nfdi4bi-kg
Repository for the NFDI4BIOIMAGE Knowledge Graph
Science Score: 49.0%
This score indicates how likely this project is to be science-related based on various indicators:
-
○CITATION.cff file
-
✓codemeta.json file
Found codemeta.json file -
✓.zenodo.json file
Found .zenodo.json file -
✓DOI references
Found 32 DOI reference(s) in README -
✓Academic publication links
Links to: zenodo.org -
○Academic email domains
-
○Institutional organization owner
-
○JOSS paper metadata
-
○Scientific vocabulary similarity
Low similarity (5.0%) to scientific vocabulary
Last synced: 6 months ago
·
JSON representation
Repository
Repository for the NFDI4BIOIMAGE Knowledge Graph
Basic Info
- Host: GitHub
- Owner: NFDI4BIOIMAGE
- License: mit
- Language: Python
- Default Branch: main
- Size: 619 KB
Statistics
- Stars: 0
- Watchers: 7
- Forks: 0
- Open Issues: 4
- Releases: 1
Created 11 months ago
· Last pushed 8 months ago
Metadata Files
Readme
License
Zenodo
README.org
#+title: NFDI4BI-KG
#+author: All contributors
#+date: [2025-03-24 Mon]
* Repository for the NFDI4BIOIMAGE Knowledge Graph
:PROPERTIES:
:ID: fc647655-1e49-41e7-96f2-6e7ce03c577d
:END:
** NFDI4BIOIMAGe on WikiData
:PROPERTIES:
:ID: 785808b2-c95a-4685-a1ab-976170415ba5
:END:
:PROPERTIES: :nfdi:knowledgegraph:wikidata:meeting:
:ID: 0602d4d7-f97f-4043-853e-9daa9fc36ba5
:END:
*** The NFDI4BI scholia page
:PROPERTIES:
:ID: 599fa125-1c19-4a6e-970b-3c37066c7adc
:END:
https://scholia.toolforge.org/topic/Q113500855
**** Observations:
:PROPERTIES:
:ID: 785a8f5a-9e2a-46bd-9fc2-451ca960d3a0
:END:
- Participants are way incomplete
- No linked topics
- publications?
- events?
- data?
*** Editing wikidata
:PROPERTIES:
:ID: b940169e-9fab-4ceb-9d79-3dc7398687e6
:END:
**** Online, e.g. https://www.wikidata.org/wiki/Q113500855
:PROPERTIES:
:ID: 82baecff-e2a3-4a56-a7d2-f94d3862d14a
:END:
- click "edit" next to any statement
- what's a statement?
- RDF triple:
#+begin_example sparql
?subject ?predicate ?object .
#+end_example
or
#+begin_example sparql
?subject ?property_name ?property_value .
#+end_example
- Adopted from the [[www.wikidata.org/wiki/Wikidata:Introduction][Wikidata introduction)]]
#+begin_example
"St. John's College" .
#+end_example
- Wikidata subjects (=item=): has a label, a description and any number of aliases. URI pattern: https://www.wikidata.org/entity/Q123456789
- Wikidata =statement= = =property= + =value=
| Item | Property | Value |
|------------+--------------------+---------------------------------------|
| wd:Q42 | rdfs:label | "Douglas Adams"^^xsd:string |
| wd:Q42 | schema:description | "A British writer"^^xsd:string@en |
| wd:Q42 | schema:description | "Ein britischer Autor"^^xsd:string@de |
| wd:Q42 | schema:description | "Un écrivain français"^^xsd:string@fr |
| wd:Q42 | wdp:P69 | Q691283 |
| wp:P69 | rdfs:label | "educated at"^^xsd:string@en |
| wd:Q691283 | label | "St. John's College"^^xsd:string |
- Each property-value pair (=statement=) can have additional annotations, such as references, validity dates, ...
Example:[[https://www.wikidata.org/wiki/Q113500855][NFDI4BIOIMAGE]]'s chairperson
*** Query all properties and values on NFDI4BIOIMAGE's item
:PROPERTIES:
:ID: 69b0670b-6859-49d4-84f9-549a4f026153
:END:
#+begin_src sparql :url https://query.wikidata.org/sparql
PREFIX wd:
PREFIX p:
PREFIX bd:
select * where {
wd:Q113500855 ?property ?value .
