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Biobanks metadata with MIABIS structure #39

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082a500
feat: change of biobank resource to map MIABIS concepts
svituz May 8, 2023
3881873
feat: changes example for biobank
svituz May 8, 2023
ef274ca
adds: biobank ttl example
svituz May 8, 2023
a9e6919
feat: change of biobank resource to map MIABIS concepts
svituz May 8, 2023
95b30e3
feat: changes example for biobank
svituz May 8, 2023
74e94d5
feat: changes description of biobanks
svituz May 8, 2023
690684f
--amend
svituz May 8, 2023
e63d007
feat/miabis_biobanks
svituz Jun 5, 2023
a578d7e
fix: fixes obib term for biobank organization in biobank example
svituz Jun 5, 2023
e84820d
feat: changes the relation between collection and biobank, changes th…
svituz Jul 21, 2023
9cc7e64
feat: changes biobank to be more similar to Dataset and compatible wi…
svituz Sep 8, 2023
190e602
feat: removes dct:alternative and other minor changes
svituz Sep 15, 2023
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66 changes: 46 additions & 20 deletions data/example-rdf/turtle/biobank.ttl
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Original file line number Diff line number Diff line change
@@ -1,26 +1,52 @@
@prefix : <http://purl.org/ejp-rd/metadata-model/v1/example-rdf/> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix ejp: <http://purl.org/ejp-rd/vocabulary/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix lang: <http://id.loc.gov/vocabulary/iso639-1/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix vcard: <http://www.w3.org/2006/vcard/ns#> .
@prefix ordo: <http://www.orpha.net/ORDO/> .
@prefix datacite: <http://purl.org/spar/datacite/> .

:biobank a ejp:Biobank ;
dct:publisher :organisation ;
dct:title "Austrian Bone Marrow Donor Registry" ;
dct:description "Donor registry";
ejp:populationCoverage :population_coverage ;
dcat:theme ordo:Orphanet_171895 ;
foaf:page <http://www.stammzellspende.at> .

:organisation a foaf:Organisation ;
dct:title "Fonds Österreichisches Stammzellregister" ;
dct:spatial :location .
:collection
a obo:OBIB_0000616, dcat:Resouce;
dct:identifier "collection-id";
dct:title "Muscle Tissue Collection";
dct:description "Example collection of samples";
dct:alternative "MTC";
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@svituz svituz Sep 15, 2023

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not in the current model

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@Orphanet Orphanet Sep 15, 2023

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

should be dcat:Resource;

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@svituz svituz Sep 15, 2023

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I changed it in the new commit

dcat:theme ordo:Orphanet_589;
dcat:keyword "Myastenia gravis"
dct:publisher :biobank;
dcat:landingPage <https://mtc.brd.org>;
dct:language <http://lexvo.org/id/iso639-3/eng>;
ejprd:personalData "true";
dcat:contactPoint [ a vcard:Individual;
vcard:email <mailto:info@ejprdbiobank.org>;
vcard:hasGivenName "John";
vcard:hasFamilyName "Smith";
vcard:hasHonorificSuffix "PhD"
].

:population_coverage a sio:SIO_001166 ;
rdfs:label "National" .
:biobank
a obo:OBIB_0000623, foaf:Organization;
dct:identifier "biobank-id";
dct:title "Biobank of Rare Diseases";
dct:alternative "BRD";
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@svituz svituz Sep 15, 2023

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not in the current model

dct:description "Biobank with collections of biopsies of muscular diseases";
dcat:landingPage <https://brd.org>;
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@svituz svituz Sep 15, 2023

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should be foaf:homepage

dct:spatial <http://publications.europa.eu/resource/authority/country/AUT>;;
obo:RO_0000053 :biobankOrganization; # has characteristic. The object MUST be of type Legal en
obo:OBIB_0000732 :collection .
dcat:contactPoint [ a vcard:Organization;
vcard:url <https://brd.org/contacts>
].


:location a dct:Location ;
dct:title "Austria" .
:biobankOrganization
a obo:OMRSE_00000038;
foaf:name "University of Muscle Diseases" .
142 changes: 59 additions & 83 deletions docs/biobank.md
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`ejp:Biobank` concept is a custom extension we added to the DCAT2 vocabulary. In our extension we defined `ejp:Biobank` is a subclass of `dcat:Resource`.
To represent biobanks, the [Minimum Information About BIobank data Sharing](https://github.com/BBMRI-ERIC/miabis) (MIABIS) has been used as a reference.

MIABIS contains two concepts at Resource level:

* Sample Collection: represents a set of samples with at least one common characteristic.
* Biobank: is defined as an organization or an organizational unit that stores samples and data related to the samples. In MIABIS Core 2.0 biobanks do not contain samples directly, but they are hosting sample collections.


