5 votes

Curation at the NCBI: Genomes, Genes, & Sequence Standards

Garth Brown¹, Catherine Farrell¹, Jennifer Hart¹, Melissa Landrum¹, Donna Maglott¹, Bonnie Maidak¹, Michael Murphy¹, Terence Murphy¹, Bhanu Rajput¹, Kim D. Pruitt¹, Lillian Riddick¹, David Webb¹, Janet Weber¹ & Wendy Wu¹

Correspondence: (Login to view email address)

1. National Center for Biotechnology Information (NCBI)

PDF (2.6 MB)

Document Type:

Poster

Date:

Received 26 May 2009 16:13 UTC; Posted 27 May 2009

Subjects:

Genetics & Genomics, Bioinformatics

Tags:

• Entrez Gene
• Genome Annotation
• RefSeq
• CCDS
• transcript
• protein

Abstract:

The National Center for Biotechnology Information (NCBI) provides curation support for many genomes, and disseminates information in several resources including Entrez Gene, reference sequences (RefSeq), the Consensus CDS (CCDS) database, and the Genome Reference Consortium (GRC). These projects are supported by several collaborations to provide:1) support to the international consortium maintaining the assemblies for human and mouse (GRC); 2) sequence standards for chromosomes, genes, transcripts and proteins (RefSeq); 3) reports of integrated information including nomenclature, publications, phenotypes and diseases, sequences, ontologies, interactions (Gene); and 4) identification of proteins that are consistently annotated on the human and mouse reference genomes, and consistently updated by collaborating members (CCDS).

NCBI curation of any one data type (e.g., a gene) is closely integrated with evaluation of the genome assembly, and determining annotation by way of RefSeq transcript and protein sequences. Database and work-flow infrastructure is designed to support reporting and tracking issues with the assembly, gene, or evidence data to collaborating groups, and to support collaborative review and discussions of issues that arise. Curation depends on publicly available information to represent the gene extent, alternatively spliced transcripts, and protein isoforms. Scientific consults occur regularly and wet-bench validation needs are supported by some of the collaborations. Curation of genome annotation results in improved data presentation at the three major genome browser sites (Ensembl, NCBI, UCSC) and has resulted in efforts to define common curation guidelines to maximize consistency and minimize conflicts.

The presentation focuses on curation of the human genome, genes, and RefSeq sequence standards.

Collection:

3rd International Biocuration Conference

Presented at:

3rd International Biocuration Conference, 16 April 2009

Discussion

Votes:

5 votes

(Login to vote)

Comments:

0 comments

(Login to post a comment)

Share:

(Login to share with a colleague)

Additional information

License:

This document is licensed to the public under the Creative Commons Attribution 3.0 License

How to cite this document:

Brown, Garth, Farrell, Catherine, Hart, Jennifer, Landrum, Melissa, Maglott, Donna, Maidak, Bonnie, Murphy, Michael, Murphy, Terence, Rajput, Bhanu, Pruitt, Kim, Riddick, Lillian, Webb, David, Weber, Janet, and Wu, Wendy. Curation at the NCBI: Genomes, Genes, & Sequence Standards. Available from Nature Precedings <http://dx.doi.org/10.1038/npre.2009.3287.1> (2009)

Version info:

Other versions of this document in Nature Precedings

None.

Other versions of this document elsewhere on the web

None known.

Submit a new version link