}
limit 30
#+end_src
#+RESULTS:
| property | value |
|--------------------------------------------+------------------------------------------------------------------------------------------|
| http://schema.org/version | 2326231438 |
| http://schema.org/dateModified | 2025-03-17T12:28:24Z |
| http://schema.org/description | Nationale Forschungsdateninfrastruktur für Mikroskopie und Bildanalyse |
| http://schema.org/description | National Research Data Infrastructure for Microscopy and Bioimage Analysis |
| http://www.w3.org/2000/01/rdf-schema#label | NFDI4BIOIMAGE |
| http://www.w3.org/2000/01/rdf-schema#label | NFDI4BIOIMAGE |
| http://wikiba.se/ontology#statements | 80 |
| http://wikiba.se/ontology#sitelinks | 0 |
| http://wikiba.se/ontology#identifiers | 6 |
| http://www.wikidata.org/prop/direct/P31 | http://www.wikidata.org/entity/Q30089794 |
| http://www.wikidata.org/prop/direct/P31 | http://www.wikidata.org/entity/Q98270496 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q420 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q431 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q441 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q7193 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q7215 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q11190 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q14620 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q21198 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q26383 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q101929 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q207011 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q489328 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q735602 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q2098469 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q30089794 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q96678462 |
| http://www.wikidata.org/prop/direct/P101 | http://www.wikidata.org/entity/Q115433545 |
| http://www.wikidata.org/prop/P31 | http://www.wikidata.org/entity/statement/Q113500855-4170d701-4400-d41b-c518-6ec24ec3eb97 |
| http://www.wikidata.org/prop/P31 | http://www.wikidata.org/entity/statement/Q113500855-a736a4bd-48d9-0052-bae1-a753dedefd55 |
#+begin_src sparql :url https://query.wikidata.org/sparql
PREFIX wd:
PREFIX p:
PREFIX bd:
select * where {
wd:Q113500855 wdt:P31 ?instance_of .
?instance_of ?iprop ?ival .
}
limit 30
#+end_src
#+RESULTS:
| instance_of | iprop | ival |
|------------------------------------------+----------------------------------------------+--------------------------------------------------------------------------------------------------------------|
| http://www.wikidata.org/entity/Q30089794 | http://schema.org/version | 2320780942 |
| http://www.wikidata.org/entity/Q30089794 | http://schema.org/dateModified | 2025-03-06T13:15:55Z |
| http://www.wikidata.org/entity/Q30089794 | http://schema.org/description | Aktivitäten rund um den Lebenszyklus von Forschungsdaten |
| http://www.wikidata.org/entity/Q30089794 | http://schema.org/description | activities around the life cycle of research-related data |
| http://www.wikidata.org/entity/Q30089794 | http://schema.org/description | desarrollo y ejecución de arquitecturas, políticas, prácticas y procedimientos de los datos de investigación |
| http://www.wikidata.org/entity/Q30089794 | http://schema.org/description | dejavnosti v življenjskem ciklu raziskovalnih podatkov |
| http://www.wikidata.org/entity/Q30089794 | http://schema.org/description | діяльності навколо життєвого циклу даних, пов’язаних з дослідженнями |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | Forschungsdatenmanagement |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | research data management |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | gestión de datos de investigación |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | Araştırma verisi yönetimi |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | 研究資料管理 |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | 研究資料管理 |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | 調査データ管理 |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | управління даними досліджень |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | hantering av forskningsdata |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | gestió de dades de recerca |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | gestion des données de recherche |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2000/01/rdf-schema#label | upravljanje raziskovalnih podatkov |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | FDM |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | RDM |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | RDM |
| http://www.wikidata.org/entity/Q30089794 | http://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/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | 調査データ・マネジメント |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | 調査データマネジメント |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | RDM |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | research data management |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | forskningsdatahantering |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | management des données de recherche |
| http://www.wikidata.org/entity/Q30089794 | http://www.w3.org/2004/02/skos/core#altLabel | traitement des données de recherche |
*** Other ways to edit wikidata
:PROPERTIES:
:ID: 6856d416-79ee-45ea-9f34-0e6c1da6c0fb
:END:
- OpenRefine ("reconciliation")
- QuickStatements -> https://quickstatements.toolforge.org/
- See more at https://www.wikidata.org/wiki/Wikidata:Tools
-
*** Suggestions for adding/editing
:PROPERTIES:
:ID: 0bd42be1-749a-4598-9ca9-f932f3ef0ca6
:END:
- Yourself
- Name
- Affiliation
- *ORCID*
- other IDs
- Degree
- Field of work
- Website
- Social media, github handles
- Publications -> https://orcid-scraper.toolforge.org
- ...
