{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T02:41:21Z","timestamp":1792204881365,"version":"4.4.0"},"reference-count":18,"publisher":"Oxford University Press (OUP)","issue":"5","license":[{"start":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T00:00:00Z","timestamp":1792195200000},"content-version":"vor","delay-in-days":38,"URL":"https:\/\/creativecommons.org\/licenses\/by\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000030","name":"Centers for Disease Control and Prevention","doi-asserted-by":"publisher","award":["R01-TS000341"],"award-info":[{"award-number":["R01-TS000341"]}],"id":[{"id":"10.13039\/100000030","id-type":"DOI","asserted-by":"publisher"}]}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2026,9,9]]},"abstract":"<jats:title>Abstract<\/jats:title>\n                  <jats:sec>\n                    <jats:title>Objectives<\/jats:title>\n                    <jats:p>Patient-directed SMART on FHIR lets registries acquire longitudinal electronic health record data, but the payload requires substantial engineering before use. We present Registry Forge, an open-source pipeline that converts it into curation-ready outputs.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Materials and methods<\/jats:title>\n                    <jats:p>Registry Forge parses C-CDA, HTML, RTF, PDF, and FHIR inputs, joins records to a canonical identifier, and emits a browser dashboard, an OMOP CDM v5.4 data set, GA4GH Phenopackets v2, a code inventory, and disease-specific narrative extractions.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Results<\/jats:title>\n                    <jats:p>Applied to the ALS Research Collaborative Study (94 participants, 56 US health systems), it processed 22\u00a0686 files and 1791 FHIR Bundles (109\u00a0599 resources); only 15.0% of files were full C-CDA XML; HTML (48.4%) and RTF (34.3%) predominated.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Discussion<\/jats:title>\n                    <jats:p>Payloads are far more heterogeneous than often assumed; the architecture is designed for extension, though generalizability remains to be demonstrated.<\/jats:p>\n                  <\/jats:sec>\n                  <jats:sec>\n                    <jats:title>Conclusion<\/jats:title>\n                    <jats:p>Registry Forge closes the gap between acquisition and curation-ready data with no server infrastructure and is openly available.<\/jats:p>\n                  <\/jats:sec>","DOI":"10.1093\/jamiaopen\/ooag200","type":"journal-article","created":{"date-parts":[[2026,9,30]],"date-time":"2026-09-30T11:58:10Z","timestamp":1790769490000},"source":"Crossref","is-referenced-by-count":0,"title":["Registry Forge: an open-source end-to-end pipeline for patient-directed SMART on FHIR registries"],"prefix":"10.1093","volume":"9","author":[{"ORCID":"https:\/\/orcid.org\/0000-0002-5206-7552","authenticated-orcid":false,"given":"Danielle","family":"Boyce","sequence":"first","affiliation":[{"name":"ALS Therapy Development Institute , Watertown, MA 02472,","place":["United States"]},{"name":"Biomedical Informatics and Data Science Section, Johns Hopkins University , Baltimore, MD 21205,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Alan","family":"Premasiri","sequence":"additional","affiliation":[{"name":"ALS Therapy Development Institute , Watertown, MA 02472,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Shawn","family":"Sullivan","sequence":"additional","affiliation":[{"name":"ALS Therapy Development Institute , Watertown, MA 02472,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Beth","family":"Levine","sequence":"additional","affiliation":[{"name":"ALS Therapy Development Institute , Watertown, MA 02472,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]},{"given":"Fernando G","family":"Vieira","sequence":"additional","affiliation":[{"name":"ALS Therapy Development Institute , Watertown, MA 02472,","place":["United States"]}],"role":[{"vocabulary":"crossref","role":"author"}]}],"member":"286","published-online":{"date-parts":[[2026,10,16]]},"reference":[{"key":"2026101622030734000_ooag200-B1","doi-asserted-by":"publisher","first-page":"899","DOI":"10.1093\/jamia\/ocv189","article-title":"SMART on FHIR: a standards-based, interoperable apps platform for electronic health records","volume":"23","author":"Mandel","year":"2016","journal-title":"J Am Med Inform Assoc."},{"key":"2026101622030734000_ooag200-B2","first-page":"326","article-title":"HL7 FHIR: an agile and RESTful approach to healthcare information exchange","author":"Bender","year":"2013","journal-title":"Proc IEEE Int Symp Comput Based Med Syst"},{"key":"2026101622030734000_ooag200-B3","first-page":"25642","article-title":"Office of the national coordinator for health information technology. 21st century cures act: interoperability, information blocking, and the ONC health IT certification program","volume":"85","year":"2020","journal-title":"Fed Regist"},{"key":"2026101622030734000_ooag200-B4","author":"HL7 International. SMART App Launch Implementation Guide. HL7 FHIR","year":"2026"},{"key":"2026101622030734000_ooag200-B5","doi-asserted-by":"publisher","first-page":"1060","DOI":"10.1136\/amiajnl-2014-002883","article-title":"Are meaningful use stage 2 certified EHRs ready for interoperability? Findings from the SMART C-CDA collaborative","volume":"21","author":"D\u2019Amore","year":"2014","journal-title":"J Am Med Inform Assoc."