A corpus of GA4GH phenopackets: case-level phenotyping for genomic diagnostics and discovery

Human Genetics and Genomics Advances, Journal Year: 2024, Volume and Issue: 6(1), P. 100371 - 100371

Published: Oct. 11, 2024

Language: Английский

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Connecting electronic health records to a biomedical knowledge graph to link clinical phenotypes and molecular endotypes in atopic dermatitis

Scientific Reports, Journal Year: 2025, Volume and Issue: 15(1)

Published: Jan. 24, 2025

Precision medicine is defined by the U.S. Food & Drug Administration as "an innovative approach to tailoring disease prevention and treatment that considers differences in people's genes, environments, lifestyles". To succeed providing personalized patients, it will be necessary integrate medical, biological molecular data order identify all complex subtypes understand their pathobiological mechanism. Since biomedical knowledge graphs (BKGs) are limited integration of prior do not real-world (RWD) would allow for incorporation patient level information, we propose a first step towards using RWD, BKGs graph machine learning (ML) enable fully integrated precision strategy. In this study, established link between RWD BKG. Our methodology introduced novel representation ML applied This facilitated interpretation extension findings, particularly subtype identification with contained We our deepen understanding atopic dermatitis, condition underlying pathophysiological Through analysis, identified seven subgroups patients each characterized clinical genomic characteristics.

Language: Английский

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The power of mouse models in the diagnostic odyssey of patients with rare congenital anomalies

Mammalian Genome, Journal Year: 2025, Volume and Issue: unknown

Published: March 18, 2025

Abstract Congenital anomalies are structural or functional abnormalities present at birth, which can be caused by genetic environmental influences. The availability of genome sequencing has significantly increased our understanding congenital anomalies, but linking variant identification to relevance and definitive diagnosis remains challenging. Many genes have unknown poorly understood functions, with a lack clear genotype-to-phenotype correlations, it difficult move from discovery diagnosis. Thus, for most there still exists “diagnostic odyssey” presents significant burden patients, families society. Animal models essential in the gene process because they allow researchers validate candidate function disease progression within intact organisms. However, use advanced model systems continues limited due complexity efficiently generating clinically relevant animals. Here we focus on precisely engineered mice variant-to-function studies resolving molecular diagnoses creating powerful preclinical covering advances genomics, editing phenotyping approaches as well necessity future initiatives aligning animal modelling deep patient multimodal datasets.

Language: Английский

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Towards a standard benchmark for phenotype-driven variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework

BMC Bioinformatics, Journal Year: 2025, Volume and Issue: 26(1)

Published: March 22, 2025

Computational approaches to support rare disease diagnosis are challenging build, requiring the integration of complex data types such as ontologies, gene-to-phenotype associations, and cross-species into variant gene prioritisation algorithms (VGPAs). However, performance VGPAs has been difficult measure is impacted by many factors, for example, ontology structure, annotation completeness or changes underlying algorithm. Assertions capabilities often not reproducible, in part because there no standardised, empirical framework openly available patient assess efficacy VGPAs—ultimately hindering development effective tools. In this paper, we present our benchmarking tool, PhEval, which aims provide a standardised evaluate phenotype-driven VGPAs. The inclusion test corpora corpus generation tools PhEval suite allows open comparison methods on sets. solve issues availability experimental tooling configuration when comparing By providing cohorts from real-world case-reports controlling evaluated VGPAs, enables transparent, portable, comparable reproducible As these key component diagnostic pipelines, thorough method assessment essential improving care

Language: Английский

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Non-coding RNAs (miRNAs – circRNAs - lncRNAs) and genes interact with the regulation of vitiligo

Archives of Dermatological Research, Journal Year: 2025, Volume and Issue: 317(1)

Published: April 5, 2025

Language: Английский

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An update on knowledge graphs and their current and potential applications in drug discovery

Expert Opinion on Drug Discovery, Journal Year: 2025, Volume and Issue: unknown, P. 1 - 21

Published: April 14, 2025

Knowledge graphs are becoming prominent tools in computational drug discovery. They effectively integrate heterogeneous biomedical data and generate new hypotheses knowledge. This article is based on a literature review using Google Scholar PubMed to retrieve articles existing knowledge relevant the discovery field. The authors compare types of entities, relationships, sources they encompass. Additionally, provide examples their use field discuss potential strategies for advancing this research area. crucial discovery, but construction leads challenges integration consistency. Future should prioritize standardization modeling. More efforts needed diverse types, such as chemical structures epigenetic data, enhance effectiveness. advancements large language models be pursued aid development graphs, intuitive querying capabilities non-expert users, explain -derived predictions, thereby making these more accessible insights interpretable wider audience.

