Directory Sync

The Directory-sync library is designed to synchronize between a FHIR store associated with a biobank and a Directory, such as the (BBMRI Directory)[https://directory.bbmri-eric.eu]. This is a two-way process, information is extracted from the FHIR store and sent to the Directory, and information is pulled from the Directory and inserted into the FHIR store. For this to work, the data in the FHIR store should conform to the (BBMRI Profile)[https://simplifier.net/bbmri.de].

This is meant to make the lives of biobank administrators a little easier, since they must currently perform this synchronization by hand.

The library can update the Directory with the following information, on a per-collection basis:

• number of donors/patients
• number of samples
• sex
• diagnosis
• age range
• sample types
• storage temperatures

It is also possible to send data in the star model format. This aggregates the data into hypercubes.

Data relating to biobank contact details can be retrieved from the Directory and stored in the FHIR store.

The Sync class is the main entrypoint into this library. See the Javadoc in Sync.java for more details.

The library was written to be used from within the (Connector)[https://github.com/samply/share-client]. However, it could be used from within any component that needs Directory-sync functionality.

Based on the mapping from https://samply.github.io/bbmri-fhir-ig/mappings.html.

Usage

<dependency>
    <groupId>de.samply</groupId>
    <artifactId>directory-sync</artifactId>
    <version>0.1.0</version>
</dependency>

Directory fields and support status

Biobank

BBMRI-ERIC-Field	Source of Truth	Status
id	Both!	Used as primary means of biobank identification, should not change
name	Directory	active
acronym	Directory	TODO
description	Directory	TODO
bioresource_reference	Directory	TODO
url	Directory	TODO
juridical_person	Directory	TODO
country	Directory	TODO
it_support_available	Directory	TODO
it_staff_size	Directory	TODO
is_available	Directory	TODO
his_available	Directory	TODO
partner_charter_signed	Directory	TODO
head_title_before_name	Directory	TODO
head_firstname	Directory	TODO
head_lastname	Directory	TODO
head_title_after_name	Directory	TODO
head_role	Directory	TODO
contact	see section contact
latitude	Directory	TODO
longitude	Directory	TODO
network	see section network
collaboration_commercial	Directory	TODO
collaboration_non_for_profit	Directory	TODO
capabilities	Directory	TODO
quality	Directory	TODO

Contact Information

Unsolved problem: How do we identify corresponding contacts in the directory and FHIR? Contacts have no identifier in FHIR.

BBMRI-ERIC-Field	Source of Truth	Status
title_before_name	Directory	TODO
first_name	Directory	TODO
last_name	Directory	TODO
title_after_name	Directory	TODO
phone	Directory	TODO
email	Directory	TODO
address	Directory	TODO
zip	Directory	TODO
city	Directory	TODO
country	Directory	TODO

Collection

BBMRI-ERIC-Field	Source of Truth	Status
id	Both!	Used as primary means of biobank identification, should not change
country	Directory	TODO
biobank	--	Not expected to change
name	Directory	TODO
acronym	Directory	TODO
description	Directory	TODO
bioresource_reference	Directory	TODO
parent_collection	--	No FHIR Mapping yet, so no sync
network	see section network
type	Directory	TODO
data_categories	Directory	TODO
quality		Directory
order_of_magnitude	FHIR	TODO
order_of_magnitude_donors	FHIR	TODO
size	FHIR	active
number_of_donors	FHIR	TODO
timestamp	FHIR (??)	TODO
id_card	Directory	TODO
head_title_before_name	Directory	TODO
head_firstname	Directory	TODO
head_lastname	Directory	TODO
head_title_after_name	Directory	TODO
head_role	Directory	TODO
contact	see section contact
latitude	Directory	TODO
longitude	Directory	TODO
sex	FHIR	TODO
diagnosis_available	FHIR	TODO
age Low	FHIR	TODO
age High	FHIR	TODO
age Unit	FHIR	Fixed to years
body_part_examined	--	No FHIR Mapping yet, so no sync
imaging_modality	--	No FHIR Mapping yet, so no sync
image_dataset_type	--	No FHIR Mapping yet, so no sync
materials	FHIR	TODO
storage_temperature	FHIR	TODO
sample_access_fee	Directory	TODO
sample_access_joint_project	Directory	TODO
sample_access_description	Directory	TODO
sample_access_uri	Directory	TODO
data_access_fee	Directory	TODO
data_access_joint_project	Directory	TODO
data_access_description	Directory	TODO
data_access_uri	Directory	TODO
image_access_fee	Directory	TODO
image_access_joint_project	Directory	TODO
image_access_description	Directory	TODO
image_access_uri	Directory	TODO
collaboration_commercial	Directory	TODO
collaboration_non_for_profit	Directory	TODO
sample_processing_sop	Directory	TODO
sample_transport_sop	Directory	TODO
sample_storage_sop	Directory	TODO
data_processing_sop	Directory	TODO
data_transport_sop	Directory	TODO
data_storage_sop	Directory	TODO

Docu

Anfrage	Subject	Stratifier	Scoring
order_of_magnitude	Specimen	Collection	cohort
order_of_magnitude_donors	Patient	Collection	cohort
size	Specimen	Collection	cohort
number_of_donors	Patient	Collection	cohort
age Low	Patient	Collection	continuous-variable
age High	Patient	Collection	continuous-variable
age Unit	hardcoded years	--	--
materials	Specimen	Collection, Type	cohort
storage_temperature	Specimen	Collection, storageTemp	cohort
sex	Patient	Collection, gender	cohort
diagnosis_available	Collection, Condition

License

Copyright 2020 The Samply Development Community

Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at

http://www.apache.org/licenses/LICENSE-2.0

Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.