Atc why oh why wiki

In Figure 1, the source code terms were in Dutch and were also translated into English. Usagi will leverage the English translations to map to the standard vocabulary. If you mouse hover over the drop downs, a pop-up will appear defining each column. Usagi will not use the Additional info column s as information to associate source codes to Vocabulary concept codes; however this additional information may help the individual reviewing the source code mapping and should be included.

Finally you can set some restrictions for Usagi when mapping. For example, in Figure 3, the user is mapping the source codes only to concepts in the Condition domain. By default, Usagi only maps to Standard Concepts, but if the the option 'Filter standard concepts' is turned off, Usagi will also consider Classification Concepts. Hover your mouse over the different filters for additional information about the filter.

For example, in the case of drugs there might already be ATC codes assigned to each drug. Even though an ATC code does not uniquely identify a single RxNorm drug code, it does help limit the search space to only those concepts that fall under the ATC code in the Vocabulary. To use the ATC code, follow these steps:.

You can also use other sources of information than the ATC code to restrict as well. In the example shown in the figure above, we used a partial mapping derived from UMLS to restrict the Usagi searh.

In that case we will need to use 'Auto concept ID column'. Figure 3: Defining filter rules when mapping. The file import will take a few minutes as it is running the term similarity algorithm to map source codes.

Figure 4: Usagi Matching Screen. In Figure 4, you see the Usagi screen is made up of 3 main sections: an overview table, the selected mapping section, and place to perform searches. Note that in any of the tables, you can right-click to select the columns that are shown or hidden to reduce the visual complexity.

The Overview Table shows the current mapping of source codes to concepts. Right after importing source codes, this mapping contains the automatically generated suggested mappings based on term similarity and any search options.

In the example in Figure 4, the English names of Dutch condition codes were mapped to standard concepts in the Condition domain, because the user restricted the search to that domain. Usagi compared the source code descriptions to concept names and synonyms to find the best match.

Because the user had selected 'Include source terms' Usagi also considered the names and synonyms of all source concepts in the vocabulary that map to a particular concept. Figure 5: Reviewing an Usagi Match. It is suggested that someone with experience with coding systems help map source codes to their associated standard vocabulary.

That individual will work through code by code in the Overview Table to either accept the mapping Usagi has suggested or choose a new mapping.

There was a matching score of 0. Figure 6: Searching for a New Concept. Usagi's suggestion was restricted by the concept identified in our automatically derived mapping from UMLS, and the result might not be optimal. In the Search Facility, we could search for other concepts using either the actual term itself or a search box query.

When using the manual search box, one should keep in mind that Usagi uses a fuzzy search, and does not support structured search queries, so for example not supporting boolean operators like AND and OR.

On the right of the Query section of the Search Facility, there is a Filters section, this provides options to trim down the results from the OMOP Vocabulary when searching for the search term. In this case we know we want to only find standard concepts, and we allow concepts to be found based on the names and synonyms of source concepts in the vocabulary that map to those standard concepts. When looking for appropriate concepts to map to, it is important to consider the 'social life' of a concept.

The meaning of a concept might depend partially on its place in the hierarchy, and sometimes there are 'orphan concepts' in the vocabulary with few or no hierarchical relationships, which would be ill-suited as target concepts. Figure 7: Concept information panel. Figure 7 shows the concept information panel. It shows general information about a concept, as well as its parents, children, and other source codes that map to the concept.

Users can use this panel to navigate the hierarchy and potentially choose a different target concept. Continue to move through this process, code by code, until all codes have been checked. In the list of source codes at the top of the screen, by selecting the column heading you can sort the codes. Often we suggest going from the highest frequency codes to the lowest.

In the bottom left of the screen you can see the number of codes that have approved mappings, and how many code occurrences that corresponds to. Troye Sivan Wiki. Zella Day Wiki. Against The Current Wikia Explore. Albums Browse In Our Bones. Community Corner Recent blog posts Forum. Explore Wikis Community Central. Register Don't have an account?

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