Biobanks metadata with MIABIS structure

[svituz]

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

1. 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.
2. Basing biobank related concepts on OBIB is a sound idea that we may want to encourage.
3. 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

1. 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:
   

2. 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?

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

[svituz]

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

[svituz]

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]

should be foaf:homepage

[svituz]

not in the current model

[svituz]

not in the current model

[Orphanet]

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

should be dcat:Resource;

[svituz]

I changed it in the new commit

[Orphanet]

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

should be dcat:Resource;