BBMRI.de/GBA Implementation Guide
1.2.0 - CI Build
BBMRI.de/GBA Implementation Guide
1.2.0 - CI Build
BBMRI.de/GBA Implementation Guide - Local Development build (v1.2.0). See the Directory of published versions
This section describes how the profiles defined in this guide relate to several other data models, mainly from other biobank-related projects. Partial paths in italic imply slice names.
The BBMRI-ERIC Directory can be found here.
The BBMRI-ERIC Directory Biobank entity corresponds to the Biobank profile from this guide.
| BBMRI-ERIC | Biobank Profile |
|---|---|
| id | identifier:Bbmri-EricId.value |
| name | name |
| acronym | alias |
| description | extension:description.value |
| bioresource_reference | extension:bioresourceReference.value |
| url | telecom:url.value |
| juridical_person | extension:juridicalPerson.value |
| country | address.country |
| it_support_available | extension:itSupport.extension:itSupportAvailable.value |
| it_staff_size | extension:itSupport.extension:itStaffSize.value |
| is_available | extension:itSupport.extension:isAvailable.value |
| his_available | extension:itSupport.extension:hisAvailable.value |
| partner_charter_signed | extension:partnerCharterSigned.value |
| head_title_before_name | contact:head.name.prefix |
| head_firstname | contact:head.name.given |
| head_lastname | contact:head.name.family |
| head_title_after_name | contact:head.name.suffix |
| head_role | contact:head.extension:role.value |
| contact | see section contact |
| latitude | address.extension:geolocation.extension:latitude |
| longitude | address.extension:geolocation.extension:longitude |
| network | see section network |
| collaboration_commercial | extension:collaboration.extension:commercial.value |
| collaboration_non_for_profit | extension:collaboration.extension:nonForProfit.value |
| capabilities | extension:capabilities.value |
| quality | extension:qualityStandards.value |
In FHIR, the contact information is included in the Organization resource, which is profiled as Biobank in this guide.
| BBMRI-ERIC | Biobank.contact |
|---|---|
| title_before_name | prefix |
| first_name | given |
| last_name | family |
| title_after_name | suffix |
| phone | contact:contact.telecom:phone.value |
| contact:contact.telecom:email.value | |
| address | contact:contact.address.line |
| zip | contact:contact.address.postalCode |
| city | contact:contact.address.city |
| country | contact:contact.address.country |
The BBMRI-ERIC Directory Collection entity corresponds to the Collection profile from this guide. Like Biobank, it is based on the Organization resource but has different constraints.
| BBMRI-ERIC | Collection |
|---|---|
| id | identifier:Bbmri-EricId.value |
| country | contact:contact.address.country (If not present, biobank country is used) |
| biobank | partOf |
| name | name |
| acronym | alias |
| description | extension.description.value |
| bioresource_reference | extension:bioresourceReference.value |
| parent_collection | via OrganizationAffiliation(TODO) |
| network | see section network |
| type | extension:collectionType.value |
| data_categories | extension:dataCategory.value |
| quality | extension:qualityStandards.value |
| order_of_magnitude | calculated on-the-fly from bridgehead data |
| order_of_magnitude_donors | calculated on-the-fly from bridgehead data |
| size | calculated on-the-fly from bridgehead data |
| number_of_donors | calculated on-the-fly from bridgehead data |
| timestamp | calculated on-the-fly from bridgehead data |
| id_card | extension:idCard.value |
| head_title_before_name | contact:head.name.prefix |
| head_firstname | contact:head.name.given |
| head_lastname | contact:head.name.family |
| head_title_after_name | contact:head.name.suffix |
| head_role | contact:head.extension:role.value |
| contact | see section contact |
| latitude | address.extension:geolocation.extension:latitude |
| longitude | address.extension:geolocation.extension:longitude |
