BBMRI.de/GBA Implementation Guide - Local Development build (v1.2.0). See the Directory of published versions

Overview

This section lists the profiles defined in this IG and briefly highlights important aspects. Fields marked with mustSupport are used by the queries and shall be filled if the information is available. Information from other fields may used in future versions and can be provided optionally.

Biobank

​A Biobank. Designed to contain all information necessary to populate a BBMRI Directory biobank entry, see Mappings page. Note that two contact slices exist, one for the biobank head (which only requires a name and no actual contact information) and one for the actual endpoint researches should contact for inquiries about data and samples (which requires an email address and a county, but does not require a name, although it should be provided where available).

Your biobank needs a Directory identifier, which is structured as follows: bbmri-eric:ID:<CC>_<local id>, where <CC> should be replaced by the valid ISO-3166-1 alpha 2 country code for your country of residence (e.g. “DE” for Germany) and <local id> with a unique local ID generated by the national node. All local parts of the ID should be limited to roman letters and numbers (a-z, A-Z, 0-9).

Collection

​A Collection within a Biobank. Designed to contain all information necessary to populate a BBMRI Directory collection entry, see Mappings page. The contact is structured as described in the Biobank section.

Use this data element to provide more details about the specimen collection/sampling event.

The identifier should be used to provide a unique identifier of the specimens collection/cohort. The structure should be the following bbmri-eric:ID:<CC>_<local id>:collection:<local id>. Where <CC> has to be replaced by the valid ISO-3166-1 alpha 2 country code for the country of residence and <local id> with a local ID generated by the national node to be unique within its context. We advise to use the ID of the entity in the national Directory if one is present. For example https://directory.bbmri.de/menu/main/app-molgenis-app-biobank-explorer#/biobank/bbmri-eric:ID:DE_ACBB. All local parts should be limited to roman letters and numbers (a-z, A-Z, 0-9).

Even if you do not use collections in your biobank, you still need to register a fictional “default” collection to the Directory. This is needed by the Negotiator and also for Directory synchronizazion, if you choose to activiate it.

NetworkMembership

Used to describe a Biobank’s membership in a Biobank Network (used to fill the BBMRI directory). The biobank is the participatingOrganization and should be referenced as a FHIR resource, the organization is the network and can be referenced without creating a FHIR resource by using its BBMRI ID in the reference.identifier field.

Patient

The birth date may be truncated to year in order to provide anonymity. While gender is defined in FHIR as the administrative gender, in some contexts this may contain/be read as the biological sex. Since most Biobanks only store a single value anyway, we do not differentiate between aspects of sex/gender, for more information see https://www.hl7.org/fhir/patient.html#gender. For deceased patients, deceased shall contain the date and time of death, although the precision may vary, e.g. only a date may be provided.

CauseOfDeath

This resource captures the ICD-10 coded cause of death for deceased patients.

TobaccoUse

TobaccoUse captures the smoking status of a patient at a given time. While the time of observation should be provided in effective, this field may be empty if no such information is available, although this highly reduces the value of this information since it can no longer be sufficiently linked to a specific sample.

Condition

Contains an ICD-10 coded diagnosis for a patient. If possible, the onset date should be documented in onset. If only the system entry time is provided, it should be stored in recordedDate and will be used as a substitute. Systems may also populate the abatement field which will allow researches advanced temporal queries in future releases.

BMI, BodyHeight and BodyWeight

BodyHeight and BodyWeight may be used to calculate the appropriate value for BMI, although currently no validation of this calculation takes place. While the time of observation should be provided in effective, this field may be empty if no such information is available, although this highly reduces the value of this information since it can no longer be sufficiently linked to a specific sample.

Specimen

Contains information related to a sample.

If you use collections at your biobank, you need to add a reference to the collection to the sample. This is done via Speciman → extension → custodian.