Terminology server¶
An HL7 FHIR-compliant terminology server is available in the research environment. The terminology server provides programmatic access to reference data for code systems (terminologies, vocabularies, classifications, ontologies) commonly used within the research environment.
Endpoint¶
An FHIR REST API endpoint can be found at: https://genomics.ontoserver.csiro.au/fhir
Examples¶
The links below are example requests to the terminology server API. Click on a link to open a new tab showing the API request URL and the API response in JSON format.
- Lookup ICD-10 code H35.6
- Lookup OPCS code X352
- Lookup HPO code HP:0000488
- Find ICD-10 codes where the description matches "epilepsy" (first 10 results))
- Find all SNOMED CT concepts subsumed by General Anaesthesia Procedure (expansion of an implicit value set)
Documentation¶
Code systems¶
(Note: the URLs in this table are used as identifiers in FHIR and don't always resolve to an actual web page)
| Name | URL | Version |
|---|---|---|
| Evidence and Conclusion Ontology | http://purl.obolibrary.org/obo/eco.owl | http://purl.obolibrary.org/obo/eco/releases/2019-05-14/eco.owl |
| Foundational Model of Anatomy | http://purl.org/sig/ont/fma.owl | http://purl.org/sig/ont/fma_4.12.0.owl |
| GEL Recruited Cancer Disease Sub Types | http://genomicsengland.co.uk/recruited-cancer-disease-sub-types | 28/02/2019 |
| GEL Recruited Cancer Disease Types | http://genomicsengland.co.uk/recruited-cancer-disease-types | 28/02/2019 |
| GEL Recruited Disorders List | http://genomicsengland.co.uk/recruited-disorders | |
| GeneticCoordinateSystem | http://hl7.org/fhir/uv/genomics-reporting/CodeSystem/genetic-coordinate-system | 0.3.0 |
| Genotype Ontology | http://purl.obolibrary.org/obo/geno.owl | 20190628 |
| HGNCGeneGroups | http://www.genenames.org/genegroup | 13/11/2020 |
| HGNCGeneIDs | http://www.genenames.org/geneId | 13/11/2020 |
| HUGO Gene Nomenclature | http://www.genenames.org | 20100712 |
| Human Ancestry Ontology | http://purl.obolibrary.org/obo/hancestro/hancestro.owl | http://purl.obolibrary.org/obo/hancestro/releases/2018-11-23/hancestro.owl |
| Human Developmental Stages | http://purl.obolibrary.org/obo/hsapdv.owl | http://purl.obolibrary.org/obo/hsapdv/releases/2018-05-20/hsapdv.owl |
| Human Disease Ontology | http://purl.obolibrary.org/obo/doid.owl | http://purl.obolibrary.org/obo/doid/releases/2019-05-13/doid.owl |
| Human Phenotype Ontology | http://purl.obolibrary.org/obo/hp.owl | 20191108 |
| ICD-10 | http://hl7.org/fhir/sid/icd-10 | 2016 |
| ICD-O-3-MORPH | http://hl7.org/fhir/sid/icd-o-3-morph | 20190819 |
| ICD-O-3-TOPO | http://hl7.org/fhir/sid/icd-o-3-topo | 20190819 |
| LOINC v2.63 | http://loinc.org | 2.63 |
| LOINC v2.64 | http://loinc.org | 2.64 |
| MONDO: Monarch Disease Ontology | http://purl.obolibrary.org/obo/mondo.owl | http://purl.obolibrary.org/obo/mondo/releases/2019-04-29/mondo.owl |
| NCI Thesaurus OBO Edition | http://purl.obolibrary.org/obo/ncit.owl | http://purl.obolibrary.org/obo/ncit/releases/2019-09-09/ncit.owl |
| OPCS Classification of Interventions and Procedures | http://digital.nhs.uk/opcs | 4.8 |
| Online Mendelian Inheritance in Man | http://www.omim.org | 07/08/2018 |
| Orphanet Rare Disease Ontology | http://www.orpha.net/ontology/orphanet.owl | 2.7 |
| Phenotypic Quality Ontology | http://purl.obolibrary.org/obo/pato.owl | http://purl.obolibrary.org/obo/pato/releases/2018-11-12/pato.owl |
| SNOMED CT United Kingdom composition module | http://snomed.info/sct | http://snomed.info/sct/83821000000107/version/20190601 |
| SNOMED Clinical Terms Australian extension | http://snomed.info/sct | http://snomed.info/sct/32506021000036107/version/20190531 |
| Sequence Ontology | http://purl.obolibrary.org/obo/so/so-simple.owl | http://purl.obolibrary.org/obo/so/so-xp.owl/so-simple.owl |
| SequencingTechnique | http://csiro.au/CodeSystem/sequencing-technique | 0.1.0 |
| Uber-anatomy ontology | http://purl.obolibrary.org/obo/uberon.owl | http://purl.obolibrary.org/obo/uberon/releases/2018-11-25/uberon.owl |
| v3.RoleCode | http://terminology.hl7.org/CodeSystem/v3-RoleCode | 12/08/2018 |