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INTRODUCTION OF DATABASES

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DATABASE

  • Store useful information
  • Store data for sharing and reuse
  • When and where to use the information

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STORING INFORMATION

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NCBI

https://www.ncbi.nlm.nih.gov/

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NCBI

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PUBMED

  • Most widely used platform for literature searching.

https://pubmed.ncbi.nlm.nih.gov/

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PUBMED

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PUBMED

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GENBANK

https://www.ncbi.nlm.nih.gov/genbank/

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GENBANK

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GENBANK

  • Locus: ID
  • Source: species
  • Features: gene, CDS …
    • source: whole genome
    • gene
      • Position
      • Gene name
    • CDS
      • Note: function
      • Protein name
      • Start coden
      • Sequence
    • Regulatory
      • class
      • Influence gene

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REFSEQ

https://www.ncbi.nlm.nih.gov/refseq/

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REFSEQ

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REFSEQ

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�ENSEMBL�

https://asia.ensembl.org/index.html

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�ENSEMBL�

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�ENSEMBL�

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EMBL-EBI

https://www.ebi.ac.uk/

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EMBL-EBI

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RNA-SEQ

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REFSEQ FTP

https://ftp.ncbi.nlm.nih.gov/refseq/

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REFSEQ FTP

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REFSEQ FTP

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GFF FORMAT

  1. seqname - name of the chromosome
  2. source - database or project name
  3. feature - feature type name, e.g. Gene, Variation, Similarity
  4. start - Start position of the feature
  5. end - End position of the feature

​

  1. score - A floating point value.
  2. strand - defined as + (forward) or - (reverse).
  3. frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..
  4. attribute - A semicolon-separated list of tag-value pairs, providing additional information about each feature.

​

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GEO

https://www.ncbi.nlm.nih.gov/geo/

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GEO

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USCS GENOME BROWSER

https://genome.ucsc.edu/

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USCS GENOME BROWSER

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USCS GENOME BROWSER

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PROTEOMICS

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UNIPROT

https://www.uniprot.org/

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UNIPROT

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UNIPROT

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PRIDE

https://www.ebi.ac.uk/pride/

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PRIDE

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PROTEIN STRUCTURE

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PROTEIN DATA BANK

https://www.rcsb.org/

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PROTEIN DATA BANK

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PROTEIN DATA BANK

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PROTEIN DATA BANK

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FUNCTIONS

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GO – GENE ONTOLOGY

http://geneontology.org/

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GO – GENE ONTOLOGY

https://www.biostars.org/p/450726/

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KEGG

https://www.genome.jp/kegg/

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KEGG

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KEGG

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PFAM

http://pfam.xfam.org/

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PFAM

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RFAM

https://rfam.xfam.org/

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RFAM

https://rfam.xfam.org/

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RFAM

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CANCER OMICS DATA

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TCGA

https://portal.gdc.cancer.gov/

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TCGA

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TCGA

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CPTAC

https://proteomics.cancer.gov/programs/cptac

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CPTAC