Phenotype informatics

Phenotype informatics

Phenotype informatics

Phenotypes are the observable consequences of genotype, environment, and their interaction, and they remain the principal currency by which disease is recognised, model organisms are characterised, and plant traits are catalogued. Our work develops the informatics infrastructure that makes phenotype data computable across species and clinical settings: the phenotype ontologies themselves, the cross-species crosswalks that link them, the tools that capture and standardise phenotype descriptions from text and images, and the computational pipelines that connect phenotype evidence back to genes

DeepViral

Rare disease Phenotype informatics genomics

Predicts virus–host protein-protein interactions from sequence and infectious-disease phenotypes; trained jointly across coronaviruses, influenza, and other RNA viruses. Get it GitHub: https://github.com/bio-ontology-research-group/DeepViral ★ 12 Developed in projects CompleX: Variant Prioritization in Complex Disease Category: Variant and Disease Prioritization

predCAN

Rare disease Phenotype informatics genomics

Ontology-based prediction of cancer driver genes by integrating phenotype, pathway and function knowledge with somatic-variant features. Get it GitHub: https://github.com/bio-ontology-research-group/predCAN ★ 5 Developed in projects CompleX: Variant Prioritization in Complex Disease Category: Variant and Disease Prioritization

GenomeLinter

Rare disease Phenotype informatics genomics

AI-powered clinical decision-support tool that ingests annotated VCFs and synthesises diagnostic interpretations for rare-disease patients without requiring deep bioinformatics expertise. Get it GitHub: https://github.com/bio-ontology-research-group/genome-linter Category: Variant and Disease Prioritization

INDIGENA

Rare disease Phenotype informatics genomics

Inductive prediction of disease–gene associations from phenotype ontologies; generalises to unseen diseases via ontology-aware embeddings. Get it GitHub: https://github.com/bio-ontology-research-group/indigena ★ 1 Developed in projects CompleX: Variant Prioritization in Complex Disease Category: Variant and Disease Prioritization

STARVar

Rare disease Phenotype informatics genomics

Symptom-based tool for automatic ranking of variants using evidence from the biomedical literature and population genomes; combines text mining with phenotype matching. Get it GitHub: https://github.com/bio-ontology-research-group/STARVar ★ 7 Developed in projects CompleX: Variant Prioritization in Complex Disease Category: Variant and Disease Prioritization

EmbedPVP

Rare disease Phenotype informatics genomics

Embedding-based phenotype-aware variant predictor that ranks candidate causative variants using joint sequence- and phenotype-derived representations. Get it GitHub: https://github.com/bio-ontology-research-group/EmbedPVP ★ 8 Developed in projects CompleX: Variant Prioritization in Complex Disease Category: Variant and Disease Prioritization

DeepSVP

Rare disease Phenotype informatics genomics

Prioritizes structural and copy-number variants by combining patient phenotype with gene-function similarity learned from biomedical ontologies. Get it GitHub: https://github.com/bio-ontology-research-group/DeepSVP ★ 18 Developed in projects CompleX: Variant Prioritization in Complex Disease A public Saudi pangenome as reference for genomics in the Middle East Category: Variant and Disease Prioritization

PhenomeNET-VP

Rare disease Phenotype informatics genomics

Phenotype-driven variant prioritization for whole-exome and whole-genome sequencing data; widely used implementation of the phenotype-aware variant ranking approach. Get it GitHub: https://github.com/bio-ontology-research-group/phenomenet-vp ★ 43 Developed in projects CompleX: Variant Prioritization in Complex Disease Category: Variant and Disease Prioritization