Language: Английский

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Developing Contextual Ontology for Chronic Diseases: AI-Enhanced Extension and Prediction in an Asthma Case Study

Applied Sciences, Journal Year: 2025, Volume and Issue: 15(8), P. 4353 - 4353

Published: April 15, 2025

The growing complexity and interdependence of healthcare data, especially for chronic diseases such as asthma, demand innovative approaches effective knowledge representation. This study introduces a general contextual ontology model diseases, extended specifically to asthma. Leveraging real-world datasets, the asthma integrates key factors symptoms, triggers, treatments, patient demographics, providing comprehensive framework disease management. was validated using intrinsic metrics classification, reusability, completeness in applications. To validate ontology, we used decision trees extract rules after identifying most relevant parameters needed generate Semantic Web Rule Language. These facilitate reasoning, validation, decision-making within ontology. results highlight potential developing extending it address specific We designed by integrating with artificial intelligence algorithms, parameters, extracting enhance representation support clinical decision-making. can be applied other case studies.

Language: Английский

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The 2024 Nucleic Acids Research database issue and the online molecular biology database collection

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(D1), P. D1 - D9

Published: Nov. 30, 2023

Abstract The 2024 Nucleic Acids Research database issue contains 180 papers from across biology and neighbouring disciplines. There are 90 reporting on new databases 83 updates resources previously published in the Issue. Updates most recently elsewhere account for a further seven. acid include NAKB structural information Genbank, ENA, GEO, Tarbase JASPAR. Issue's Breakthrough Article concerns NMPFamsDB novel prokaryotic protein families AlphaFold Protein Structure Database has an important update. Metabolism is covered by Reactome, Wikipathways Metabolights. Microbes RefSeq, UNITE, SPIRE P10K; viruses ViralZone PhageScope. Medically-oriented familiar COSMIC, Drugbank TTD. Genomics-related Ensembl, UCSC Genome Browser Monarch. New arrivals cover plant imaging (OPIA PlantPAD) crop plants (SoyMD, TCOD CropGS-Hub). entire Issue freely available online website (https://academic.oup.com/nar). Over last year NAR Molecular Biology Collection been updated, reviewing 1060 entries, adding 97 eliminating 388 discontinued URLs bringing current total to 1959 databases. It at http://www.oxfordjournals.org/nar/database/c/.

Language: Английский

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A corpus of GA4GH Phenopackets: case-level phenotyping for genomic diagnostics and discovery

medRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: May 29, 2024

Summary The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 approved by ISO as a standard sharing clinical genomic information about an individual, including phenotypic descriptions, numerical measurements, genetic information, diagnoses, treatments. A phenopacket can be used input file software that supports phenotype-driven diagnostics algorithms facilitate patient classification stratification identifying new diseases There has been great need collection of phenopackets to test pipelines algorithms. Here, we present phenopacket-store. Version 0.1.12 phenopacket-store includes 4916 representing 277 Mendelian chromosomal associated with 236 genes, 2872 unique pathogenic alleles curated from 605 different publications. This represents the first large-scale case-level, standardized derived case reports literature detailed descriptions data will useful many purposes, development testing prioritizing genes diagnostic genomics, machine learning analysis phenotype data, stratification, genotype-phenotype correlations. corpus also provides best-practice examples curating literature-derived using GA4GH Schema.

Language: Английский

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Towards a standard benchmark for variant and gene prioritisation algorithms: PhEval - Phenotypic inference Evaluation framework

bioRxiv (Cold Spring Harbor Laboratory), Journal Year: 2024, Volume and Issue: unknown

Published: June 16, 2024

Computational approaches to support rare disease diagnosis are challenging build, requiring the integration of complex data types such as ontologies, gene-to-phenotype associations, and cross-species into variant gene prioritisation algorithms (VGPAs). However, performance VGPAs has been difficult measure is impacted by many factors, for example, ontology structure, annotation completeness or changes underlying algorithm. Assertions capabilities often not reproducible, in part because there no standardised, empirical framework openly available patient assess efficacy - ultimately hindering development effective tools.

Language: Английский

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