Introduction to pyrophen

What is FHIR?

The standards development organization Health Level Seven (HL7) is a non-profit ANSI-accredited standards development organization dedicated to providing standards and solutions for global health data interoperability.

HL7 develops Fast Healthcare Interoperability Resource (FHIR) is a a standard describing data formats and elements (known as “resources”) and an application programming interface (API) for exchanging electronic health records (EHR) (Wikipedia entry). The NIH is supporting FHIR for research user.

It is here that we see the major current use case for the HPO FHIR Codeset.

FHIR provides a set of modular components called “Resources” that can easily be assembled into working systems that solve real world clinical and administrative problems. FHIR enables access to data distributed across systems, databases, and devices in real time, similar to the World-Wide Web.

What is a FHIR Code system?

A FHIR code system declares the existence of and describes a code system or code system supplement and its key properties, and optionally defines a part or all of its content. Also known as Ontology, Terminology, or Enumeration

What is a FHIR Value set?

A FHIR value set specifies a set of codes drawn from one or more code systems, intended for use in a particular context. Value sets link between CodeSystem definitions and their use in coded elements.

What is the Human Phenotype Ontology (HPO)

The Human Phenotype Ontology (HPO, HPO) was launched in 2008 to provide a comprehensive logical standard to describe and computationally analyze phenotypic abnormalities found in human disease. The HPO is now a worldwide standard for phenotype exchange and is used by many software tools for computational phenotype analysis. The HPO provides a standardized vocabulary of phenotypic abnormalities encountered in human disease. Each term in the HPO describes a phenotypic abnormality, such as Atrial septal defect. The HPO is currently being developed using the medical literature, Orphanet, DECIPHER, and OMIM. HPO currently contains over 15,000 terms and over 200,000 annotations to hereditary diseases.

What is the purpose of this codeset?

The codeset that is generated by pyrophen provides a specified set of HPO codes for use in FHIR coded elements.