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This Week in Nucleic Acids Research: Nov 13, 2013

A German-led team presents an updated online resource produced by members of the Human Phenotype Ontology project. The site describes nearly 10,100 classes and more than 13,300 sub-classes of unusual phenotypes in humans, study authors note, as well as annotations for almost 7,300 hereditary conditions. "The HPO aims to provide a powerful and manually curated resource to support efforts to discover disease sub-classes and to translate this knowledge into clinical care, by providing the means to capture, store, and exchange phenotypic data," they write. "The clinical data that have been captured in this fashion are computable and can be easily integrated into computational algorithms for translational biomedical research."

Investigators from Italy and the US outline a database designed to catalog pan-genomic patterns from sequenced microbial genomes and metagenomes, including some metagenomic samples assessed for the Human Microbiome Project. The online site houses information mined from thousands of bacterial, archaeal, and metagenomic datasets for gene family information — from core and pan genome patterns to gene family conservation, phylogeny, and function — the study authors note. The database "identifies and reports each family present in at least one genome, organizing them into pan, core, or maker families, reconciles their functional annotations when possible, and systematically surveys their presence in multiple body sites of the human microbiome," they write.

In an effort to boost ties between translational genomics and molecular breeding research for soybeans, a University of Missouri team has updated an online resource known as the soybean knowledge base, or SoyKB. Along with data organized by gene/protein, small RNA, SNP, metabolite, and plant line classifications, those involved say the site contains several sets of data stemming from omic, molecular breeding, and soybean trait studies. Additional data types are incrementally incorporated into SoyKB, they note, as are tools for working with and interpreting information from the database.

The Scan

Not as High as Hoped

The Associated Press says initial results from a trial of CureVac's SARS-CoV-2 vaccine suggests low effectiveness in preventing COVID-19.

Finding Freshwater DNA

A new research project plans to use eDNA sampling to analyze freshwater rivers across the world, the Guardian reports.

Rise in Payments

Kaiser Health News investigates the rise of payments made by medical device companies to surgeons that could be in violation of anti-kickback laws.

Nature Papers Present Ginkgo Biloba Genome Assembly, Collection of Polygenic Indexes, More

In Nature this week: a nearly complete Ginkgo biloba genome assembly, polygenic indexes for dozens of phenotypes, and more.