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