Archived Builds

PKT Human Disease Knowledge Graph Benchmark Builds

This page provides an overview of the PKT Human Disease Knowledge Graph Benchmark and lists all builds and by release and build date.

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PKT Human Disease Knowledge Graph
Build Archive

PKT Human Disease Knowledge Graph

👉 For additional details on the Human Disease Benchmark Builds, please see the associated manuscript: https://doi.org/10.48550/arXiv.2307.05727.

The PKT Human Disease KG was built to model mechanisms of human disease, which includes the Central Dogma and represents multiple biological scales of organization including molecular, cellular, tissue, and organ. The knowledge representation was designed in collaboration with a PhD-level molecular biologist (below).

(Click Figure to Enlarge)

The PKT Human Disease KG was constructed using 12 OBO Foundry ontologies, 31 Linked Open Data sets, and results from two large-scale experiments (Supplementary material).

The 12 OBO Foundry ontologies were selected to represent chemicals and vaccines (i.e., ChEBI) and Vaccine Ontology [VO]), cells and cell lines (i.e., Cell Ontology [CL], Cell Line Ontology [CLO]), gene/gene product attributes (i.e., Gene Ontology [GO]), phenotypes and diseases (i.e., Human Phenotype Ontology [HPO], Mondo Disease Ontology [Mondo]), proteins, including complexes and isoforms (i.e., PRO), pathways (i.e., Pathway Ontology [PW]), types and attributes of biological sequences (i.e., Sequence Ontology [SO]), and anatomical entities (the Uber Anatomy Ontology [Uberon]). The Relation Ontology (RO) is used to provide relationships between the core OBO Foundry ontologies and database entities.
The PKT Human Disease KG contained 18 node types (Table 1 below) and 33 edge types (listed by relation in Table 3 [below]). Note that the number of nodes and edge types reflects those that are explicitly added to the core set of OBO Foundry ontologies and does not take into account the node and edge types provided by the ontologies.
These nodes and edge types were used to construct 12 different PKT Human Disease benchmark KGs by altering the Knowledge Model (i.e., class- vs. instance-based), Relation Strategy (i.e., standard vs. inverse relations), and Semantic Abstraction (i.e., OWL-NETS (yes/no) with and without Knowledge Model harmonization [OWL-NETS Only vs. OWL-NETS + Harmonization]) parameters.
Benchmarks within the PheKnowLator ecosystem are different versions of a KG that can be built under alternative knowledge models, relation strategies, and with or without semantic abstraction. They provide users with the ability to evaluate different modeling decisions (based on the prior mentioned parameters) and to examine the impact of these decisions on different downstream tasks. Please note that the actual content of each KG may differ slightly across the builds.

Table 1. PKT Human Disease Knowledge Graph Primary Node Types.

Node	Universal Resource Identifier
Anatomical Entities	http://purl.obolibrary.org/obo/UBERON
Biological Processes	http://purl.obolibrary.org/obo/GO
Catalysts	http://purl.obolibrary.org/obo/CHEBI
Cells	http://purl.obolibrary.org/obo/CL
Cell Lines	http://purl.obolibrary.org/obo/CLO
Cellular Components	http://purl.obolibrary.org/obo/GO
Chemicals	http://purl.obolibrary.org/obo/CHEBI
Cofactors	http://purl.obolibrary.org/obo/CHEBI
Diseases	http://purl.obolibrary.org/obo/MONDO
Genes	http://www.ncbi.nlm.nih.gov/gene/
Molecular Functions	http://purl.obolibrary.org/obo/GO
Pathwaysa	http://purl.obolibrary.org/obo/PWhttps://reactome.org/content/detail/R-HSA-
Phenotypes	http://purl.obolibrary.org/obo/HP
Proteins	http://purl.obolibrary.org/obo/PR
Sequencesb	http://purl.obolibrary.org/obo/SO
Transcripts	https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST
Vaccinesb	http://purl.obolibrary.org/obo/VO
Variants	https://www.ncbi.nlm.nih.gov/snp/rs

Table 2. PKT Human Disease Knowledge Graph Primary Node Types.

Relations	Edge Types
participates in (RO_0000056) has participant (RO_0000057)	chemical-pathway; gene-pathway; protein-biological process; protein-pathway
has function (RO_0000085) function of (RO_0000079)	pathway-molecular function; protein-molecular function
located in (RO_0001025) location of (RO_0001015)	protein-anatomy; protein-cella; protein-cellular component; transcript-anatomy; transcript-cella
has component (RO_0002180)	pathway-cellular component
has phenotype (RO_0002200) phenotype of (RO_0002201)	disease-phenotype
has gene product (RO_0002205) gene product of (RO_0002204)	gene-protein
interacts with (RO_0002434)	chemical-gene; chemical-protein
genetically interacts with (RO_0002435)	gene-gene
molecularly interacts with (RO_0002436)	chemical-biological process; chemical-cellular component; chemical-molecular function; protein-catalyst; protein-cofactor; protein-protein
transcribed to (RO_0002511) transcribed from (RO_0002510)	gene-transcript
ribosomally translates to (RO_0002513) ribosomal Translation of (RO_0002512)	transcript-protein
causally influences (RO_0002566) causally influenced by (RO_0002559)	variant-gene
is substance that treats (RO_0002606) is treated by substance (RO_0002302)	chemical-disease; chemical-phenotype
causes or contributes to condition (RO_0003302)	gene-disease; gene-phenotype; variant-disease; variant-phenotype
realized in response to (RO_0009501)	biological process-pathway

Build Archive

Please use the the links below to access specific builds. Within a specific date you will find links to access all of the KG files, metadata, and logs. Details on each of the KG file types is available here.