NCBI: something old, something new
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Transcript of NCBI: something old, something new
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NCBI: something old, something new
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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.
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The National Center for Biotechnology Information (NCBI)
Part of National Library of Medicine (NLM) at
National Institutes of Health (NIH)
Bethesda,MD
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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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20100
500,000
1,000,000
1,500,000
2,000,000
2,500,000
3,000,000
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
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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
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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
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Getting Started: NCBI Home Page http://www.ncbi.nlm.nih.gov
Search All Databases in Entrez
Learn more:NewsletterEducationmailing lists
Search resources by name
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NCBI Resources by name
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How to: NCBI help pages
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The NCBI Handbook
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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
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Genetic Testing Registry (GTR)
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BLAST
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Entrez Assembly
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Entrez Genome redesign
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Microbial Genome Resources
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NCBI on Facebook and Twitter
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David Lipman on GenBank 25th Anniversary