| sex | calculated on-the-fly from bridgehead data |
| diagnosis_available | calculated on-the-fly from bridgehead data |
| age Low | calculated on-the-fly from bridgehead data |
| age High | calculated on-the-fly from bridgehead data |
| age Unit | calculated on-the-fly from bridgehead data |
| body_part_examined | calculated on-the-fly from bridgehead data (once available) |
| imaging_modality | calculated on-the-fly from bridgehead data (once available) |
| image_dataset_type | calculated on-the-fly from bridgehead data (once available) |
| materials | calculated on-the-fly from bridgehead data |
| storage_temperature | calculated on-the-fly from bridgehead data |
| sample_access_fee | extension:accessPolicy.extension:fee.value (when extension:accessPolicy.extension:resource.value = “sample”) |
| sample_access_joint_project | extension:accessPolicy.extension:jointProject.value (when extension:accessPolicy.extension:resource.value = “sample”) |
| sample_access_description | extension:accessPolicy.extension:description.value (when extension:accessPolicy.extension:resource.value = “sample”) |
| sample_access_uri | extension:accessPolicy.extension:uri.value (when extension:accessPolicy.extension:resource.value = “sample”) |
| data_access_fee | extension:accessPolicy.extension:fee.value (when extension:accessPolicy.extension:resource.value = “data”) |
| data_access_joint_project | extension:accessPolicy.extension:jointProject.value (when extension:accessPolicy.extension:resource.value = “data”) |
| data_access_description | extension:accessPolicy.extension:description.value (when extension:accessPolicy.extension:resource.value = “data”) |
| data_access_uri | extension:accessPolicy.extension:uri.value (when extension:accessPolicy.extension:resource.value = “data”) |
| image_access_fee | extension:accessPolicy.extension:fee.value (when extension:accessPolicy.extension:resource.value = “image”) |
| image_access_joint_project | extension:accessPolicy.extension:jointProject.value (when extension:accessPolicy.extension:resource.value = “image”) |
| image_access_description | extension:accessPolicy.extension:description.value (when extension:accessPolicy.extension:resource.value = “image”) |
| image_access_uri | extension:accessPolicy.extension:uri.value (when extension:accessPolicy.extension:resource.value = “image”) |
| collaboration_commercial | extension:collaboration.extension:commercial.value |
| collaboration_non_for_profit | extension:collaboration.extension:nonForProfit.value |
| sample_processing_sop | extension:resourceManagement.extension:processingSop.value (when extension:resourceManagement.extension:resource.value = “sample”) |
| sample_transport_sop | extension:resourceManagement.extension:transportSop.value (when extension:resourceManagement.extension:resource.value = “sample”) |
| sample_storage_sop | extension:resourceManagement.extension:storageSop.value (when extension:resourceManagement.extension:resource.value = “sample”) |
| data_processing_sop | extension:resourceManagement.extension:processingSop.value (when extension:resourceManagement.extension:resource.value = “data”) |
| data_transport_sop | extension:resourceManagement.extension:transportSop.value (when extension:resourceManagement.extension:resource.value = “data”) |
| data_storage_sop | extension:resourceManagement.extension:storageSop.value (when extension:resourceManagement.extension:resource.value = “data”) |
This project does not contain a specific profile for biobank networks. While such networks could be represented as Organization resources, it is outside the scope for this project. To record a biobank’s membership in a network, we use a profiled OrganizationAffiliation: NetworkMembership. There, the reference to the network happens via its BBMRI Directory id since we do not have an actual FHIR resource.
The information for a MIABIS Biobank is found in the Biobank profile.
