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NFDI4BI-KG

Repository for the NFDI4BIOIMAGE Knowledge Graph

Introduction

The NFDI4BI scholia page

https://scholia.toolforge.org/topic/Q113500855

Observations:

  • Participants are way incomplete
  • No linked topics
  • publications?
  • events?
  • data?

Editing wikidata

  • click “edit” next to any statement
  • what’s a statement?
  • RDF triple:
    ?subject ?predicate ?object .
          

    or

    ?subject ?property_name ?property_value .
          
  • Adopted from the Wikidata introduction)
<http://example.org/DouglasAdams> <http://example.org/educated_at> "St. John's College" .
  
ItemPropertyValue
wd:Q42rdfs:label“Douglas Adams”^^xsd:string
wd:Q42schema:description“A British writer”^^xsd:string@en
wd:Q42schema:description“Ein britischer Autor”^^xsd:string@de
wd:Q42schema:description“Un écrivain français”^^xsd:string@fr
wd:Q42wdp:P69Q691283
wp:P69rdfs:label“educated at”^^xsd:string@en
wd:Q691283label“St. John’s College”^^xsd:string
  • Each property-value pair (statement) can have additional annotations, such as references, validity dates, …

Example:NFDI4BIOIMAGE’s chairperson

Example queries

Query all properties and values on NFDI4BIOIMAGE’s item

PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX ps: <http://www.wikidata.org/prop/statement/>
PREFIX pq: <http://www.wikidata.org/prop/qualifier/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX bd: <http://www.bigdata.com/rdf#>

select * where {
  wd:Q113500855 ?property ?value .
  }
limit 30
propertyvalue
http://schema.org/version2326231438
http://schema.org/dateModified2025-03-17T12:28:24Z
http://schema.org/descriptionNationale Forschungsdateninfrastruktur für Mikroskopie und Bildanalyse
http://schema.org/descriptionNational Research Data Infrastructure for Microscopy and Bioimage Analysis
http://www.w3.org/2000/01/rdf-schema#labelNFDI4BIOIMAGE
http://www.w3.org/2000/01/rdf-schema#labelNFDI4BIOIMAGE
http://wikiba.se/ontology#statements80
http://wikiba.se/ontology#sitelinks0
http://wikiba.se/ontology#identifiers6
http://www.wikidata.org/prop/direct/P31http://www.wikidata.org/entity/Q30089794
http://www.wikidata.org/prop/direct/P31http://www.wikidata.org/entity/Q98270496
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q420
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q431
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q441
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q7193
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q7215
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q11190
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q14620
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q21198
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q26383
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q101929
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q207011
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q489328
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q735602
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q2098469
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q30089794
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q96678462
http://www.wikidata.org/prop/direct/P101http://www.wikidata.org/entity/Q115433545
http://www.wikidata.org/prop/P31http://www.wikidata.org/entity/statement/Q113500855-4170d701-4400-d41b-c518-6ec24ec3eb97
http://www.wikidata.org/prop/P31http://www.wikidata.org/entity/statement/Q113500855-a736a4bd-48d9-0052-bae1-a753dedefd55
PREFIX wd: <http://www.wikidata.org/entity/>
PREFIX wdt: <http://www.wikidata.org/prop/direct/>
PREFIX wikibase: <http://wikiba.se/ontology#>
PREFIX p: <http://www.wikidata.org/prop/>
PREFIX ps: <http://www.wikidata.org/prop/statement/>
PREFIX pq: <http://www.wikidata.org/prop/qualifier/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX bd: <http://www.bigdata.com/rdf#>

select * where {
  wd:Q113500855 wdt:P31 ?instance_of .
  ?instance_of ?iprop ?ival .
  }
limit 30
instance_ofipropival
http://www.wikidata.org/entity/Q30089794http://schema.org/version2320780942
http://www.wikidata.org/entity/Q30089794http://schema.org/dateModified2025-03-06T13:15:55Z
http://www.wikidata.org/entity/Q30089794http://schema.org/descriptionAktivitäten rund um den Lebenszyklus von Forschungsdaten
http://www.wikidata.org/entity/Q30089794http://schema.org/descriptionactivities around the life cycle of research-related data
http://www.wikidata.org/entity/Q30089794http://schema.org/descriptiondesarrollo y ejecución de arquitecturas, políticas, prácticas y procedimientos de los datos de investigación
http://www.wikidata.org/entity/Q30089794http://schema.org/descriptiondejavnosti v življenjskem ciklu raziskovalnih podatkov
http://www.wikidata.org/entity/Q30089794http://schema.org/descriptionдіяльності навколо життєвого циклу даних, пов’язаних з дослідженнями
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#labelForschungsdatenmanagement
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#labelresearch data management
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#labelgestión de datos de investigación
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#labelAraştırma verisi yönetimi
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#label研究資料管理
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#label研究資料管理
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#label調査データ管理
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#labelуправління даними досліджень
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#labelhantering av forskningsdata
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#labelgestió de dades de recerca
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#labelgestion des données de recherche
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2000/01/rdf-schema#labelupravljanje raziskovalnih podatkov
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabelFDM
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabelRDM
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabelRDM
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabelリサーチ・データ・マネジメント
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabel調査データ・マネジメント
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabel調査データマネジメント
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabelRDM
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabelresearch data management
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabelforskningsdatahantering
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabelmanagement des données de recherche
http://www.wikidata.org/entity/Q30089794http://www.w3.org/2004/02/skos/core#altLabeltraitement des données de recherche

Other ways to edit wikidata

-

Suggestions for adding/editing

Your affiliation(s)

  • ROR ID
  • Website

Public OMERO istance

NFDI4BI Use cases

NFDI4BI Use cases

Task areas

NFDI Sections and Workgroups

Graphs

Default graph

The default graph will contain the URIs of all named graphs, not more.

