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ontology-mapping.md

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Ontology mapping

The ontology mapping file is used to map variables declared in the column mapping file to ontology codes and to contain the ancestry of the classes those codes represent. The ontology codes will be used to create entries in the concept dimension. The ancestry information will be used to create nodes in the ontology tree.

ONTOLOGY_MAP_FILE format

Category code Data label Ontology code Label URI Ancestors
Vital Signs Heart Rate SNOMEDCT/364075005 Heart rate http://purl.bioontology.org/ontology/SNOMEDCT/364075005 SNOMEDCT/78564009,SNOMEDCT/364072008
SNOMEDCT/78564009 Pulse rate http://purl.bioontology.org/ontology/SNOMEDCT/78564009 SNOMEDCT/46680005,SNOMEDCT/310611001,SNOMEDCT/248627000
SNOMEDCT/310611001 Cardiovascular measure http://purl.bioontology.org/ontology/SNOMEDCT/310611001 SNOMEDCT/364066008
SNOMEDCT/248627000 Pulse characteristics http://purl.bioontology.org/ontology/SNOMEDCT/248627000 SNOMEDCT/364093006
SNOMEDCT/364093006 Feature of peripheral pulse http://purl.bioontology.org/ontology/SNOMEDCT/364093006 SNOMEDCT/364089000
SNOMEDCT/364089000 Systemic arterial feature http://purl.bioontology.org/ontology/SNOMEDCT/364089000 SNOMEDCT/364088008
SNOMEDCT/364088008 Arterial feature http://purl.bioontology.org/ontology/SNOMEDCT/364088008 SNOMEDCT/364087003
SNOMEDCT/364087003 Blood vessel feature http://purl.bioontology.org/ontology/SNOMEDCT/364087003 SNOMEDCT/364066008
SNOMEDCT/364072008 Cardiac feature http://purl.bioontology.org/ontology/SNOMEDCT/364072008 SNOMEDCT/364066008,SNOMEDCT/414236006
SNOMEDCT/364066008 Cardiovascular observable http://purl.bioontology.org/ontology/SNOMEDCT/364066008 SNOMEDCT/363788007
SNOMEDCT/414236006 Feature of anatomical entity http://purl.bioontology.org/ontology/SNOMEDCT/414236006 SNOMEDCT/414237002
SNOMEDCT/414237002 Feature of entity http://purl.bioontology.org/ontology/SNOMEDCT/414237002 SNOMEDCT/363787002
SNOMEDCT/363788007 Clinical history/examination observable http://purl.bioontology.org/ontology/SNOMEDCT/363788007 SNOMEDCT/363787002
SNOMEDCT/46680005 Vital signs http://purl.bioontology.org/ontology/SNOMEDCT/46680005 SNOMEDCT/363787002
SNOMEDCT/363787002 Observable entity http://purl.bioontology.org/ontology/SNOMEDCT/363787002

Table, tab separated, txt file. It contains information about concepts and the ontology tree that are uploaded to TranSMART. The first two columns refer to columns in the column mapping file. The rows were these columns are not empty, are used for associating observations with concept codes. The others are only used to build the tree.

Description of the columns:

  • Category Code The category name used in the column mapping file.
  • Data Label The variable name used in the column mapping file.
  • Ontology code Concept code to be used to classify observations.
  • Label Name of the concept.
  • URI Link to resource with metadata about the concept.
  • Ancestors Comma-separated list of ontology codes of classes of which this concept is a subclass.

An example ontology mapping file can be found in the TEST_17_1 example study.

Generating an ontology mapping file

An ontology mapping file can be generated using a ontologymapping.params file.

The following parameters are supported:

  • COLUMN_MAP_FILE (Example: clinical/OBS336-201_columns.txt)
  • ONTOLOGY_MAP_FILE (Example: ontology_codes.txt)
  • ONTOLOGY_SERVICE_TYPE (Example: default)

Two ontology types are currently implemented:

The following parameters are available for the default service type:

  • ONTOLOGY_SERVER_URL: The URL of the ontology server.
  • ONTOLOGY_SERVER_SEARCH_PATH: The relative path used to search for recommended terms (Example: /search)
  • ONTOLOGY_SERVER_DETAILS_PATH: The relative path used to lookup details of ontology terms (Example: /codes/details)

The following parameters are available for the bioontology service type:

  • ONTOLOGY_SERVER_URL: The URL of the ontology server (Example: 'https://data.bioontology.org').
  • ONTOLOGY_SERVER_API_KEY: The API key token, required to access the server. An API key can be obtained by registering at https://bioportal.bioontology.org/.
  • ONTOLOGY_SERVER_ONTOLOGIES: The comma-separated list of ontologies to query (Example: SNOMEDCT).

An example fetching parameters file can be found in the TEST_17_1 example study.

Note: If you want to rerun a previously completed job, you need to pass the -n options to transmart-batch.