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Domain 'concepts'

The concepts subfolder contains CSV import files for saving concepts in bulk. This is a possible example of its content:

concepts/
  ├── diagnoses.csv
  ├── findings.csv
  ├── misc.csv
  └──  ...

The way those CSV files are processed is controlled by a reserved part of the CSV file header line that holds metadata about the CSV file itself. Here is an example of a header line:

Uuid Void/Retire Fully specified name:en Short name:en Description:en ... _version:1 _order:1000

Concept Name Updating vs Concept Name Deleting + Creating

The concepts domain loader will attempt to match incoming concept names with existing concept names when possible. It will first try to match on the concept name UUID if one is specified. If no explicit UUID is specified it will try to match on the exact combination of name text, name type and locale.

If a matching name is found, the loader will update this existing name. If a matching name is not found, the loader will save a new name. Any existing concept names that were not matched are voided in a accordance with the WYSIWYG principle.

NOTE: OpenMRS does not allow changing the name text of an existing ConceptName entity. If a UUID matches and the name does not for an existing concept name, the processing will fail for the row. One should assign a new UUID when changing a concept name, which will result in a new ConceptName entity to be created and for the existing ConceptName entity to be voided.

Implicit Generation of Concept Names UUIDs

When no UUID is explicitely defined for a concept name, one is generated implicitly by Initializer in a determinsitic way. Implicit concept names UUIDs are generated from the following seed information:

  1. The concept UUID,
  2. The concept name text value,
  3. The concept name type (FSN, short name or synonym),
  4. The concept name locale.

Each combination of those four arguments always produce the same concept name UUID.

Concept Headers

Headers Fully specified name:<locale>, Short name:<locale>, Index term <n>:<locale>, Synonym <n>:<locale>, and Description:<locale>

Those are locale specific headers that need to indicate the locale for the values of their column.
For example for a column to contain short names in English (locale 'en') simply name the header Short name:en. The same logic applies for the other locale specific headers.

At least one fully specified name per locale must be specified for a concept. All other concept names are optional. The fully specified name is a secondary identifier for the concepts domain, it will be used to attempt fetching the concept if no UUID is provided. A concept may contain one short name per Locale. A concept may contain more than one index term and synonym per Locale.

The concept name type to associate with a given name is inferred from the concept name header, namely either FULLY_SPECIFIED, SHORT, INDEX_TERM or none (which implicitly means that the name is a synonym.)

To allow for more than one Index term and Synonym while maintaining unique column headers, one simply needs to add an indexing suffix <n> to the header prior to the locale. Some examples:

  • Fully specified name:en
  • Fully specified name:fr
  • Short name:en
  • Index term 1:fr
  • Synonym 1:en
  • Synonym 2:en
Headers Fully specified name:<locale>:Preferred, Short name:<locale>:Preferred, Index term <n>:<locale>:Preferred and Synonym <n>:<locale>:Preferred

By default, the first name found for a given locale in a particular CSV row will be marked as being locale preferred. If one wants to indicate that a different localized name should be locale preferred, this can be done via a preferred (case insensitive) column associated with the name column. For example, to indicate that the concept name added as Synonym 1:en should be locale preferred, one should set a truthy value:

Synonym 1:en Synonym 1:en:Preferred
Diabetes TRUE
Headers Fully specified name:<locale>:Uuid, Short name:<locale>:Uuid, Index term <n>:<locale>:Uuid and Synonym <n>:<locale>:Uuid

One may specify the uuid to associate with a given concept name in order to fully control references to this concept name. This is done by adding a a uuid column associated with the name column. For example, to associate a fixed UUID with the Synonym 1:en name, one would add a column with the uuid as a value named:

Synonym 1:en Synonym 1:en:Uuid
Diabetes d4bce1d7-1a1b-4108-b87f-e630e43c7374
Header Description:<locale>

Similarly as with concept names the description is localised.

Header Data class (mandatory)
Header Data type (mandatory)
Header Version (optional)

Here is an example of valid CSV to define basic concepts:

Uuid Fully specified name:en Short name:en Description:en Data class Data type
Nationality Nat. The status of belonging to a particular nation. Question Text
db2f4fc4-.. Language Lang. The method of human communication. Question Text
Header Answers (optional)

To provide a semicolon-separated list of answer concepts to the concept to be created or edited. Note that if this header/column is present, when processing an existing concept, all answers not specified here will be removed. If the column is not present, any existing answers will be preserved (allowing answers to be managed via the conceptsets domain).

