documentation:software:atlas:vocabulary
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documentation:software:atlas:vocabulary [2016/08/19 15:40] jhardin |
documentation:software:atlas:vocabulary [2019/05/30 20:47] (current) anthonysena |
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| - | ====== Vocabulary ====== | + | ===== IMPORTANT NOTE ===== |
| + | |||
| + | All ATLAS documentation has moved to [[https://github.com/OHDSI/ATLAS/wiki|GitHub]]. Please disregard the content below as it is legacy and kept for posterity. | ||
| + | |||
| + | ====== Vocabulary (LEGACY) ====== | ||
| Atlas provides the ability to search and explore the [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary|OMOP standardized vocabulary]]. This functionality was originally built as part of the [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:hermes|Hermes working group]] and now Hermes has been fully incorporated into Atlas. | Atlas provides the ability to search and explore the [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary|OMOP standardized vocabulary]]. This functionality was originally built as part of the [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:hermes|Hermes working group]] and now Hermes has been fully incorporated into Atlas. | ||
| - | Select "Vocabulary" in the Atlas left hand menu to bring up the search screen. You will see 4 tabs: search, advanced, results and import. Each section will be described in more detail. | + | Select "Vocabulary" in the Atlas left hand menu to bring up the search screen. You will see 2 tabs: search and import. Each section will be described in more detail. |
| + | {{ documentation:software:atlas:atlas_vocab_search.png |}} | ||
| ===== Search ===== | ===== Search ===== | ||
| ---- | ---- | ||
| Type in a search term and Atlas will search the entire standardized vocabulary for concepts that match that term. It will do a wildcard search so if you search for a term like "dementia" it will look for concepts that contain the term dementia. Once the search is complete, the results will show in the results tab. | Type in a search term and Atlas will search the entire standardized vocabulary for concepts that match that term. It will do a wildcard search so if you search for a term like "dementia" it will look for concepts that contain the term dementia. Once the search is complete, the results will show in the results tab. | ||
| - | ===== Advanced ===== | + | {{ documentation:software:atlas:atlas_vocab_dementia.png |}} |
| + | ===== Advanced Options ===== | ||
| ---- | ---- | ||
| - | This will allow you to perform a search query and specifically filter the results down to a specific set of vocabularies and domains. | + | This option is available below the 'search' button and will allow you to perform a search query and specifically filter the results down to a specific set of vocabularies and domains. |
| ===== Results ===== | ===== Results ===== | ||
| Line 22: | Line 28: | ||
| - Standard Concept: Allows for filtering down to [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:concept|standard concepts]]. | - Standard Concept: Allows for filtering down to [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:concept|standard concepts]]. | ||
| - Invalid Reason: This will enable for filtering out invalid concepts. | - Invalid Reason: This will enable for filtering out invalid concepts. | ||
| - | - Has Records: If you have configured a [[https://github.com/OHDSI/WebAPI/wiki/Source-Configuration|source daimon]] for your CDM, this filter will enable you to determine which concepts contain data in your CDM. | + | - Has Records: If you have configured a [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:webapi:webapi_installation_guide|source daimon]] for your CDM, this filter will enable you to determine which concepts contain data in your CDM. |
| - Has Descendant Records: Similar to "Has Records", it enables you to filter on concepts where descendant concepts contain data in your CDM. | - Has Descendant Records: Similar to "Has Records", it enables you to filter on concepts where descendant concepts contain data in your CDM. | ||
| Line 42: | Line 48: | ||
| * Filtering: There is a filter text box that appears in the upper right hand corner of the results table. Typing a term in this box will dynamically filter the results. | * Filtering: There is a filter text box that appears in the upper right hand corner of the results table. Typing a term in this box will dynamically filter the results. | ||
| * Sorting: The table allows for sorting on each column | * Sorting: The table allows for sorting on each column | ||
| - | * Shopping Cart: Clicking on the shopping cart will allow you to select the concept for use in new [[https://github.com/OHDSI/Atlas/wiki/Concept-Sets|Concept Set]]. If you do not have a concept set open, this will automatically start a new concept set for you. | + | * Shopping Cart: Clicking on the shopping cart will allow you to select the concept for use in new [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:atlas:concept_sets|Creating concept sets]]. If you do not have a concept set open, this will automatically start a new concept set for you. |
| + | |||
| + | {{documentation:software:atlas:atlas_vocab_dementia_boxes.png|}} | ||
| ===== Import ===== | ===== Import ===== | ||
| ---- | ---- | ||
| - | The import tab provides a means for importing concepts into a new concept set. Concept Sets are described in more detail [[https://github.com/OHDSI/Atlas/wiki/Concept-Sets|here]]. This section allows you to import concepts in the following ways: | + | The import tab provides a means for importing concepts into a new concept set. Concept Sets are described in more detail [[http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:atlas:concept_sets|here]]. This section allows you to import concepts in the following ways: |
| - Concept Identifiers: use a list of comma delimited concept_ids to import concepts into a concept set | - Concept Identifiers: use a list of comma delimited concept_ids to import concepts into a concept set | ||
| - Source Codes: use a list of comma delimited source code values to import these concept into a concept set | - Source Codes: use a list of comma delimited source code values to import these concept into a concept set | ||
| - Concept Set: enables you to import a JSON object that represents a concept set | - Concept Set: enables you to import a JSON object that represents a concept set | ||
documentation/software/atlas/vocabulary.1471621223.txt.gz · Last modified: 2016/08/19 15:40 by jhardin
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