Table 1

Adaptations made to existing DDSS to create GPACSS

Adaptation	Component	Approach
Overall design	SMART-on-FHIR enabled EHR	Logica platform (https://www.logicahalth.org/; formerly Health Services Platform Consortium)
Overall design	Archive	Custom archive stores key files RESTful interface.
Coordination and communication	User interface	SMART-on-FHIR application (GPACSS FHIR app client, figure 2). Interface allows user access to DDSS directly from patient record. Choice to launch with no findings or with findings previously saved.
Coordination and communication	Coordination	GPACSS ‘Coordinator’ application programming interface (API) saves the NLP output Matching of UMLS codes in NLP output to DDSS findings Send the matched flagged findings to the DDSS at launch (figure 2)
Natural language processing	Extraction of findings	NLP: open source Apache cTAKES V.4.0.23 cTAKES default modules to handle sentence boundary detection, tokenisation, normalisation, tagging parts of speech, recognising named entities and negation. cTAKES pretrained module to recognise UMLS concepts in text.
	Mapping in DDSS	DDSS findings mapped within the DDSS to one or more UMLS and Human Phenotype Ontology codes. Mapping strategy minimises false negatives in term capture while tolerating false positives (identifying information unrelated or irrelevant to the diagnostic process).
	Display in DDSS	Findings identified by NLP display a flag icon. Clicking the flag enables viewing of metadata.

DDSS, diagnostic decision support system; EHR, electronic health record; GPACSS, Genotype-Phenotype Archiving and Communication System with SimulConsult; UMLS, Unified Medical Language System.