Differences

This shows you the differences between two versions of the page.

--- documentation:software:atlas:vocabulary [2016/08/19 15:19] – jhardin
+++ documentation:software:atlas:vocabulary [2019/05/30 20:47] (current) – anthonysena
@@ Line 1: / Line 1: @@
-Atlas provides the ability to search and explore the [OMOP standardized vocabulary](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:vocabulary). This functionality was originally built as part of the [Hermes working group](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:software:hermes) and now Hermes has been fully incorporated into Atlas.
+~~NOTOC~~
-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.
+===== 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.
+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 =====
 ----
 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 =====
@@ Line 17: / Line 26: @@
   - Class: This will allow for filtering down to a specific class of concepts.
   - Domain: This will allow for filtering down to a specific domain.
-  - Standard Concept: Allows for filtering down to [standard concepts](http://www.ohdsi.org/web/wiki/doku.php?id=documentation:cdm:concept).
+  - 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.
-  - Has Records: If you have configured a [source daimon](https://github.com/OHDSI/WebAPI/wiki/Source-Configuration) 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.
@@ Line 39: / 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.
   * 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 [Concept Set](https://github.com/OHDSI/Atlas/wiki/Concept-Sets).  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 =====
 ----
-The import tab provides a means for importing concepts into a new concept set. Concept Sets are described in more detail [here](https://github.com/OHDSI/Atlas/wiki/Concept-Sets). 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
   - 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