From 9f234ab08edf6804d15edd2e4de92f9ac6c90d3a Mon Sep 17 00:00:00 2001 From: dermatologist Date: Mon, 28 Oct 2024 13:47:06 -0500 Subject: [PATCH] Update README.md with additional features and examples --- README.md | 19 +++++++++++++++---- 1 file changed, 15 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index 5152fa1..cd187e9 100644 --- a/README.md +++ b/README.md @@ -8,7 +8,13 @@ Virtual flattened view of *FHIR Bundle / ndjson / FHIR server / BigQuery!* :fire: **FHIRy** is a [python](https://www.python.org/) package to facilitate health data analytics and machine learning by converting a folder of [FHIR bundles](https://www.hl7.org/fhir/bundle.html)/ndjson from [bulk data export](https://hl7.org/fhir/uv/bulkdata/export/index.html) into a [pandas](https://pandas.pydata.org/docs/user_guide/index.html) data frame for analysis. You can import the dataframe into ML packages such as Tensorflow and PyTorch. **FHIRy also supports FHIR server search and FHIR tables on BigQuery.** -## UPDATE + +Test this with the [synthea sample](https://synthea.mitre.org/downloads) or the downloaded ndjson from the [SMART Bulk data server](https://bulk-data.smarthealthit.org/). Use the 'Discussions' tab above for feature requests. + +:sparkles: Checkout [this template](https://github.com/dermatologist/kedro-multimodal) for Multimodal machine learning in healthcare! + + +## UPDATE 1 Recently added support for **LLM based natural language queries** of FHIR bundles/ndjson using [llama-index](examples/llm_example.py). Please install the llm extras as follows. Please be cognizant of the privacy issues with publically hosted LLMs. Any feedback will be highly appreciated. [See usage](examples/llm_example.py)! ``` @@ -16,10 +22,15 @@ pip install fhiry[llm] ``` [See usage](examples/llm_example.py). -Test this with the [synthea sample](https://synthea.mitre.org/downloads) or the downloaded ndjson from the [SMART Bulk data server](https://bulk-data.smarthealthit.org/). Use the 'Discussions' tab above for feature requests. - -:sparkles: Checkout [this template](https://github.com/dermatologist/kedro-multimodal) for Multimodal machine learning in healthcare! +## UPDATE 2 +Added support for converting a FHIR Bundle to its textual representation for LLMs. You can also convert individual FHIR resources including *Patient, Condition, Observation, Procedure, Medication, AllergyIntolerance and DocumentReference*. +``` +from fhiry import FlattenFhir +bundle = json.load(jsonfile) +flatten_fhir = FlattenFhir(bundle) +print(flatten_fhir.flattened) +``` ## Installation