Continuous Evaluation of Relational Learning in Biomedicine (CERLIB)

PheKnowLator KG

Introduction

PheKnowLator (Phenotype Knowledge Translator), is a Python 3 library that constructs semantically-rich, large-scale biomedical knowledge graphs under different semantic models. For this challenge, the PheKnowLator knowledge graphs have been designed to model mechanisms of human disease and were built using 12 open biomedical ontologies, 24 linked open datasets, and results from two large-scale, experimentally-derived datasets. For additional information see the associated GitHub website: https://github.com/callahantiff/PheKnowLator/wiki/v2.0.0.

Relation types

We will evaluate predictions on the following 15 Relation Ontology (RO) relations, which are utilized in 34 distinct edge types (additional details can be found here: https://github.com/callahantiff/PheKnowLator/wiki/v2.0.0#edge-data):

Relation	Edge Types
Participates in (http://purl.obolibrary.org/obo/RO_0000056)	chemical-pathway; gene-pathway; protein-gobp; protein-pathway
Has function (http://purl.obolibrary.org/obo/RO_0000085)	pathway-gomf; protein-gomf
Located in (http://purl.obolibrary.org/obo/RO_0001025)	protein-anatomy; protein-cell; protein-gocc; rna-anatomy; rna-cell
Has component (http://purl.obolibrary.org/obo/RO_0002180)	pathway-gocc
Has phenotype (http://purl.obolibrary.org/obo/RO_0002200)	disease-phenotype
Has gene product (http://purl.obolibrary.org/obo/RO_0002205)	gene-protein
Interacts with (http://purl.obolibrary.org/obo/RO_0002434)	chemical-gene; chemical-protein; chemical-rna
Genetically interacts with (http://purl.obolibrary.org/obo/RO_0002435)	gene-gene
Molecularly interacts with (http://purl.obolibrary.org/obo/RO_0002436)	chemical-gobp; chemical-gocc; chemical-gomf; protein-catalyst; protein-cofactor; protein-protein
Transcribed to (http://purl.obolibrary.org/obo/RO_0002511)	gene-rna
Ribosomally translates to (http://purl.obolibrary.org/obo/RO_0002513)	rna-protein
Causally influences (http://purl.obolibrary.org/obo/RO_0002566)	variant-gene
Is substance that treats (http://purl.obolibrary.org/obo/RO_0002606)	chemical-disease; chemical-phenotype
Causes or contributes to condition (http://purl.obolibrary.org/obo/RO_0003302)	gene-disease; gene-phenotype; variant-disease; variant-phenotype
Realized in response to (http://purl.obolibrary.org/obo/RO_0009501)	gobp-pathway

Data sources and contact

In addition to the SPARQL Endpoint and RDF download link, we also provide access to the data in other formats (n-triples, networkx MultiDigraph, txt files) via a publicly accessible Google Cloud Storage Bucket. See the README in the bucket for additional documentation.

Github: https://github.com/callahantiff/PheKnowLator
Primary contact: Tiffany Callahan

Data download and evaluation

Dataset download: https://storage.googleapis.com/pheknowlator/ISMB_Challenge_Data/PheKnowLator_v2.0.0_full_instance_inverseRelations_noOWL_OWLNETS.nt

Endpoint: http://sparql.pheknowlator.com/sparql

Query for evaluation:

PREFIX obo: <http://purl.obolibrary.org/obo/>
PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>

SELECT ?s ?p ?o 
WHERE { 
  VALUES ?p {
    obo:RO_0000056
    obo:RO_0000085
    obo:RO_0001025
    obo:RO_0002180
    obo:RO_0002200
    obo:RO_0002205
    obo:RO_0002434
    obo:RO_0002435
    obo:RO_0002436
    obo:RO_0002511
    obo:RO_0002513
    obo:RO_0002566
    obo:RO_0002606
    obo:RO_0003302
    obo:RO_0009501
  }
  ?s ?p ?o 
}

Rankings

Ranking

New submission

To submit, create a compressed (gzip or zip) tab-separated file containing (subject, predicate, object, score) quadruples. An example file could be:

<https://reactome.org/content/detail/R-HSA-2172127> <http://purl.obolibrary.org/obo/RO_0000057> <http://www.ncbi.nlm.nih.gov/gene/5710> 0.9
<http://purl.obolibrary.org/obo/CHEBI_4034> <http://purl.obolibrary.org/obo/RO_0002434> <https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000546491> 0.1
<http://purl.obolibrary.org/obo/CHEBI_49662> <http://purl.obolibrary.org/obo/RO_0002434> <https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000344604> 0.231
<http://purl.obolibrary.org/obo/PR_P63010> <http://purl.obolibrary.org/obo/RO_0002436> <http://purl.obolibrary.org/obo/PR_P51812> 0.111
<http://purl.obolibrary.org/obo/MONDO_0009452> <http://purl.obolibrary.org/obo/RO_0002200> <http://purl.obolibrary.org/obo/HP_0001290> 0
<http://purl.obolibrary.org/obo/CHEBI_46195> <http://purl.obolibrary.org/obo/RO_0002434> <https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000546299> 1.0
<http://purl.obolibrary.org/obo/PR_Q8ND25> <http://purl.obolibrary.org/obo/RO_0002512> <https://uswest.ensembl.org/Homo_sapiens/Transcript/Summary?t=ENST00000320619> 0.4291
<http://www.ncbi.nlm.nih.gov/gene/2065> <http://purl.obolibrary.org/obo/RO_0002559> <https://www.ncbi.nlm.nih.gov/snp/rs115311663> 0.1
<http://purl.obolibrary.org/obo/PR_Q13480-2> <http://purl.obolibrary.org/obo/RO_0002436> <http://purl.obolibrary.org/obo/PR_P16333-1> 0.5
<http://purl.obolibrary.org/obo/CHEBI_78802> <http://purl.obolibrary.org/obo/RO_0002436> <http://purl.obolibrary.org/obo/GO_0006875> 0

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