These two concepts of MIABIS have been modelled similarly to Dataset and denoted more specifically using classes from [OBIB](https://www.ebi.ac.uk/ols4/ontologies/obib) ontology.


### Metadata model figure
Expand All @@ -16,86 +24,54 @@

```ttl
@prefix : <http://purl.org/ejp-rd/metadata-model/v1/example-rdf/> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix ejp: <http://purl.org/ejp-rd/vocabulary/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix sio: <http://semanticscience.org/resource/> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> .
@prefix rdfs: <http://www.w3.org/2000/01/rdf-schema#> .
@prefix dcat: <http://www.w3.org/ns/dcat#> .
@prefix xsd: <http://www.w3.org/2001/XMLSchema#> .
@prefix owl: <http://www.w3.org/2002/07/owl#> .
@prefix dct: <http://purl.org/dc/terms/> .
@prefix lang: <http://id.loc.gov/vocabulary/iso639-1/> .
@prefix foaf: <http://xmlns.com/foaf/0.1/> .
@prefix obo: <http://purl.obolibrary.org/obo/> .
@prefix vcard: <http://www.w3.org/2006/vcard/ns#> .
@prefix ordo: <http://www.orpha.net/ORDO/> .
@prefix skos: <http://www.w3.org/2004/02/skos/core#> .

:biobank a ejp:Biobank ;
dct:publisher :organisation ;
dct:title "Austrian Bone Marrow Donor Registry" ;
ejp:populationCoverage :population_coverage ;
dcat:theme ordo:Orphanet_171895 ;
foaf:page <http://www.stammzellspende.at> .

ordo:Orphanet_171895 a skos:Concept . # Declaration to comply with dcat:theme range of skos:Concept

:organisation a foaf:Organisation ;
dct:title "Fonds Österreichisches Stammzellregister" ;
dct:spatial :location .

:population_coverage a sio:SIO_001166 ;
rdfs:label "National" .

:location a dct:Location ;
dct:title "Austria" .
```

***

### Validation artifacts

##### ShEx figure

<p align="center">
<a href="../images/shex/biobank.svg" target="_blank">
<img src="../images/shex/biobank.svg">
</a>
</p>

***
##### ShEx

``` ShEx
PREFIX : <http://purl.org/ejp-rd/metadata-model/v1/shex/>
PREFIX dcat: <http://www.w3.org/ns/dcat#>
PREFIX dct: <http://purl.org/dc/terms/>
PREFIX ejp: <http://purl.org/ejp-rd/vocabulary/>
PREFIX foaf: <http://xmlns.com/foaf/0.1/>
PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>
PREFIX sio: <http://semanticscience.org/resource/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

:biobankShape IRI {
a [ejp:Biobank];
dct:title xsd:string;
dct:description xsd:string*;
ejp:populationCoverage @:populationCoverageShape*;
dcat:theme IRI+;
dct:publisher @:organisationShape;
foaf:page IRI*
}

:locationShape IRI {
a [dct:Location];
dct:title xsd:string;
dct:description xsd:string*;
}

:organisationShape IRI {
a [foaf:Organisation];
dct:title xsd:string;
dct:description xsd:string*;
dct:spatial @:locationShape;
foaf:page IRI*
}

:populationCoverageShape IRI {
a [sio:SIO_001166];
rdfs:label ["National" "International" "Regional"]
}
```
@prefix datacite: <http://purl.org/spar/datacite/> .


:collection
a obo:OBIB_0000616, dcat:Resouce;
dct:identifier "collection-id";
dct:title "Muscle Tissue Collection";
dct:description "Example collection of samples";
dct:alternative "MTC";
dcat:theme ordo:Orphanet_589;
dcat:keyword "Myastenia gravis"
dct:publisher :biobank;
dcat:landingPage <https://mtc.brd.org>;
dct:language <http://lexvo.org/id/iso639-3/eng>;
ejprd:personalData "true";
dcat:contactPoint [ a vcard:Individual;
vcard:email <mailto:info@ejprdbiobank.org>;
vcard:hasGivenName "John";
vcard:hasFamilyName "Smith";
vcard:hasHonorificSuffix "PhD"
].

:biobank
a obo:OBIB_0000623, foaf:Organization;
dct:identifier "biobank-id";
dct:title "Biobank of Rare Diseases";
dct:alternative "BRD";
dct:description "Biobank with collections of biopsies of muscular diseases";
dcat:landingPage <https://brd.org>;
dct:spatial <http://publications.europa.eu/resource/authority/country/AUT>;;
obo:RO_0000053 :biobankOrganization; # has characteristic. The object MUST be of type Legal en
obo:OBIB_0000732 :collection .
dcat:contactPoint [ a vcard:Organization;
vcard:url <https://brd.org/contacts>
].


:biobankOrganization
a obo:OMRSE_00000038;
foaf:name "University of Muscle Diseases" .``
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