**** Your affiliation(s)
:PROPERTIES:
:ID: 1031e141-2a68-40a5-a7e6-9735f8863819
:END:
- ROR ID
- Website
**** Public OMERO istance
:PROPERTIES:
:ID: 7ab130e3-dce8-4e51-9c6f-96e6e462ff05
:END:
**** NFDI4BI Use cases
:PROPERTIES:
:ID: c2db42f5-551a-4731-a61d-66a82e6e4761
:END:
**** NFDI4BI Use cases
:PROPERTIES:
:ID: bb3f0446-7437-4fcd-b064-cb073b31dd2f
:END:
**** Task areas
:PROPERTIES:
:ID: 53ffd7ac-cf7a-4d37-9620-25138c6cf50d
:END:
**** NFDI Sections and Workgroups
:PROPERTIES:
:ID: 1bee5ed1-c28d-4eb3-8ba9-085aa5b4bdd3
:END:
* NFDI self hosted KG
:PROPERTIES:
:ID: f275722e-acb8-48c0-9875-ca191e1fb562
:header-args:sparql: :url https://kg.nfdi4bioimage.de/N4BIKG/sparql
:END:
Since June 16 2025, the NFDI4BIOIMAGE Knowledge Graph is operational at https://kg.nfdi4bioimage.de.
** Graphs
:PROPERTIES:
:ID: 0e01ef08-fb7c-4336-971f-de43a7763409
:END:
*** Default graph
:PROPERTIES:
:ID: bcd055b3-f942-4f05-8652-2583307ef7c6
:END:
The default graph is the union of all named graphs.
*** Named graphs
:PROPERTIES:
:ID: 3bbe4960-5160-46ef-a6f2-93d63bfdfa7a
:END:
#+begin_src sparql
SELECT ?graph (count(?subject) as ?number_of_triples)
WHERE {
graph ?graph { ?subject ?predicate ?object }
}
group by ?graph
#+end_src
#+RESULTS:
| graph | number_of_triples |
|----------------------------------------------------------+-------------------|
| https://kg.nfdi4bioimage.de/n4bikg/core | 8 |
| https://kg.nfdi4bioimage.de/n4bikg/n4bi_zenodo_community | 3482 |
| https://kg.nfdi4bioimage.de/n4bikg/owl | 3993 |
** Example queries
:PROPERTIES:
:ID: 88e593e5-defe-4211-ab3d-c407739d75f7
:END:
*** spo
:PROPERTIES:
:ID: bd5e3d52-41fe-4676-b6bf-78a0be8a0a55
:END:
#+begin_src sparql
PREFIX owl:
PREFIX rdfs:
PREFIX rdf:
prefix dcite:
select ?s ?p ?plabel ?o ?olabel where
{
?s ?p ?o
optional {
?p rdfs:label ?plabel.
}
optional {
?o rdfs:label ?olabel .
}
}
limit 10
#+end_src
#+RESULTS:
| s | p | plabel | o | olabel |
|-----------------------------------------------------+-----------------------------------------------------+-------------------------+----------------------------------------------------------------------------+-----------------|
| https://nfdi4bioimage.de/rdf/node | http://www.w3.org/1999/02/22-rdf-syntax-ns#type | | https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0001039 | nfdi consortium |
| https://nfdi4bioimage.de/rdf/node | http://purl.org/dc/elements/1.1/description | | Nationale Forschungsdateninfrastruktur für Mikroskopie und Bildanalyse | |
| https://nfdi4bioimage.de/rdf/node | http://purl.org/dc/elements/1.1/description | | National Research Data Infrastructure for Microscopy and Bioimage Analysis | |
| https://nfdi4bioimage.de/rdf/node | https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0000136 | foundation date | 2023-03-01 | |
| https://nfdi4bioimage.de/rdf/node | https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0001006 | has external identifier | https://wikidata.org/entity/Q113500855 | |
| https://nfdi4bioimage.de/rdf/node | https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0001008 | has url | https://nfdi4bioimage.de | |
| https://nfdi4bioimage.de/rdf/node | https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0010015 | has acronym | N4BI | |
| https://nfdi4bioimage.de/rdf/node | https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0010015 | has acronym | NFDI4BIOIMAGE | |
| https://nfdi4bioimage.de/rdf/node | https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0000195 | represents collection | https://zenodo.org/communities/nfdi4bioimage | |
| https://nfdi.fiz-karlsruhe.de/ontology/NFDI_0001039 | http://www.w3.org/1999/02/22-rdf-syntax-ns#type | | http://www.w3.org/2002/07/owl#Class | |
*** Creators and contributors for a record
:PROPERTIES:
:ID: bd5e3d52-41fe-4676-b6bf-78a0be8a0a55
:END:
#+begin_src sparql
PREFIX owl:
PREFIX rdfs:
PREFIX rdf:
prefix dcite:
prefix nfdicore: dcite:creator ?creator .
