Super-basic intro to NCBI. Meant to accompany live demo

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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