Header Members (optional)

To provide a semicolon-separated list of concepts to be members of the concept set to be created or edited. Note that the concept will be marked to be a set as soon as set members are provided. Note that if this header/column is present, when processing an existing concept, all members not specified here will be removed. If the column is not present, any existing members will be preserved (allowing members to be managed via the conceptsets domain).

Here is an example of the 'nested' columns:

... Answers Members ...
... CONCEPT_NAME; source:134; db2f4fc4-.. ...
... CONCEPT_NAME; source:134; db2f4fc4-.. ...

As the example suggests, it is possible to provide lists of concepts identifiers to fill the values of the columns 'answers' or 'members' under the form of concept names in OpenMRS' default locale (eg. "Hypertension"), concept same-as mappings (eg. "CIEL:117399") and concept UUIDs (eg. "211b7c44-e346-47ab-866c-7ac638cd5352"). The concepts that could not be fetched through their provided identifier will fail the creation of the concept from the CSV line altogether, and the parser will continue to the next CSV line.

This also the case for concepts referenced by names that do not exist in the default locale, even though they may exist in other allowed locales. Eg. if the default locale is 'en' and that the hypertension concept is referenced by its 'es' name "hipertensión", then it will not be fetched and this will result in an error.

NOTE In the current implementation the listing order of the concepts in the CSV file does matter since unexisting concepts will fail the CSV line processing. It is recommended to take this into account and to insert CSV lines for concepts with nested lists low enough in the CSV file so that all nested concepts are found when the CSV line is being processed.

Same as mappings

As of version 2.4 the header Same as mappings is discouraged in favour of the newer Mappings|SAME-AS. See Mappings headers section below:

Mappings headers

Concepts support one or more mappings to concept reference terms. Each of these mappings are configurable with a mapping type, a source, and a code. In order to specify mappings on a given concept, the values for those mappings can be set under ad-hoc headers starting with the special prefix Mappings|. Mappings headers should be specified in the following format:

Option 1: Column header specifies the mapping type, but not the source. In this case, the column values must be one or more source:code pairs. If specifying multiple source:code pairs, these must be separated by semi-colons. Example:

... Mappings|SAME-AS Mappings|NARROWER-THAN
... CIEL:5089; SNOMED CT:27113001 LOINC:3141-9

NOTE: One may also use the column header Same as mappings as an alternative to Mappings:SAME-AS for backwards-compatibility with earlier versions.

Option 2: Column header specifies both the mapping type and the source. In this case, the column values must only be the codes. If specifiying multiple codes for the same mapping type and source, these must be separated by semi-colons, or they can alternatively be added as separate columns. In the case of adding them as separate columns, and additional suffix is supported on the header to enable each column header to be unique. Example:

... Mappings|SAME-AS|CIEL Mappings|SAME-AS|SNOMED CT Mappings|SAME-AS|PIH|Code Mappings|SAME-AS|PIH|Name
... 5089 27113001 5089 WEIGHT (KG)
Attribute headers

Concepts support attributes. The values for those attributes can be set under ad-hoc headers starting with the special prefix Attribute|. The value indicated on a CSV line will be resolved to its final value based on the type of the attribute. Let us look at an example:

... Attribute|Last Audit Date ...
... 2017-05-15 ...

This attribute points to an attribute type identified by "Last Audit Date". The attribute type identifier (a name here) suggests that it might be an attribute of custom datatype Date. This means that its value, represented by the string 2017-05-15, will eventually be resolved as the Java date Mon May 15 00:00:00 2017 set as an attribute of the concept described by the CSV line.

Below are the headers specific to concepts numeric:

Header Absolute low
Header Critical low
Header Normal low
Header Normal high
Header Critical high
Header Absolute high
Header Units
Header Allow decimals
Header Display precision

NOTE The concept will be considered as a candidate to be a concept numeric if and only if its data type is set to Numeric.

Below are the headers specific to concepts complex:

Header Complex data handler (mandatory for concepts complex)

This should be the class name of a valid complex data handler class at runtime. Eg. ImageHandler, BinaryDataHandler, ... etc. See here for the list of handlers shipped with Core 2.x.

NOTE The concept will be considered as a candidate to be a concept complex if and only if its data type is set to Complex.

Further examples:

Please look at the test configuration folder for sample import files for all domains, see here.