pankgraph

PanKgraph

PanKgraph — PanKbase Knowledge Graph (NIDDK)

27.1M triples
13 classes
103 properties
1.6M subjects

PanKgraph is a state-of-the-art Knowledge Graph developed for the study of the human pancreas. By leveraging large language models (LLMs) and diverse data types, PanKgraph enables users to uncover biological connections and insights into diabetes pathogenesis. Previously disjointed entities such as genes, single nucleotide polymorphisms (SNPs), and pancreatic expression quantitative trait loci (eQTLs) can now be explored and connected in innovative ways.

PanKbase is a comprehensive, centralized resource for the study of the human pancreas and diabetes. The PanKbase collective aims to integrate diverse type 1 diabetes (T1D) datasets with expert-curated knowledge in a centralized, open-source data hub. Since users will ultimately be able to contribute their own data, this will be a repository for reproducible, collaborative research within the pancreas and T1D realms.

PanKbase is an actively evolving resource that plans to offer integrated and computation-ready multi-omic data including genomics, epigenomics, transcriptomics, metabolomics, and proteomics, as well as other data types such as imaging and physiological data. Datasets are currently sourced from key external programs, from which human donor-derived pancreatic data and metadata are aggregated, harmonized, and disseminated.

Find genes expressed in pancreas acinar cells and regulating cell-matrix adhesion 
PREFIX cl: <http://purl.obolibrary.org/obo/CL_>
PREFIX go: <http://purl.obolibrary.org/obo/GO_>
PREFIX ro: <http://purl.obolibrary.org/obo/RO_>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX biolink: <https://w3id.org/biolink/vocab/>

SELECT DISTINCT ?gene ?function {
    ?stmt1 rdf:subject ?gene ; rdf:predicate biolink:functional_association ; rdf:object ?function .
    ?stmt2 rdf:subject ?gene ; rdf:predicate biolink:expressed_in ; rdf:object cl:0002064 .
    ?function ro:0002211 go:0007160 .
}

graph TD
classDef projected fill:lightgreen;
classDef literal fill:orange;
classDef iri fill:yellow;
  v3("?function"):::projected 
  v2("?gene"):::projected 
  v1("?stmt1")
  v4("?stmt2")
  c8([obo:GO_0007160]):::iri 
  c3([biolink:functional_association]):::iri 
  c5([biolink:expressed_in]):::iri 
  c6([obo:CL_0002064]):::iri 
  v1 --"rdf:subject"-->  v2
  v1 --"rdf:predicate"-->  c3
  v1 --"rdf:object"-->  v3
  v4 --"rdf:subject"-->  v2
  v4 --"rdf:predicate"-->  c5
  v4 --"rdf:object"-->  c6
  v3 --"obo:RO_0002211"-->  c8
Run in FRINK
SPARQL Endpoint https://frink.apps.renci.org/pankgraph/sparql
Triple Pattern Fragments https://frink.apps.renci.org/ldf/pankgraph
ClassEntities
PropertyTriples