bug?

sorting by concept set name triggers route

If you click on the Title column header on the /atlas/#/conceptsets page you get an error. The event callback is based on a class, but it appears the class is assigned the to TH as well so when you attempt to sort you trigger a route with an undefined identifier:

/WebAPI/conceptset/undefined

Unable to create concept set when concepts are imported

After importing a new concept set on the import tab, the entire concept set is selected but does not create a new concept set. For now I've worked around it by first clicking on new concept set, and then importing the set afterwards

Always show left-hand menu items

Found it odd that there was show/hide on menu items. The link on 'Selected concepts' did not work once it was shown, so couldn't get to that page.

New Job Routes

Active - Not completed and started in last 48 hours
Recent - Started in last 48 hours

Deleting Cohort doesn't Close it

Need to remove the reference to the observable when a cohort is deleted so that the "current asset" link on the left menu is removed.

Should check concept sets as well, same should happen here.

Refresh Jobs Button

Add a button to refresh job status

Cohort Name Goes Away in Cohort Reporting Tab

When working with a specific cohort in cohort reporting, if you navigate to vocabulary search and then back to cohort reporting you are still examining the same cohort you were before but the name at the top reverts back to 'Click Here to Choose a Cohort'.

refactor report manager component

create individual report components for reuse across penelope/heracles/achilles (cohort/label, cohort, source) reporting needs.

place of service record counts?

Are they not available?

display concept record counts across data sets within concept manager and concept set manager components

Concept Set - concept duplication

To reproduce: open a concept set that contains concepts. Then, open another concept set that contains concepts. The result: you will have a list of concepts from both sets.

My current work around is to clear the concept list before loading the 2nd concept set.

add error handling for lack of availability of r service bus nodes

This should handle availability issues of both RSB as well as RPool

No tests

Any plans to add unit or e2e tests?

Concept Set Save Button Issue

While working with Urmila we found that sometimes the Save button on the Concept Set page would save, but not change to disabled acknowledging that the save occurred.

Allow choice of how to handle restriction to observation period in cohort definition

Currently, cohort definition presumes that the index date falls within an observation period, and all subsequent inclusion criteria are to be evaluated within the confines of that same observation period. Generally, I think this is the right approach. However, there can be instances when the user wants to look beyond the observation period (e.g. find patients with prior history of a condition anytime in their past). We should consider if we can make this choice explicit in the cohort definition process, so 1) at a minimum, users are aware that their criteria are restricted to the observation period (e.g. at this as text on the UI and within the print friendly view) and 2) consider if choosing to be in the observation period or using all time independent from observation period should be an option.

When using import with source codes, does not clear after concepts are removed

After importing source code list, and adding as a concept set the source code list is not cleared when the concept set is closed. I have to manually select all the codes in the box and then delete them

show both descendant record counts as well as record counts

Past Vocabulary Searches

The past searches look like links however they do not navigate to the past search.

Upgrade DataTables library to enable exports and other new features

V1.0.0 Release Steps

Release Version V1.0.0

• Use latest master as candidate V1.1.0 of WebAPI and deploy to development
• Generate Atlas Release Notes
• Generate WebAPI Release Notes
• Complete user acceptance testing
• Obtain sign off
• Tag Atlas as V1.0.0
• Tag WebAPI as V1.1.0
• Update Jenkins automation to point to "released" branch to obtain latest stable build for OHDSI.org
• Merge charon branch into master & remove
• Communicate production change to team
• Update OHDSI.org
• Communicate release via OHDSI forums

Import CIRCE components into ATLAS

CIRCE components are going to be hosted out of ATLAS for the 1.0 release. This issue is tracking the progress of moving components from CIRCE to ATLAS.

Once completed, can address issue #47 by migrating to font awesome.

cohort-conceptset-manager cleanup

Remove references to this component as it is no longer needed

Remove Cohort Reporting left hand menu item

This has now been integrated into the cohort editing screen so it will be easier to access that way to generate reports and to view them.

Remove references to unsecured (http) resources

When Atlas is deployed on a secured server (https), requests for external http resources (i.e. css and js) fail. We should always use https, right?

Table headers and contents are not properly aligned in the Generation Status tab of the Cohort Definitions

In the Cohort Definition - Generation Status Tab, the table headers and contents are not properly aligned. The headers are left aligned and the contents are right aligned.

add a feedback link to menu

direct people to github to post issues, suggestions, etc.