MIABIS on FHIR Implementation Guide
1.0.0 - CI Build

MIABIS on FHIR Implementation Guide - Local Development build (v1.0.0) built by the FHIR (HL7® FHIR® Standard) Build Tools. See the Directory of published versions

Artifacts Summary

This page provides a list of the FHIR artifacts defined as part of this implementation guide.

Behavior: Search Parameters

These define the properties by which a RESTful server can be searched. They can also be used for sorting and including related resources.

Search Group by extension containing members

Search parameter for searching Group by provided members via extension

Search by Sample Collection ID

Allows searching for specimens by the sample collection ID stored in the miabis-sample-collection-extension.

Structures: Resource Profiles

These define constraints on FHIR resources for systems conforming to this implementation guide.

Biobank

This profile represents a Biobank, which is defined as an entity that stores samples and data related to the samples.

Collection

Collection represents a set of samples and/or data items collected and/or derived in a common context and stored under a common stewardship and available for future research

Collection Organization

Collection Organization represent a formal part of a organization, like ist name, contact information, publications, etc.

Condition

This profile is used to represent only the diagnosis of the patient. It is not used to represent diagnosis linked to the sample. For the diagnosis linked to the sample, use the observation resource.

Network

This resource represents a group of interconnected biobanks, collections, and/or research resources

Network Organization

Network Organization represent a formal part of a Network, like ist name, contact information, url, etc.

Observation

Observation containing an ICD-10/9 code of a diagnosis linked to a specific Sample

Sample

Sample is a portion or quantity of biological material that is collected from a sample donor, or a digital representation of a biological entity of the sample donor, such as an image.

Sample Donor

Sample donor is a person who is a source of either a biological material or a digital representation of a biological entity such as an image.

Structures: Extension Definitions

These define constraints on FHIR data types for systems conforming to this implementation guide.

Bioprocessing and Analytical Capabilities Extension

Bio processing and analytical services that the biobank can offer to the clients.

Collection Dataset Type Extension

Types of datasets (groups of related data) obtained or otherwise derived from donors or their specimens.

Collection Design Extension

The overall design of the collection that explains how the collection was/is built up.

Common Collaboration Topics Extension

Topics that the network partners collaborate on.

Dataset Extension

The data categories from which data are available or can be linked to the sample donor

Description extension

Description of the collection in English.

Inclusion Criteria Extension

Information on type of parameters that determine which subjects will become collection participants.

Infrastructural Capabilities Extension

The technical infrastructural capabilities that the biobank can offer to the clients.

Number Of Subjects

Total number of subjects included in the collection.

Organisational Capabilities Extension

The organisational capabilities and services that the biobank can provide to support clients.

Publications Extension

Key publications produced using the Sample Collection.

Quality Management Standard Extension

The standards that the biobank is certified or accredited for.

Sample Collection

Allows linking a Sample to a Sample Collection using an identifier instead of a direct FHIR reference.

Sample Collection Setting Extension

The context in which the Sample Collection was/is conducted.

Sample Source Extension

The source from which the samples were collected or isolated.

Sample content diagnosis

The ICD-10 code describing the diagnosis of the Sample content, such as whether the Sample contains carcinogenic material

Sample storage temperature

The long-term temperature at which the sample is stored after preparation, based on SPREC v3

Use and Access Conditions Extension

The conditions that may change the availability of the samples/data in the collection.

Terminology: Value Sets

These define sets of codes used by systems conforming to this implementation guide.

Bio processing and Analytical Capabilities Value Set

Value set containing codes representing bio processing and analytical services that the biobank can offer to the clients.

Collection Design Value Set

Value set containing codes representing the overall design of the collection that explains how the collection was/is built up.

Collection Sample Type Value Set

Value set containing codes for the collection sample types of the provided samples

Common Collaboration Topics Value Set

Value set containing codes representing common collaboration topics of members of a network.

DetailedSampleTypeVS

This value set contains codes for the detailed sample type of the sample.

DiagnosisVS

Value set containig ICD-10 codes for diagnosis

Inclusion Criteria ValueSet

Value set containing codes describing information on type of parameters that determine which subjects will become collection participants.

Infrastructural Capabilities ValueSet

Value set containing codes representing the technical infrastructural capabilities that the biobank can offer to the clients.

MIABIS Collection Dataset Type

Value set containing codes describing the type of dataset that is part of a collection.

Material Type Value Set

Value set containing codes for the material type of the sample.

Organisational Capabilities Value Set

Value set containing codes representing the organisational capabilities and services that the biobank can provide to support clients

Sample Collection Setting Value Set

Value set containing codes for the context in which the sample collection was conducted.

Sample Source Value Set

Value set containing the possible sources of a sample.

Sex Value Set

Biological sex of the sample donor. Can be one or more of the provided values:

Storage Temperature Value Set

Value set containing codes for different storage temperatures.

Use and Access Conditions Value Set

Value set containing codes describing the conditions that may change the availability of the samples/data in the collection.

characteristicVS

Value set containing codes for specifying which characteristic is being described.

dataset type Value Set

The data categories from which data are available or can be linked to the sample donor. Can be one or more of the provided values

Terminology: Code Systems

These define new code systems used by systems conforming to this implementation guide.

Bioprocessing and Analytical Capabilities Code System

Code system representing the bio processing and analytical services that the biobank can offer to the clients.

Common Collaboration Topics Code System

Codes describing topics that the network partners collaborate on

DetailedSampleType

Code system for the detailed sample type of a sample

Inclusion Criteria

Code system describing information on type of parameters that determine which subjects will become collection participant

Infrastructural Capabilities Code System

Code system representing the technical infrastructural capabilities that the biobank can offer to the clients.

MIABIS Characteristics code system

Codes for specifying which characteristic is being described.

MIABIS Code system for the source of the sample

This Code system defines codes for the source of the sample

MIABIS Collection Dataset Type

Codes describing the type of dataset that is part of a collection.

MIABIS Collection Design code System

Codes describing the overall design of the collection that explains how the collection was/is built up.

MIABIS Collection Sample Type Code System

Codes for the collection sample types of the provided samples

MIABIS ContactType code system

Contact Type of the managing person of collection or dataset

MIABIS Dataset Type Code System

Codes for the type of dataset in used in Sample Donor resource

MIABIS Material Type Code System

Codes for the material type of a sample

MIABIS Sample Collection Setting Code System

Code set for the context in which the sample collection was conducted.

MIABIS Sex Code System

Codes for providing information about sex of the patient

MIABIS Storage Temperature Code System

Code System used to describe the storage temperature of a sample

MIABIS Use and Access Conditions Code System

Code system representing the conditions that may change the availability of the samples/data in the collection.

Organisational Capabilities

This code system represents the organisational capabilities and services that the biobank can provide to support clients.

Example: Example Instances

These are example instances that show what data produced and consumed by systems conforming with this implementation guide might look like.

BiobankInstance

Example instance of a Biobank

CollectionInstance

Example instance of a Collection of Samples

CollectionOrgInstance

Example instance of a Collection Organization

Condition Instance

Example instance of a Condition

Example Donor

Example instance of a Donor

Example observation

Example instance of an Observation

NetworkInstance

Example instance of a Network

NetworkOrgInstance

Example instance of a Network as an Organization

SampleInstance

Example instance of a Sample