?creator dcite:givenName ?creator_given_name ;
dcite:familyName ?creator_family_name .
?creator dcite:affiliation ?affiliation .
filter(isiri(?affiliation))
?affiliation rdfs:label ?affiliation_name .
}
limit 40
#+end_src
#+RESULTS:
| creator | creator_given_name | creator_family_name | affiliation | affiliation_name |
|---------------------------------------+--------------------+---------------------------+---------------------------+--------------------------------------------|
| https://orcid.org/0000-0001-9568-895X | Christian | Schmidt | https://ror.org/0546hnb39 | University of Konstanz |
| https://orcid.org/0000-0001-9568-895X | Christian | Schmidt | https://ror.org/04cdgtt98 | German Cancer Research Center |
| https://orcid.org/0000-0001-9568-895X | Christian | Christian Schmidt | https://ror.org/0546hnb39 | University of Konstanz |
| https://orcid.org/0000-0001-9568-895X | Christian | Christian Schmidt | https://ror.org/04cdgtt98 | German Cancer Research Center |
| https://orcid.org/0000-0001-7734-3771 | Stefanie | Stefanie Weidtkamp-Peters | https://ror.org/01vnkaz16 | NFDI4BIOIMAGE |
| https://orcid.org/0000-0001-7734-3771 | Stefanie | Stefanie Weidtkamp-Peters | https://ror.org/024z2rq82 | Heinrich Heine University Düsseldorf |
| https://orcid.org/0000-0001-7734-3771 | Stefanie | Weidtkamp-Peters | https://ror.org/01vnkaz16 | NFDI4BIOIMAGE |
| https://orcid.org/0000-0001-7734-3771 | Stefanie | Weidtkamp-Peters | https://ror.org/024z2rq82 | Heinrich Heine University Düsseldorf |
| https://orcid.org/0000-0001-6523-7496 | Susanne | Kunis | https://ror.org/04qmmjx98 | Osnabrück University |
| b0 | Tom | Boissonnet | https://ror.org/024z2rq82 | Heinrich Heine University Düsseldorf |
| b1 | Bettina | Hagen | https://ror.org/04xx1tc24 | Max Planck Institute for Biology of Ageing |
Some records must have the full name set as 'family name'.
*** ORCID properties
:PROPERTIES:
:ID: 7329c725-8e84-49eb-ad67-d3c7a238c970
:END:
#+begin_src sparql
PREFIX owl:
PREFIX rdfs:
PREFIX rdf:
prefix dcite:
prefix nfdicore: dcite:givenName ?first;
dcite:familyName ?last .
}
#+end_src
#+RESULTS:
| first | last |
|----------+---------------------------|
| Stefanie | Stefanie Weidtkamp-Peters |
| Stefanie | Weidtkamp-Peters |
*** Count number of creators and contributors per record.
:PROPERTIES:
:ID: bd5e3d52-41fe-4676-b6bf-78a0be8a0a55
:END:
#+begin_src sparql :session sparql
PREFIX owl:
PREFIX rdfs:
PREFIX rdf:
prefix dcite:
prefix nfdicore:
PREFIX rdfs:
PREFIX rdf:
prefix dcite:
prefix nfdicore:
PREFIX rdfs:
PREFIX rdf:
prefix dcite:
prefix nfdicore:
Owner
- Name: NFDI4BioImage
- Login: NFDI4BIOIMAGE
- Kind: organization
- Website: https://nfdi4bioimage.de/
- Twitter: nfdi4bioimage
- Repositories: 1
- Profile: https://github.com/NFDI4BIOIMAGE
Research Data Management for Microscopy and BioImage Analysis
GitHub Events
Total
- Create event: 5
- Release event: 1
- Issues event: 4
- Delete event: 1
- Issue comment event: 3
- Member event: 2
- Push event: 14
Last Year
- Create event: 5
- Release event: 1
- Issues event: 4
- Delete event: 1
- Issue comment event: 3
- Member event: 2
- Push event: 14