Named graphs

configuration

fuseki --set tdb:unionDefaultGraph=true

Example queries

spo

PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix dcite: <https://schema.datacite.org/meta/kernel-4.6/metadata.xsd#>
select ?s ?p ?plabel ?o ?olabel where 
{
  ?s ?p ?o
  optional {
    ?p rdfs:label ?plabel.
  }
  optional {
    ?o rdfs:label ?olabel .
  }
}
limit 10
spplabeloolabel
https://zenodo.org/communities/nfdi4bioimagehttp://purl.org/dc/elements/1.1/identifiernfdi4bioimage
https://zenodo.org/communities/nfdi4bioimagehttps://nfdi.fiz-karlsruhe.de/ontology/NFDI_0001008has urlhttps://zenodo.org/communities/nfdi4bioimage
http://purl.org/dc/elements/1.1/identifierhttp://www.w3.org/1999/02/22-rdf-syntax-ns#typehttp://www.w3.org/2002/07/owl#AnnotationProperty
https://doi.org/10.1038/s41598-019-56067-whttps://schema.datacite.org/meta/kernel-4.6/metadata.xsd#IsPartOfhttps://zenodo.org/communities/nfdi4bioimage/
https://doi.org/10.1038/s41598-019-56067-whttps://schema.datacite.org/meta/kernel-4.6/metadata.xsd#Issued2019-12-20
https://doi.org/10.1038/s41598-019-56067-whttps://schema.datacite.org/meta/kernel-4.6/metadata.xsd#Updated2023-02-02
https://doi.org/10.1038/s41598-019-56067-whttps://schema.datacite.org/meta/kernel-4.6/metadata.xsd#creatorhttps://orcid.org/0000-0002-8367-5163
https://doi.org/10.1038/s41598-019-56067-whttps://schema.datacite.org/meta/kernel-4.6/metadata.xsd#resourceTypeNone
https://doi.org/10.1038/s41598-019-56067-whttps://schema.datacite.org/meta/kernel-4.6/metadata.xsd#rightCreative Commons Attribution 4.0 International
https://doi.org/10.1038/s41598-019-56067-whttps://schema.datacite.org/meta/kernel-4.6/metadata.xsd#subjectFLIM, sdt, image analysis

Creators and contributors for a record

PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix dcite: <https://schema.datacite.org/meta/kernel-4.6/metadata.xsd#>
prefix nfdicore: <https://nfdi.fiz-karlsruhe.de/ontology/>
select *
where
{
  <https://doi.org/10.5281/zenodo.14013026> dcite:contributor ?contributor ;
                                            dcite:creator ?creator .
  ?creator dcite:affiliation ?affilation .
  ?affiliation rdfs:label ?affiliation_name .
}
limit 10
contributorcreatoraffilationaffiliationaffiliation_name
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39https://ror.org/01v7r4v08DataPLANT
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39b1Riccardo
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39https://ror.org/01vnkaz16NFDI4BIOIMAGE
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39b2NFDI4BIOIMAGE
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39https://ror.org/05qj6w324Nationale Forschungsdateninfrastruktur
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39b3Jan
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39b4Stefan
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39b5Thomas
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39b6Wibke
b0https://orcid.org/0000-0001-9568-895Xhttps://ror.org/0546hnb39b7Hannes

Count number of creators and contributors per record.

PREFIX owl: <http://www.w3.org/2002/07/owl#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
prefix dcite: <https://schema.datacite.org/meta/kernel-4.6/metadata.xsd#>
prefix nfdicore: <https://nfdi.fiz-karlsruhe.de/ontology/>
select ?record (count(distinct ?creator) as ?ncreators) (count(distinct ?contributor) as ?ncontributor)
where
{
  ?record dcite:contributor ?contributor ;
          dcite:creator ?creator .
}
group by ?record
recordncreatorsncontributor
https://doi.org/10.5281/zenodo.1150272119
https://doi.org/10.5281/zenodo.510115811
https://doi.org/10.5281/zenodo.1530877312
https://doi.org/10.5281/zenodo.1493763211
https://doi.org/10.5281/zenodo.1103174711
https://doi.org/10.1038/s41598-019-56067-w11
https://doi.org/10.5281/zenodo.1417878951
https://doi.org/10.5281/zenodo.1495114213
https://doi.org/10.5281/zenodo.14044640101
https://doi.org/10.5281/zenodo.1135068932
https://doi.org/10.5281/zenodo.1522561613
https://doi.org/10.5281/zenodo.1404438091
https://doi.org/10.5281/zenodo.1110961631
https://doi.org/10.5281/zenodo.14909526101
https://doi.org/10.5281/zenodo.1537355532
https://doi.org/10.5281/zenodo.1418610115
https://doi.org/10.5281/zenodo.1401302651

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