Biobanks metadata with MIABIS structure #39

svituz · 2023-05-10T13:38:43Z

This PR changes the metadata schema for biobanks in order to be compliant with the MIABIS schema

NB: currently it is missing the PNG with the representation of the schema

henrietteharmse

Here are some initial feedback for a discussion.

Valid points

The dcat:Resource in the EJP RD model is missing the dct:indentifier property that is very clearly part of DCAT2 and even if it was not part of DCAT2 it should have been added to realize the Findable aspect of data and metadata. This seems to be an oversight of the EJP RD model.
Basing biobank related concepts on OBIB is a sound idea that we may want to encourage.
The EJP RD model does not include dcat:contactPoint on dcat:Resource. Why? This would seem to make sense as both DCAT2 and FDP have it.

To discuss

The intent of the EJP RD meta-model is to only deal with meta-data. It therefore would seem that collections should not form part of meta-data as these in fact represent record data of biobanks. It would be similar to adding patient and diagnosis information for patient registries to the meta-data model. The fact that a collection seem to be a record-level element seems to be supported by the definition of OBIB_0000645 "A object aggregate that consists of specimens, participates in a study and is part of a biobank." Here is diagram representing collection data:
Should the EJPRD model include fdp-o:metadataIdentifier information? This seems very specific to FDP and not general the EJPRD meta-data model. Also, it seems that fdp-o:metadataIdentifier is deprecated based on [https://w3id.org/fdp/fdp-o#](See https://w3id.org/fdp/fdp-o#). However, when looking at https://specs.fairdatapoint.org/
it seems to still in use.

Possible error?

dct:isPartOf :catalog but :catalog is not defined.

svituz · 2023-06-05T15:10:10Z

I changed the mapping of the concepts of biobanks and collections.
I do agree that the previous mapping of the concepts defined by OBIB and MIABIS didn't completely fit.

Now the MIABIS Collection is mapped to obib:biobank and the MIABIS Biobank is mapped to obib:biobank_organization. The two entities are linked by the relations :biobank obib:owns :collection and :collection obib:is_owned_by :biobank. The biobank organization has now a dcat:publisher -> foaf:Organization, similarly to the Patient Registry and to the old version of the biobank model.
This new version should be more similar to the old EJP model, with the difference that it uses OBIB concepts and relations. Indeed the old ejp:Biobank is now obib:biobank while the foaf:Organization is now denoted more specifically using the obib:biobank_organization term.

This mapping should also clarify the doubt about collections being records of the biobank: the collection metadata describes the samples while the MIABIS biobank contains only organizational data. For example, the metadata about the diseases treated is registered in the collection, from a MIABIS point of view.

Other minor changes: I removed the FDP specific attributes from the examples and the dcat:isPartOf :catalog

…e biobankShape to be a foaf:Organization and introdue the legal entity for biobank

…th both MIABIS and previous EJP model

svituz · 2023-09-08T09:24:03Z

I changed again the mapping. Now it is really similar to the EJP previous model.
The main changes have been restricted to:

The old ejp:Biobank entity has been replaced by dcat:Dataset and obo:OBIB_0000616 (obib:biobank) to be compatible with MIABIS
The old foaf:Organization representing the Organization that owns the Biobank has been enhanced as follows:
- It has been also assigned the obo:OBIB_0000623 (obib:biobank_organization) to specify it is a Biobank Organization as defined by MIABIS
- the obo:OBIB_0000732 (obib:owns) relates the biobank to the collectionShape
- the obo:RO_0000053 (obo:has_charasteristic) predicate has been added. This generic predicate from obo is used to link the biobank to an object of type obo:OMRSE_00000038 (obo:legal_entity) to link it to the Legal Entity (e.g. a university) that represents the Organization

svituz · 2023-09-15T10:43:00Z

data/example-rdf/turtle/biobank.ttl

+  dct:title "Biobank of Rare Diseases";
+  dct:alternative "BRD";
+  dct:description "Biobank with collections of biopsies of muscular diseases";
+  dcat:landingPage <https://brd.org>;


should be foaf:homepage

svituz · 2023-09-15T10:43:16Z

data/example-rdf/turtle/biobank.ttl

+  a obo:OBIB_0000623, foaf:Organization;
+  dct:identifier "biobank-id";
+  dct:title "Biobank of Rare Diseases";
+  dct:alternative "BRD";


not in the current model

svituz · 2023-09-15T10:43:24Z

data/example-rdf/turtle/biobank.ttl

+  dct:identifier "collection-id";
+  dct:title "Muscle Tissue Collection";
+  dct:description "Example collection of samples";
+  dct:alternative "MTC";


not in the current model

I think, there is a typo here:
dcat:Resouce;

should be dcat:Resource;

I changed it in the new commit

Orphanet · 2023-09-15T10:57:16Z

data/example-rdf/turtle/biobank.ttl

+  dct:identifier "collection-id";
+  dct:title "Muscle Tissue Collection";
+  dct:description "Example collection of samples";
+  dct:alternative "MTC";


I think, there is a typo here:
dcat:Resouce;

should be dcat:Resource;

henrietteharmse reviewed May 12, 2023

View reviewed changes

henrietteharmse requested review from Orphanet and luizbonino May 12, 2023 15:17

svituz added 10 commits July 21, 2023 15:02

feat: change of biobank resource to map MIABIS concepts

082a500

feat: changes example for biobank

3881873

adds: biobank ttl example

ef274ca

feat: change of biobank resource to map MIABIS concepts

a9e6919

feat: changes example for biobank

95b30e3

feat: changes description of biobanks

74e94d5

--amend

690684f

feat/miabis_biobanks

e63d007

fix: fixes obib term for biobank organization in biobank example

a578d7e

feat: changes the relation between collection and biobank, changes th…

e84820d

…e biobankShape to be a foaf:Organization and introdue the legal entity for biobank

svituz force-pushed the feat/miabis_biobanks branch from 3eda2b2 to e84820d Compare July 21, 2023 14:30

henrietteharmse requested a review from markwilkinson August 29, 2023 10:55

feat: changes biobank to be more similar to Dataset and compatible wi…

9cc7e64

…th both MIABIS and previous EJP model

svituz commented Sep 15, 2023

View reviewed changes

Orphanet requested changes Sep 15, 2023

View reviewed changes

svituz mentioned this pull request Sep 15, 2023

Change the Biobank model to be compliant with MIABIS #60

Open

feat: removes dct:alternative and other minor changes

190e602

henrietteharmse added the status: awaiting decision Awaiting decision by members on whether this change/extension should be applied label Dec 8, 2023

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Biobanks metadata with MIABIS structure #39

Biobanks metadata with MIABIS structure #39

svituz commented May 10, 2023

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edited

svituz commented Jun 5, 2023

svituz commented Sep 8, 2023

svituz Sep 15, 2023

svituz Sep 15, 2023

svituz Sep 15, 2023

Orphanet Sep 15, 2023

svituz Sep 15, 2023

Orphanet Sep 15, 2023

Biobanks metadata with MIABIS structure #39

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Biobanks metadata with MIABIS structure #39

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