Adam Wright
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View article: React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase
React-to-Me: A Conversational Interface for Interactive Exploration of the Reactome Pathway Knowledgebase Open
The Reactome Pathway Knowledgebase ( www.reactome.org ) provides expert-curated information on human biological pathways, molecular interactions, and disease mechanisms. However, its complex data model and keyword-based search interface pr…
View article: The Reactome Knowledgebase 2026
The Reactome Knowledgebase 2026 Open
The Reactome Knowledgebase (https://reactome.org) is a freely accessible, expert-curated, open-source, and open-data resource that describes human biology in molecular detail. It spans normal physiology as well as disease mechanisms, inclu…
View article: Anterior interosseous nerve syndrome: an unusual case of peripheral nerve compression in a high-level baseball pitcher
Anterior interosseous nerve syndrome: an unusual case of peripheral nerve compression in a high-level baseball pitcher Open
Baseball pitchers have commonly been reported to have an increased risk of ulnar neuropathy due to throwing mechanics at the elbow. However, this patient population has a low incidence of other peripheral compressive neuropathies, includin…
View article: Guidelines for gene and genome assembly nomenclature
Guidelines for gene and genome assembly nomenclature Open
The rapid increase in the number of reference-quality genome assemblies presents significant new opportunities for genomic research. However, the absence of standardized naming conventions for genome assemblies and annotations across datas…
View article: WormBase 2024: status and transitioning to Alliance infrastructure
WormBase 2024: status and transitioning to Alliance infrastructure Open
WormBase has been the major repository and knowledgebase of information about the genome and genetics of Caenorhabditis elegans and other nematodes of experimental interest for over 2 decades. We have 3 goals: to keep current with the fast…
View article: Updates to the Alliance of Genome Resources central infrastructure
Updates to the Alliance of Genome Resources central infrastructure Open
The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively studied model organisms. The Alliance is organized as individual knowledge centers with strong con…
View article: FAIR Header Reference genome: a TRUSTworthy standard
FAIR Header Reference genome: a TRUSTworthy standard Open
The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR bioHeaders Reference genome (FHR), a meta…
View article: Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes Open
Germline and somatic mutations can give rise to proteins with altered activity, including both gain and loss-of-function. The effects of these variants can be captured in disease-specific reactions and pathways that highlight the resulting…
View article: FAIR Header Reference genome: A TRUSTworthy standard
FAIR Header Reference genome: A TRUSTworthy standard Open
The lack of interoperable data standards among reference genome data-sharing platforms inhibits cross-platform analysis while increasing the risk of data provenance loss. Here, we describe the FAIR-bioHeaders Reference genome (FHR), a meta…
View article: Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes
Pathway-based, reaction-specific annotation of disease variants for elucidation of molecular phenotypes Open
Disease variant annotation in the context of biological reactions and pathways can provide a standardized overview of molecular phenotypes of pathogenic mutations that is amenable to computational mining and mathematical modeling. Reactome…
View article: Evaluating the Predictive Accuracy of Reactome's Curated Biological Pathways
Evaluating the Predictive Accuracy of Reactome's Curated Biological Pathways Open
Reactome is a database of human biological pathways manually curated from the primary literature and peer-reviewed by experts. To evaluate the utility of Reactome pathways for predicting functional consequences of genetic perturbations, we…