NCBI: something old, something new

What is NCBI?

• Create automated systems for knowledge about molecular biology, biochemistry, and genetics.

• Perform research into advanced methods of analyzing and interpreting molecular biology data.

• Enable biotechnology researchers and medical care personnel to use the systems and methods developed.

On November 4, 1988 that President Ronald Reagan signed the Health Omnibus Extension Act to create The National Center for Biotechnology Information as part of National Library of Medicine at NIH.

The National Center for Biotechnology Information (NCBI)

Part of National Library of Medicine (NLM) at

National Institutes of Health (NIH)

Bethesda,MD

NCBI: down on the farm

• Genome assembly and annotation

• Pre-computed relationships for:– Protein clusters– “Nearby” nucleic acid– EST unigene clusters– Putative homologous

genes– Conserved protein domains– SNPs– Reciprocal links

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Web users: 2.7 million per day

Data downloaded: 23 TB per dayPeak web hits: 7,000 per second

Web page views: 26 million per day

NCBI Daily Users

NCBI: Integrated platform for data analysis and visualization

Primary Data sets: BioProject, BioSample, Genome, Assembly, AnnotationCurated data sets: Refseq genomes, Gene, Protein Clusters, Pathogenic Factors, Targeted LociEntrez search and retrieval systemAnalysis Tools: Annotation pipeline, genome alignments, protein clustering, multiple alignments, (assembly, SNP)Validation Tools: assembly and annotation quality assesmentVisualization Tools: genomeMap, distance tree, proteinMap, Genome Comparison

How to navigate through NCBI resources

Text search in Entrez Search in MapViewer All databases Marker/gene name

Specialized databases Accession # Use limits page Organism name

Sequence search Pre-computed similaritiesBLAST Blink Genome BLAST CDD

Splign/ProSplign TaxPlot

Use Genome specific resources

Getting Started: NCBI Home Page http://www.ncbi.nlm.nih.gov

Search All Databases in Entrez

Learn more:NewsletterEducationmailing lists

Search resources by name

NCBI Resources by name

How to: NCBI help pages

The NCBI Handbook

Keeping up with what’s new

NCBI News on Bookshelf

www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=newsncbi

NCBI News on Bookshelf

www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=newsncbi

Genetic Testing Registry (GTR)

BLAST

Entrez Assembly

Entrez Genome redesign

Microbial Genome Resources

NCBI on Facebook and Twitter

David Lipman on GenBank 25th Anniversary