Private-preview application link: http://re-uat-terminology-app-01.gel.zone/
The purpose of the Terminology Toolset is to help you work effectively with the various clinical coding standards that are in use within the Research Environment:
With the Terminology Toolset you can search for Main Programme participants, using terminology resources to specify your search criteria:
Terminology reference data is provided by a FHIR terminology server (https://genomics.ontoserver.csiro.au/fhir)
Participant clinical data is obtained from the Main Programme Data Release version 6.
The diagram below depicts the clinical data model used for specifying search criteria and for displaying the results. This model is based on the HL7 FHIR resource model.
Concept | Meaning |
---|---|
Participant | A participant in the Genomics England 100,000 Genomes Project. Participants include probands and relatives. |
Condition | A clinical condition, problem, diagnosis, or other event, situation, issue, or clinical concept that has risen to a level of concern. |
Observation | Measurements and simple assertions made about a participant |
Procedure | An action that is or was performed on or for a patient. This can be a physical intervention like an operation, or less invasive like long term services, counseling, or hypnotherapy. |
Encounter | An interaction between a patient and healthcare provider(s) for the purpose of providing healthcare service(s) or assessing the health status of a patient. |
Please click here, to see how tables and columns in the Main Programme Data Release are mapped to this model.
Specify a combination of conditions, observations and procedures to search for matching participants.
Notes:
Search for terms from the available code systems, by entering part of the code or description. Notes:
The search will only return results when terms in the search criteria are from the same code system as the underlying data. For example, ICD-10 coded participant data can only be found if the search criteria include ICD-10 terms.
You can use the "Automatically include mapped concepts" feature (described below) to find equivalent terms across different code systems.
For an overview of fields and code systems, see Terminology Service Tool: Clinical Data Mapping.
Select on or more terms from the list. Notes:
Descendants of selected terms are automatically included in the search.
Searching with high-level terms, which can have thousands of descendants, may slow down the search.
It is not currently possible to search with terms that have more than 10000 descendants.
Select "Automatically include mapped concepts" to find and add mapped concepts from other code systems to the search criteria. For example, after selecting a SNOMED CT concept, the search can automatically include ICD-10 terms that have the same meaning as the SNOMED CT concept in the search, thus potentially finding more participants. Notes:
Mapped concepts may not have the exact same meaning as the selected concepts, so this feature must be used carefully!
Mapped concepts and their descendants can be distinguished in the UI by their colour (green) and a special icon.
SNOMED CT to ICD10 and SNOMED to OPCS4 mappings are provided by NHSD. Targets that are equivalent or narrower are included. Targets that require combining multiple wider concepts have been excluded.
SNOMED CT to HPO mappings are provided by CSIRO.
When your search criteria are complete, click on "Continue" to see the search results.
For each participant that matches the search criteria, the following fields are displayed:
Notes:
Select columns to include and download a CSV file with the search results.
Notes:
Browse and explore the structure of relevant code systems.
Behind this application is an HL7 FHIR-compliant terminology server, which is also available for your own scripts and applications to implement terminology-enabled functionality.
FHIR API endpoint: https://genomics.ontoserver.csiro.au/fhir
Disclaimer: this API is currently provided for testing purposes only and without any guarantees regarding availability or content quality.
Please note: the SSL certificate of the API endpoint may trigger a security warning when accessing the URL through a browser. In the case of the terminology server, this should not pose a threat and the risk can be accepted. If you understand and accept the risk, please click the “Accept the Risk and Continue” button. The issue is being addressed and will be resolved in the future.
To learn about the FHIR terminology server standard, see http://hl7.org/fhir/stu3/terminology-module.html
For details about our specific implementation of the terminology server and more examples, please refer to https://ontoserver.csiro.au/docs/5.1/api-fhir.html#.
Example API requests:
This section describes how the standard concepts of Condition, Observation, Procedure and Encounter map to the table structure of the Genomics England Main Programme data release.
More fields will be included in future releases.
The following table shows which fields from the Main Programme data model map to conditions, and the coding standards used.
Main Programme Table | Condition Code | |
---|---|---|
ICD-10 | GEL Recruited Diseases | |
cancer_participant_tumour | diagnosis_icd_code | |
cancer_participant_disease | cancer_disease_type cancer_disease_sub_type | |
rare_diseases_participant_disease | normalised_disease_group normalised_disease_sub_group normalised_specific_disease | |
hes_apc | diag_01 ... diag_20 | |
hes_op | diag_01 ... diag_12 |
The following table shows which fields from the Main Programme data model map to observations, and the coding standards used.
Main Programme Table | Observation Code | Body Site Code | |
---|---|---|---|
HPO | SNOMED CT | SNOMED CT | |
cancer_participant_tumour | morphology_snomed_ct_code | topography_snomed_ct_code | |
rare_diseases_participant_phenotype | hpo_id (positive) |
The following table shows which fields from the Main Programme data model map to procedures, and the coding standards used.
Main Programme Table | Procedure Code | |
---|---|---|
OPCS-4 | SNOMED CT | |
hes_apc | opertn_01 ... opertn_24 | |
hes_op | opertn_01 ... opertn_24 | |
did | did_snomedct_code |
The following table shows which fields from the Main Programme data model map to encounters.
Main Programme Table | Encounter Type | Encounter ID | Encounter Date |
---|---|---|---|
participant, cancer_*, rare_diseases_* | GMC | participant_id | registration_date if available, consent_date otherwise |
ae | |||
hes_apc | Inpatient | admidate | admidate |
hes_op | Outpatient | attendkey | apptdate |
did | Diagnostic Imaging | submissiondataid | did_date3 |