Current status and new features of the Consensus Coding Sequence database

@article{Farrell2014CurrentSA,
  title={Current status and new features of the Consensus Coding Sequence database},
  author={Catherine M. Farrell and Nuala A. O'Leary and Rachel A. Harte and Jane E. Loveland and Laurens G. Wilming and Craig Wallin and Mark E. Diekhans and Daniel Barrell and Stephen M. J. Searle and Bronwen L. Aken and Susan M. Hiatt and Adam Frankish and Marie-Marthe Suner and Bhanu Rajput and Charles A. Steward and Garth R. Brown and Ruth Bennett and Michael R. Murphy and Wendy Wu and Mike P. Kay and Jennifer Hart and Jeena Rajan and Janet Weber and Catherine Snow and Lillian D. Riddick and Toby Hunt and David Webb and Mark Thomas and Pamela Tamez and Sanjida H. Rangwala and Kelly M. McGarvey and Shashikant Pujar and Andrei Shkeda and Jonathan M. Mudge and Jose Manuel Gonzalez and James G. R. Gilbert and Stephen J. Trevanion and Robert Baertsch and Jennifer L. Harrow and Tim J. P. Hubbard and James Ostell and David Haussler and Kim D. Pruitt},
  journal={Nucleic Acids Research},
  year={2014},
  volume={42},
  pages={D865 - D872}
}
The Consensus Coding Sequence (CCDS) project (http://www.ncbi.nlm.nih.gov/CCDS/) is a collaborative effort to maintain a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assemblies by the National Center for Biotechnology Information (NCBI) and Ensembl genome annotation pipelines. Identical annotations that pass quality assurance tests are tracked with a stable identifier (CCDS ID). Members of the collaboration, who are from NCBI, the… 

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References

SHOWING 1-10 OF 35 REFERENCES
The consensus coding sequence (CCDS) project: Identifying a common protein-coding gene set for the human and mouse genomes.
TLDR
The CCDS database centralizes the function of identifying well-supported, identically-annotated, protein-coding regions and indicates that the entries in the CCDS set are highly likely to represent real proteins, more so than annotations from contributing groups not included in CCDS.
NCBI Reference Sequences (RefSeq): current status, new features and genome annotation policy
TLDR
Recent growth, the status of curating the human RefSeq data set, more extensive feature annotation and current policy for eukaryotic genome annotation via the NCBI annotation pipeline are reported on.
GenBank
TLDR
GenBank® is a comprehensive database that contains publicly available nucleotide sequences for over 340 000 formally described species and integrates these records with a variety of other data including taxonomy nodes, genomes, protein structures, and biomedical journal literature in PubMed.
GENCODE: the reference human genome annotation for The ENCODE Project.
TLDR
This work has examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites, and over one-third of GENCODE protein-Coding genes aresupported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas.
Locus Reference Genomic sequences: an improved basis for describing human DNA variants
TLDR
It is hoped that widespread adoption of LRGs - which will be created and maintained by the NCBI and the European Bioinformatics Institute - along with consistent use of the Human Genome Variation Society (HGVS)-approved variant nomenclature will reduce errors in the reporting of variants in the literature and improve communication about variants affecting human health.
Tracking and coordinating an international curation effort for the CCDS Project
TLDR
The relevant background and reasoning behind the curation standards that are developed for CCDS database treatment of transcripts that are nonsense-mediated decay (NMD) candidates, for transcripts containing upstream open reading frames, for identifying the most likely translation start codons and for the annotation of readthrough transcripts are presented.
The vertebrate genome annotation (Vega) database
TLDR
The Vertebrate Genome Annotation (Vega) database was first made public in 2004 and now contains comprehensive annotation on 20 of the 24 human chromosomes, four whole mouse chromosomes and around 40% of the zebrafish Danio rerio genome.
The International Nucleotide Sequence Database Collaboration
TLDR
The INSDC is introduced, data growth patterns are outlined and the challenges of increased growth are commented on, with a clear mark on INSDC strategy.
The Universal Protein Resource (UniProt) in 2010
The primary mission of UniProt is to support biological research by maintaining a stable, comprehensive, fully classified, richly and accurately annotated protein sequence knowledgebase, with
Ensembl 2013
TLDR
The Ensembl project provides genome information for sequenced chordate genomes with a particular focus on human, mouse, zebrafish and rat, as well as variation data resources for 17 species and regulation annotations based on ENCODE and other data sets.
...
...