| MIABIS Attribute Code | Name | FHIR | |
|---|---|---|---|
| MIABIS-2.0-01 | ID | identifier | |
| MIABIS-2.0-02 | Acronym | alias | |
| MIABIS-2.0-03 | Name | Text | name |
| MIABIS-2.0-04 | URL | Text | telecom:url.value |
| MIABIS-2.0-05 | Juristic Person | extension:juridicalPerson.value | |
| MIABIS-2.0-06 | Country | address.country | |
| MIABIS-2.0-07 | Contact Information | See section contact | |
| MIABIS-2.0-08 | Description | extension:description.value |
Corresponds to Collection profile
| MIABIS Attribute Code | Name | FHIR |
|---|---|---|
| MIABIS-2.0-01 | ID | identifier |
| MIABIS-2.0-02 | Acronym | alias |
| MIABIS-2.0-03 | Name | name |
| MIABIS-2.0-08 | Description | extension.description.value |
| MIABIS-2.0-09 | Sex | calculated on-the-fly from bridgehead data |
| MIABIS-2.0-10 | Age Low | calculated on-the-fly from bridgehead data |
| MIABIS-2.0-11 | Age High | calculated on-the-fly from bridgehead data |
| MIABIS-2.0-12 | Age Unit | calculated on-the-fly from bridgehead data |
| MIABIS-2.0-13 | Data categories | extension:dataCategory |
| MIABIS-2.0-14 | Material type | calculated on-the-fly from bridgehead data |
| MIABIS-2.0-15 | Storage temperature | calculated on-the-fly from bridgehead data |
| MIABIS-2.0-16 | Collection type | extension:collectionType.value |
| MIABIS-2.0-17 | Disease | not supported |
| MIABIS-2.0-07 | Contact information | See section contact |
The contact information can be stored in the contact fields of Collection or Biobank which already specify two slices for the head and the research contact with slices on telecom to model phone and mail contact points. We currently do not support the researcher information type.
| Attribute Code | Attribute Name | FHIR |
|---|---|---|
| MIABIS-2.0-07-A | First name | name.given |
| MIABIS-2.0-07-B | Last name | name.family |
| MIABIS-2.0-07-C | Phone | telecom:phone.value |
| MIABIS-2.0-07-D | telecom:email.value | |
| MIABIS-2.0-07-E | Address | address.line |
| MIABIS-2.0-07-F | ZIP | address.postalCode |
| MIABIS-2.0-07-G | City | address.city |
| MIABIS-2.0-07-H | Country | address.country |
Corresponds to the specimen profile.
| Attribute Code | Attribute Name | FHIR |
|---|---|---|
| MIABIS-SAMPLE-01 | Sample ID | no internal IDs supported, identification via resource id |
| MIABIS-SAMPLE-02 | Detailed material type | type (not yet mapped to MIABIS types) |
| MIABIS-SAMPLE-03 | Sample storage temperature | extension:storageTemperature |
| MIABIS-SAMPLE-04 | Sample creation date and time | collection.collectedDateTime |
| MIABIS-SAMPLE-05 | Anatomical site ontology | collection.bodySite.coding.system |
| MIABIS-SAMPLE-06 | Anatomical site ontology version | collection.bodySite.coding.version |
| MIABIS-SAMPLE-07 | Anatomical site ontology code | collection.bodySite.coding.code |
| MIABIS-SAMPLE-08 | Anatomical site ontology description | collection.bodySite.coding.display |
| MIABIS-SAMPLE-09 | Anatomical site free text | collection.bodySite.text |
| MIABIS-10 | Sample content diagnosis | extension:diagnosis |
| MIABIS-11 | Use restrictions | not yet supported |
Corresponds to the Patient profile.
| Attribute Code | Attribute Name | FHIR |
|---|---|---|
| MIABIS-SAMPLEDONOR-01 | Sample donor ID | no internal ids supported, use resource id |
| MIABIS-SAMPLEDONOR-02 | Sex | gender (WARNING: Per FHIR definition this is the Administrative Gender of the patient, which may or may not equal the value for biological sex. Biobanks may report values based on different aspects of sex/gender here, see https://www.hl7.org/fhir/patient.html#gender |
| MIABIS-SAMPLEDONOR-03 | Data categories | calculated on-the-fly from bridgehead data |
| MIABIS-SAMPLEDONOR-04 | Birth year | birthDate |
Not supported
IG © 2020+ bbmri.de. Package de.bbmri.fhir#1.2.0 based on FHIR 4.0.1. Generated 2023-09-01
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