FHIR Type System - BD2KOnFHIR/uima-on-fhir GitHub Wiki

UIMA reserved feature name

• type
• address
• class
• view

UIMA CAS types

UIMA type	FHIR type	Note
uima.cas.String	org.hl7.fhir.String	FHIRString
uima.cas.Boolean	org.hl7.fhir.Boolean	FHIRBoolean
uima.cas.Integer	org.hl7.fhir.Integer	FHIRInteger
uima.cas.FSArray
uima.cas.TOP

Useful Links

FHIR

• FHIR: https://www.hl7.org/fhir/index.html
• FHIR W5: https://www.hl7.org/fhir/w5.html
• org.eclipse.mdht.git: http://git.eclipse.org/c/mdht/org.eclipse.mdht.git
• Clone
• git://git.eclipse.org/gitroot/mdht/org.eclipse.mdht.git
• ssh://git.eclipse.org/gitroot/mdht/org.eclipse.mdht.git
• http://git.eclipse.org/gitroot/mdht/org.eclipse.mdht.git

UIMA

• https://uima.apache.org/index.html
• UIMA Type System Descriptor: https://uima.apache.org/d/uimaj-2.8.1/references.html#ugr.ref.xml.component_descriptor.type_system
• UIMA Tools Guide and Reference https://uima.apache.org/d/uimaj-2.8.1/tools.html#
• UIMA Overview & SDK Setup: http://uima.apache.org/d/uimaj-2.7.0/overview_and_setup.html#
• UIMA Tutorial and Developers' Guides: http://uima.apache.org/downloads/releaseDocs/2.2.2-incubating/docs/html/tutorials_and_users_guides/tutorials_and_users_guides.html#
• Getting Started: Writing My First UIMA Annotator: http://uima.apache.org/doc-uima-annotator.html
• UIMA RDF https://uima.apache.org/downloads/sandbox/RDF_CC/RDFCASConsumerUserGuide.html

CTAKES v4.0

• https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+4.0
• https://cwiki.apache.org/confluence/display/CTAKES/cTAKES+3.2+Developer+Install+Guide
• https://healthnlp.hms.harvard.edu/deepphe/wiki/index.php/Main_Page
• https://ctakes.apache.org/downloads.cgi
• http://healthnlp.github.io/examples/

TAC 2017

• TAC 2017: Adverse Drug Reaction Extraction from Drug Labels: https://bionlp.nlm.nih.gov/tac2017adversereactions/