},{"key":"2026101622030734000_ooag200-B6","doi-asserted-by":"publisher","first-page":"103310","DOI":"10.1016\/j.jbi.2019.103310","article-title":"Developing a FHIR-based EHR phenotyping framework: a case study for identification of patients with obesity and multiple comorbidities","volume":"99","author":"Hong","year":"2019","journal-title":"J Biomed Inform."},{"key":"2026101622030734000_ooag200-B7","author":"HL7 International. US Core Implementation Guide: Document Reference Profile","year":"2026"},{"key":"2026101622030734000_ooag200-B8","author":"Observational Health Data Sciences and Informatics","year":"2026"},{"key":"2026101622030734000_ooag200-B9","doi-asserted-by":"publisher","first-page":"553","DOI":"10.1093\/jamia\/ocu023","article-title":"Feasibility and utility of applications of the common data model to multiple, disparate observational health databases","volume":"22","author":"Voss","year":"2015","journal-title":"J Am Med Inform Assoc."},{"key":"2026101622030734000_ooag200-B10","doi-asserted-by":"publisher","first-page":"817","DOI":"10.1038\/s41587-022-01357-4","article-title":"The GA4GH phenopacket schema defines a computable representation of clinical data","volume":"40","author":"Jacobsen","year":"2022","journal-title":"Nat Biotechnol"},{"key":"2026101622030734000_ooag200-B11","doi-asserted-by":"publisher","first-page":"507","DOI":"10.1136\/jamia.2009.001560","article-title":"Mayo clinical text analysis and knowledge extraction system (cTAKES): architecture, component evaluation and applications","volume":"17","author":"Savova","year":"2010","journal-title":"J Am Med Inform Assoc."},{"key":"2026101622030734000_ooag200-B12","first-page":"438","article-title":"Launching into clinical space with medspaCy: a new clinical text processing toolkit in python","volume":"2021","author":"Eyre","year":"2021","journal-title":"AMIA Annu Symp Proc."},{"key":"2026101622030734000_ooag200-B13","doi-asserted-by":"publisher","DOI":"10.21203\/rs.3.rs-8272744\/v1","article-title":"The ALS research collaborative: a long-running multimodal ALS natural history resource","author":"Boyce","year":"2025","journal-title":"Res Sq"},{"key":"2026101622030734000_ooag200-B14","doi-asserted-by":"publisher","first-page":"e81254","DOI":"10.2196\/81254","article-title":"Harmonizing logical observation identifiers names and codes (LOINC) codes and units in real-world oncology data: method development and evaluation","volume":"14","author":"Naliyatthaliyazchayil","year":"2026","journal-title":"JMIR Med Inform."},{"key":"2026101622030734000_ooag200-B15","first-page":"574","article-title":"Observational health data sciences and informatics (OHDSI): opportunities for observational researchers","volume":"216","author":"Hripcsak","year":"2015","journal-title":"Stud Health Technol Inform."},{"key":"2026101622030734000_ooag200-B16","doi-asserted-by":"publisher","first-page":"e22219","DOI":"10.2196\/22219","article-title":"What every reader should know about studies using electronic health record data but may be afraid to ask","volume":"23","author":"Kohane","year":"2021","journal-title":"J Med Internet Res"},{"key":"2026101622030734000_ooag200-B17","doi-asserted-by":"publisher","first-page":"1244","DOI":"10.13063\/2327-9214.1244","article-title":"A harmonized data quality assessment terminology and framework for the secondary use of electronic health record data","volume":"4","author":"Kahn","year":"2016","journal-title":"EGEMS (Wash DC)"},{"key":"2026101622030734000_ooag200-B18","doi-asserted-by":"publisher","first-page":"2251","DOI":"10.1093\/jamia\/ocab132","article-title":"Increasing trust in real-world evidence through evaluation of observational data quality","volume":"28","author":"Blacketer","year":"2021","journal-title":"J Am Med Inform Assoc."}],"container-title":["JAMIA Open"],"original-title":[],"language":"en","link":[{"URL":"https:\/\/academic.oup.com\/jamiaopen\/article-pdf\/9\/5\/ooag200\/72054793\/ooag200.pdf","content-type":"application\/pdf","content-version":"vor","intended-application":"syndication"},{"URL":"https:\/\/academic.oup.com\/jamiaopen\/article-pdf\/9\/5\/ooag200\/72054793\/ooag200.pdf","content-type":"unspecified","content-version":"vor","intended-application":"similarity-checking"}],"deposited":{"date-parts":[[2026,10,17]],"date-time":"2026-10-17T02:03:13Z","timestamp":1792202593000},"score":1,"resource":{"primary":{"URL":"https:\/\/academic.oup.com\/jamiaopen\/article\/doi\/10.1093\/jamiaopen\/ooag200\/8932407"}},"subtitle":[],"short-title":[],"issued":{"date-parts":[[2026,9,9]]},"references-count":18,"journal-issue":{"issue":"5","published-print":{"date-parts":[[2026,9,9]]}},"URL":"https:\/\/doi.org\/10.1093\/jamiaopen\/ooag200","relation":{},"ISSN":["2574-2531"],"issn-type":[{"value":"2574-2531","type":"electronic"}],"subject":[],"published-other":{"date-parts":[[2026,10]]},"published":{"date-parts":[[2026,9,9]]},"article-number":"ooag200"}}