The document discusses the National Center for Biotechnology Information (NCBI) and the services and databases it provides. NCBI develops and maintains molecular databases and software tools for searching and analyzing data. It provides a web portal for accessing these data and tools. The databases include those related to biomedical literature, sequences, gene expression, genome maps, structures, pathways and genetic variation. NCBI databases include primary data directly submitted as well as curated data maintained by NCBI. Key databases discussed are GenBank, PubMed, dbSNP, Protein Data Bank and Gene. NCBI provides integrated access to these resources through Entrez and tools for analysis like BLAST, Cn3D and Genome Workbench.

2.  Develop and maintain molecular and bibliographic
databases.
 Develop software for searching, and analysis of
these data.
 Provide Web access point for data and software.
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3.  Sequences
 Expression
 Genome Maps
 3D Structures
 Protein Domains
 Homologous Genes,
Proteins, Structures
 Pathways
 Genetic Variation
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4.  Biomedical Literature
 PubMed, PubMed Central, Bookshelf
 Molecular Databases and Metadatabases
 Sequences, Structures, Variation, Chemicals etc.
 Clinical / Medical Genetics
 GTR, ClinVar, MedGen, OMIM, PubMed Health, dbGaP
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5.  Primary Data /Database
 Results of a particular
technique
 Submitted to NCBI
 Submitter has editorial
control
 Curated Data /Database
 Based on primary
database records
 Third party (NCBI)
maintains and updates
 Often includes additional
analyses
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6.  Sequences (DNA)
 GenBank (International Sequence Database Collaboration)
now 2.1 X 1012 bases
 Sequence Read Archive (SRA), Next-Gen sequence reads now 9.7
X 1015 bases!
 Other databases with a primary component
 Expression
 Gene Expression Omnibus
 RNA-Seq, Microarray, Other high throughput data
 Variation
 dbSNP small scale variants
 dbVar genomic structural studies
 Database of Genotype and Phenotype (dbGaP)
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7.  Sequences
 GenPept translations of CDS regions on INSDC records
 NCBI Reference Sequences (DNA and Protein)
 Variation
 NCBI Reference SNPs (non-redundant set of variants)
 Structures
 NCBI’s MMDB
 based on PDB
 Conserved Domains
 NCBI Conserved Domain Database
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8.  Entrez integrated literature and molecular databases
 Graphical Sequence Viewer annotation viewer and
analysis tool
 BLAST sequence similarity search service
 VAST structure similarity searches
 Cn3D 3D structure viewer
 Genome Workbench standalone sequence analysis
annotation platform
 SRA Utilities
 SRA Run Browser web access for viewing, searching and
downloading next-generation reads
 SRA toolkit standalone SRA manipulator and client
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9. www.ncbi.nlm.nih.gov
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11.  Literature
 PubMed, PMC, Books
 Sequences
 Protein, Nuccore, GSS, SRA, Assembly
 Expression
 GEO profiles
 Variation
 dbSNP, dbVaR
 Protein and Nucleic acid structures
 Structure
 Small Molecules
 PubChem
 Medical Genetics
 ClinVar, MedGen, GTR
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12. Central Resources / Databases
• Taxonomy
• BioProject
• Assembly
• Gene
Follow links to others when
needed
Nucleotide, Protein, SRA
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The Entrez system: 39 (and counting) integrated databases

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14. If your question is about data for ...
 an organism -> Taxonomy
 a gene name -> Gene (common organisms)
 a large-scale project -> BioProject
 a bacterial genome -> Genome
 a genome sequence -> Assembly
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15. Organizes gene-centered data
 Biological role; genomic context; phenotypes; interactions;
literature
 Sequences
 Genomic
 Transcript
 Proteins
 Best entry point for many biomolecular searches
 Eukaryotic and Microbial Genomes
 17.3 million records for 13,566 taxa
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16.  Provide a reference standard
 Represent all molecules in the central dogma
 Selected Eukaryotes
 Genomic
 Transcripts
 Proteins
 All Prokaryotes and Viruses
 Genomic and Protein only
 Maintained by NCBI staff and outside experts
 Distinct accession series
 (NC_, AC_, NG_, NM_, NM_, NR_, XM_, XR_)
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17. Specific gene:
XXX[Symbol] AND YYY[Organism]
APRT[Symbol] AND human[Organism]
apt[Symbol] AND Escherichia coli[Organism]
All genes:
YYY[Organism] AND current only[Filter]
zebrafish[Organism]AND current
only[Filter]
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Protein-Structure Shortcut

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20. UniGene
GEO
Profiles
Expression
HomoloG
ene
Homologs
PubMed
PMC
Literature
Gene
• Genomic Structure
• Orthologs via Gpipe
Structure
Structures
SNP ClinVar
Variation
OMIMdbGaP
Nuccore
Protein
Sequences
Homologs via Blink
Proteins w Structure via
Related Strutures
SRA
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21.  Learn: <ncbi>/learn.shtml
 Factsheets: <ftp>/pub/factsheets/
 NCBI YouTube Channel: (www.youtube.com/ncbinlm)
 NCBI Helpdesk: info@ncbi.nlm.nih.gov
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