Publication¶
Registry Forge: an open-source end-to-end pipeline for patient-directed SMART on FHIR registries¶
Danielle Boyce, MPH, DPA1,2; Alan Premasiri1; Shawn Sullivan1; Beth Levine1; Fernando G. Vieira, MD1
1 ALS Therapy Development Institute, 480 Arsenal Street, Suite 201, Watertown, MA 02472, USA 2 Johns Hopkins University, Biomedical Informatics and Data Science Section, Baltimore, MD 21205, USA
JAMIA Open, volume 9, issue 5, 2026, article ooag200. doi:10.1093/jamiaopen/ooag200. Open access under the Creative Commons Attribution License (CC BY 4.0).
Read the article in JAMIA Open
Cite this article
Boyce D, Premasiri A, Sullivan S, Levine B, Vieira FG. Registry Forge: an open-source end-to-end pipeline for patient-directed SMART on FHIR registries. JAMIA Open. 2026;9(5):ooag200. doi:10.1093/jamiaopen/ooag200
| Journal | JAMIA Open |
| Citation | 2026;9(5):ooag200 |
| DOI | 10.1093/jamiaopen/ooag200 |
| Software release archive DOI | 10.71944/2P5C-NG50 |
| License | MIT (software); CC BY 4.0 (article) |
| Keywords | Patient Registries; SMART on FHIR; HL7; Electronic Health Records; Amyotrophic Lateral Sclerosis |
What the article reports¶
The article describes an open-source pipeline that turns the raw files a registry receives through patient-directed SMART on FHIR retrieval into outputs researchers can review. It parses C-CDA, HTML, RTF, PDF and FHIR files, links them to one participant identifier, and produces a browser dashboard, an OMOP CDM v5.4 data set, Phenopackets, a code inventory and disease-specific note extractions. Run in the ARC Study, it showed that only a small share of the documents participants contributed (about 15%) were full C-CDA XML; most of the rest were HTML and RTF.
Try it¶
The live demos run the pipeline over an invented ALS cohort, and the architecture page shows how the stages and modules fit together. Everything needed to run it is on the Downloads page.