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Biodatabases

This document provides an overview of essential biodiversity databases crucial for genomic research. It includes links to global resources like the National Center for Biotechnology Information (NCBI), European Molecular Biology Laboratory (EMBL), and DNA Data Bank of Japan (DDBJ). Additionally, it covers protein and RNA databases such as the Protein Data Bank (PDB), Swiss-Prot/trEMBL, and various RNA databases. The significance of literature retrieval tools like Medline and Entrez for literature citation searches is also discussed, highlighting their role in ensuring accurate scientific communication and data accuracy.

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Biodatabases

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  1. Biodatabases

  2. WWW • Deposit before you publish • Literature

  3. Google (v) • From noun to verb • How does PageRank work?

  4. NCBI-EMBL-DBJ • National Center for Biotechnology Informationhttp://www.ncbi.nlm.nih.gov/ • European Molecular Biology Labhttp://www1.embl-heidelberg.de/ • DNA Data Bank Japanrhttp://www.ddbj.nig.ac.jp/

  5. Protein databases • Protein Data Bank (PDB)http://www.rcsb.org/pdb/ • Swiss Prot / trEMBLhttp://us.expasy.org/sprot/

  6. Tigr • The Institute for Genomic Research (microbes)http://www.tigr.org/

  7. Rna databases • Small Rna databasehttp://mbcr.bcm.tmc.edu/smallRNA/smallrna.html • rRna databasehttp://rrna.uia.ac.be/ • Ribosomal databasehttp://rdp.cme.msu.edu/html/

  8. KEGG • Kyoto encyclopedia of genes and genomes • http://www.genome.ad.jp/kegg/kegg2.html

  9. Medline • http://www.ncbi.nlm.nih.gov/PubMed/ • Medline citations

  10. Entrez • http://www.ncbi.nlm.nih.gov/Entrez/ • Retrieval from multiple databases

  11. Omim • http://www.ncbi.nlm.nih.gov/omim/ • Human genes and genetic disorders

  12. Nucleic Acids Research • Nucleic Acids Research (DB issue)http://nar.oupjournals.org/content/vol31/issue1/index.shtml

  13. Sequence Retrieval System • http://srs.embl-heidelberg.de:8000/srs5/

  14. Automated retrieval • How do you do a large number of queries?

  15. Bio-GIGO? • ‘Genome’ (s) vs. diverse genetic pool • Errors or snp’s? • Duplicate, overlapping and contradictory data

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