The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 and approved by ISO as a standard for sharing clinical and genomic information about an individual, including phenotypic descriptions, numerical measurements, genetic information, diagnoses, and treatments. A phenopacket can be used as an input file for software that supports phenotype-driven genomic diagnostics and for algorithms that facilitate patient classification and stratification for identifying new diseases and treatments. There has been a great need for a collection of phenopackets to test software pipelines and algorithms. Here, we present Phenopacket Store. Phenopacket Store v.0.1.19 includes 6,668 phenopackets representing 475 Mendelian and chromosomal diseases associated with 423 genes and 3,834 unique pathogenic alleles curated from 959 different publications. This represents the first large-scale collection of case-level, standardized phenotypic information derived from case reports in the literature with detailed descriptions of the clinical data and will be useful for many purposes, including the development and testing of software for prioritizing genes and diseases in diagnostic genomics, machine learning analysis of clinical phenotype data, patient stratification, and genotype-phenotype correlations. This corpus also provides best-practice examples for curating literature-derived data using the GA4GH Phenopacket Schema.
- Klíčová slova
- global alliance for genomics and health, human phenotype ontology, phenopacket schema,
- MeSH
- databáze genetické MeSH
- fenotyp * MeSH
- genomika * metody MeSH
- lidé MeSH
- software MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
The Global Alliance for Genomics and Health (GA4GH) Phenopacket Schema was released in 2022 and approved by ISO as a standard for sharing clinical and genomic information about an individual, including phenotypic descriptions, numerical measurements, genetic information, diagnoses, and treatments. A phenopacket can be used as an input file for software that supports phenotype-driven genomic diagnostics and for algorithms that facilitate patient classification and stratification for identifying new diseases and treatments. There has been a great need for a collection of phenopackets to test software pipelines and algorithms. Here, we present phenopacket-store. Version 0.1.12 of phenopacket-store includes 4916 phenopackets representing 277 Mendelian and chromosomal diseases associated with 236 genes, and 2872 unique pathogenic alleles curated from 605 different publications. This represents the first large-scale collection of case-level, standardized phenotypic information derived from case reports in the literature with detailed descriptions of the clinical data and will be useful for many purposes, including the development and testing of software for prioritizing genes and diseases in diagnostic genomics, machine learning analysis of clinical phenotype data, patient stratification, and genotype-phenotype correlations. This corpus also provides best-practice examples for curating literature-derived data using the GA4GH Phenopacket Schema.
- Publikační typ
- časopisecké články MeSH
- preprinty MeSH
The Human Phenotype Ontology (HPO) is a widely used resource that comprehensively organizes and defines the phenotypic features of human disease, enabling computational inference and supporting genomic and phenotypic analyses through semantic similarity and machine learning algorithms. The HPO has widespread applications in clinical diagnostics and translational research, including genomic diagnostics, gene-disease discovery, and cohort analytics. In recent years, groups around the world have developed translations of the HPO from English to other languages, and the HPO browser has been internationalized, allowing users to view HPO term labels and in many cases synonyms and definitions in ten languages in addition to English. Since our last report, a total of 2239 new HPO terms and 49235 new HPO annotations were developed, many in collaboration with external groups in the fields of psychiatry, arthrogryposis, immunology and cardiology. The Medical Action Ontology (MAxO) is a new effort to model treatments and other measures taken for clinical management. Finally, the HPO consortium is contributing to efforts to integrate the HPO and the GA4GH Phenopacket Schema into electronic health records (EHRs) with the goal of more standardized and computable integration of rare disease data in EHRs.
Over two decades, the checklist has risen to prominence in healthcare improvement. This paper contributes to the debate between its proponents and critics, making the case for an Science and Technology Studies-informed understanding of the checklist that demonstrates the limitations of both the "checklist-as-panacea" and "checklist-as-socially-determined" positions. Attending to the checklist as a socio-material object endowed with affordances that call upon clinicians to act (Allen 2012, Hutchby 2001), the study revisits the efforts of a recent improvement initiative, the Enhanced Peri-Operative Care for High-risk patients trial. Rather than a singularised simple tool, this study discusses four different and relationally enacted logics of the checklist as a stop and check tool, a clinical prompt, an audit tool and a clinical record. Each logic is associated with specific temporality, beneficiaries, relationship with material forms, and interpellates (Law 2002) clinicians to initiate specific actions which can conflict. The paper seeks to make the case for intervention to improve such tools and consciously account for the consequences of their design and materiality and calls for supporting such settings and arrangements in which incoherences collected in tools can be locally negotiated.
- Klíčová slova
- affordances, checklist, healthcare improvement, multiple logics, socio-material infrastructures,
- MeSH
- kontrolní seznam * MeSH
- lidé MeSH
- poskytování zdravotní péče * MeSH
- zlepšení kvality * MeSH
- Check Tag
- lidé MeSH
- Publikační typ
- časopisecké články MeSH
- práce podpořená grantem MeSH
