documentation:software:atlas:concept_sets
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documentation:software:atlas:concept_sets [2016/08/24 15:04] jhardin |
documentation:software:atlas:concept_sets [2016/09/19 20:44] jhardin [Close] |
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| ===== Browsing concept sets ===== | ===== Browsing concept sets ===== | ||
| ---- | ---- | ||
| - | Selecting the Concept Sets menu option in Atlas will show you all of the concept sets available in the system. This table has filtering and sorting capabilities similar to the [[https://github.com/OHDSI/Atlas/wiki/Vocabulary#results|vocabulary results table]]. From this screen, you can click on an existing concept set to explore its definition or you can click the "Add Concept Set" button to start developing a new one. | + | Selecting the Concept Sets menu option in Atlas will show you all of the concept sets available in the system. This table has filtering and sorting capabilities similar to the [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:vocabulary|vocabulary results table]]. From this screen, you can click on an existing concept set to explore its definition or you can click the "Add Concept Set" button to start developing a new one. |
| ===== Creating concept sets ===== | ===== Creating concept sets ===== | ||
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| As you define the concept set expression, you can use the other tabs to explore how the expression is evaluated against the vocabulary to select concepts. | As you define the concept set expression, you can use the other tabs to explore how the expression is evaluated against the vocabulary to select concepts. | ||
| + | |||
| + | {{ documentation:software:atlas:atlas_conceptset_exclude_menu.png |}} | ||
| ===== Included concepts ===== | ===== Included concepts ===== | ||
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| ---- | ---- | ||
| The included source codes tab is used to show all of the non-standard concepts that are included when the concept set is evaluated. You can use this tab to review which source codes are included when the concept set is evaluated. This is useful when attempting to translate from a set of source codes (i.e. ICD9) to standard concepts to ensure that your definition is complete. It is also useful when attempting to ensure that the concept set will translate to other data sources that may have different source codes. | The included source codes tab is used to show all of the non-standard concepts that are included when the concept set is evaluated. You can use this tab to review which source codes are included when the concept set is evaluated. This is useful when attempting to translate from a set of source codes (i.e. ICD9) to standard concepts to ensure that your definition is complete. It is also useful when attempting to ensure that the concept set will translate to other data sources that may have different source codes. | ||
| + | |||
| + | ===== Explore evidence ===== | ||
| + | ---- | ||
| + | The evidence tab is used to display concept specific evidence from the LAERTES evidence base. The evidence base is comprised of evidence found in published literature, product labels and spontaneous reports. Use the evidence sources below to find out what evidence has been associated to the concepts included in this concept set. | ||
| ===== Export ===== | ===== Export ===== | ||
| ---- | ---- | ||
| - | The export tab is used to export the concept set expression and/or the concept id list. This is useful if we need to share a concept set definition with others outside of our organization. They can then use this information to import this definition using the [[https://github.com/OHDSI/Atlas/wiki/Vocabulary#import|import functionality under the vocabulary area]]. | + | The export tab is used to export the concept set expression and/or the concept id list. This is useful if we need to share a concept set definition with others outside of our organization. They can then use this information to import this definition using the import functionality under the vocabulary area. |
| - | ===== Saving ===== | + | ===== Compare ===== |
| + | ---- | ||
| + | The compare tab is used to compare two concept set expressions. The intention of this feature is to expose differences in the way a concept has been defined between studies and expose associated differences in the study results. | ||
| + | |||
| + | ===== Save ===== | ||
| + | ---- | ||
| + | Concept sets must be named and saved in order to persist them between Atlas sessions. There is a save button to the right of the concept set name box that is used to save this work to the database. Once the save has occurred you will notice that the copy button appears to the right of the concept set name box. | ||
| + | |||
| + | |||
| + | ===== Close ===== | ||
| + | ---- | ||
| + | When you are done using the concept set, you can use the close button to the right of the concept set name box to close it out. This will also remove the reference in your left-hand menu. | ||
| + | |||
| + | ===== Copy ===== | ||
| + | ---- | ||
| + | After you have saved the concept set you can select the copy button to the right of the concept set name box to copy it. | ||
| + | ===== Optimize===== | ||
| ---- | ---- | ||
| - | Concept sets must be named and saved in order to persist them between Atlas sessions. There is a save button in the top-right of the page that is used to save this work to the database. | + | When you have finished creating the concept set, you can use the optimize button to the right of the concept set name box to see what concepts are redundant or missing from the main concept. This feature will suggest as to how to modify the concept set by removing or adding to it to make the most parsimonious concept set. When you have reviewed the choices you can select the blue Save Options box to overwrite the current concept set or to create a new concept set. |
| - | ===== Closing ===== | + | ===== Delete===== |
| ---- | ---- | ||
| - | When you are done using the concept set, you can use the close button in the top-right of the page to close it out. This will also remove the reference in your left-hand menu. | + | You may wish to use the delete button to the right of the concept set name box to eliminate a test concept set or one which you no longer require. |
| ===== Scope of concept sets ===== | ===== Scope of concept sets ===== | ||
documentation/software/atlas/concept_sets.txt · Last modified: 2019/05/30 20:43 by anthonysena
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