Introduction | Installation | Authentication | Creating a Client | Getting Concepts | Batch Operations | Searching Concepts | Semantic Search | Similarity Search | Bulk Search | Bulk Lexical Search | Bulk Semantic Search | Autocomplete | Pagination | Manual Pagination | Automatic Pagination | Hierarchy Navigation | Concept Mappings | Error Handling | FHIR-to-OMOP Resolution | Single Coding | Non-Standard Code (Automatic Maps-to Traversal) | Batch Resolution | CodeableConcept with Vocabulary Preference | Tibble Output for Batch Resolution | Standalone Wrapper Functions | FHIR Client Interop with omophub_fhir_url() | Further Resources
Package: omophub 1.8.1
Alex Chen
omophub: R Client for the 'OMOPHub' Medical Vocabulary API
Provides an R interface to the 'OMOPHub' API for accessing 'OHDSI ATHENA' standardized medical vocabularies. Supports concept search, semantic search using neural embeddings, concept similarity, vocabulary exploration, hierarchy navigation, relationship queries, concept mappings, and FHIR-to-OMOP concept resolution with automatic pagination.
Authors:
omophub_1.8.1.tar.gz
omophub_1.8.1.zip(r-4.7)omophub_1.8.1.zip(r-4.6)omophub_1.8.1.zip(r-4.5)
omophub_1.8.1.tgz(r-4.6-any)omophub_1.8.1.tgz(r-4.5-any)
omophub_1.8.1.tar.gz(r-4.7-any)omophub_1.8.1.tar.gz(r-4.6-any)
omophub_1.8.1.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
omophub/json (API)
| # Install 'omophub' in R: |
| install.packages('omophub', repos = c('https://omophub.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/omophub/omophub-r/issues
Pkgdown/docs site:https://omophub.github.io
api-clientathenabioinformaticscdmclinical-informaticsclinical-researchfhirfhir-terminologyhealthcare-dataicd10medical-terminologymedical-vocabulariesohdsiohdsi-vocabularyomopreal-world-evidencesnomed
Last updated from:47d10cd352. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 160 | ||
| source / vignettes | OK | 195 | ||
| linux-release-x86_64 | OK | 127 | ||
| macos-release-arm64 | OK | 150 | ||
| macos-oldrel-arm64 | OK | 242 | ||
| windows-devel | OK | 101 | ||
| windows-release | OK | 102 | ||
| windows-oldrel | OK | 97 | ||
| wasm-release | OK | 145 |
Exports:fhir_resolvefhir_resolve_batchfhir_resolve_codeable_conceptget_api_keyhas_api_keyomophub_fhir_urlOMOPHubClientset_api_key
Dependencies:askpassbackportscheckmateclicurlgluehttr2lifecyclemagrittropensslpillarpkgconfigpurrrR6rappdirsrlangsystibbleutf8vctrswithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Resolve a FHIR Coding to an OMOP standard concept | fhir_resolve |
| Batch-resolve FHIR Codings | fhir_resolve_batch |
| Resolve a FHIR CodeableConcept with vocabulary preference | fhir_resolve_codeable_concept |
| Get OMOPHub API Key | get_api_key |
| Check if API Key is Available | has_api_key |
| OMOPHub FHIR Terminology Service URL | omophub_fhir_url |
| OMOPHub API Client | OMOPHubClient |
| Set OMOPHub API Key | set_api_key |
