Abstract
The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome ...annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community.
Abstract
Ensembl (https://www.ensembl.org) is a freely available genomic resource that has produced high-quality annotations, tools, and services for vertebrates and model organisms for more than two ...decades. In recent years, there has been a dramatic shift in the genomic landscape, with a large increase in the number and phylogenetic breadth of high-quality reference genomes, alongside major advances in the pan-genome representations of higher species. In order to support these efforts and accelerate downstream research, Ensembl continues to focus on scaling for the rapid annotation of new genome assemblies, developing new methods for comparative analysis, and expanding the depth and quality of our genome annotations. This year we have continued our expansion to support global biodiversity research, doubling the number of annotated genomes we support on our Rapid Release site to over 1700, driven by our close collaboration with biodiversity projects such as Darwin Tree of Life. We have also strengthened support for key agricultural species, including the first regulatory builds for farmed animals, and have updated key tools and resources that support the global scientific community, notably the Ensembl Variant Effect Predictor. Ensembl data, software, and tools are freely available.
Graphical Abstract
Graphical Abstract
To Right These Wrongs Korstad, Robert Rodgers; Leloudis, James; Barnes, Billy
01/2011
eBook
When Governor Terry Sanford established the North Carolina Fund in 1963, he saw it as a way to provide a better life for the "tens of thousands whose family income is so low that daily subsistence is ...always in doubt." Illustrated with evocative photographs by Billy Barnes,To Right These Wrongsoffers a lively account of this pioneering effort in America's War on Poverty.Robert Korstad and James Leloudis describe how the Fund's initial successes grew out of its reliance on private philanthropy and federal dollars and its commitment to the democratic mobilization of the poor. Both were calculated tactics designed to outflank conservative state lawmakers and entrenched local interests that nourished Jim Crow, perpetuated one-party politics, and protected an economy built on cheap labor. By late 1968, when the Fund closed its doors, a resurgent politics of race had gained the advantage, led by a Republican Party that had reorganized itself around opposition to civil rights and aid to the poor.The North Carolina Fund came up short in its battle against poverty, but its story continues to be a source of inspiration and instruction for new generations of Americans.
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