SMART Genomics API

SMART Genomics provide support for using genomic information in the healthcare environment by providing new resource definitions and resource extensions to the existing SMART on FHIR framework. Using SMART Genomics, medical apps can quickly access a patient's genomic information in conjunction with their standard clinical data to provide high quality, personalized care to their patients. The SMART Genomics API is based upon three main resources of Sequence, SequencingLab and GeneticObservation.

For more information on how to use the SMART Genomics API, please read the Developer's guide. For a detailed overview of the API, please review the API Reference.

Resources

Sequence

The Sequence resource is used to store data of patient's amino acid, RNA, or DNA sequences. Sequence resource is designed in an abstract and non-format-specific way such that users don’t have to be worried about various file formats (VCF, GFF, etc) and can focus on the genetics. Data encapsulated by Sequence resource include read of the sequence, genomic position where the sequence is mapped, quantity of the molecule represented by the sequence presenting in the sample, etc.

SequencingLab

Sequencing Labs are container resources that hold results about specific labs used to sequence a patient's genome. Sequencing Labs are extended from the Procedure resource which contains information about general procedures performed on patients. Sequencing Labs contain information about raw files generated from the sequencing facility as well as any associated metadata. Such metadata may include sample type, species information, assembly information, etc. The SequencingLab resource helps link patient Sequences to their original source and may be useful for clinical documentation for keeping track of how each patient's genotypes were determined.

GeneticObservation

Genetic Observations are resources that relay information about a patient's phenotype and its relationship to the patient's genotype. Genetic Observations are extended from the Observation resource which contains information about a patient's diagnostic information as well as social history. Each Genetic Observation is linked with a physical trait and a collection of genotype-phenotype relationships that are associated with that trait. Genetic Observations provide critical information to healthcare professionals about the traits a given patient exhibit based on their genomes. The genotype of a variant can be described either by linking to the relevant Sequence resource that describes it, or by a NCI code.