large, organized body of persistent data
Databases
databases are designed to ____, ____, ___, components of the data stored within the system
- Update
- Query
- Retrieve
Types of Databases
- Bibliographic
- Molecular Biology DB
Examples of Bibliographic
Journal/Articles
Books
Example of Molecular BiologyDB
Based on level of:
- Curation
- Scope
Index, store and for access of scientific literature
Bibliographic databases
Different models of Bibliographic databases
- Closed acess model
- Open access model
the model in which the publishers hold copyright
- Closed access model
model where content must be available on the internet and is free to acess
Open access model
Example of open access model of public funded research
- NIH and European fundigng agencies
Other example of journal articles
- Pubmed
- Google scholar
- ResearchGate
Example of Books
- EBSCO (E-books)
- NCBI
- frequency that a typical article from a certain journal is cited given a particular year or period
- the higher the impact factor, the more prestigious is the journal/better to publish in
Impact Factor
provide an indication of an acaemic journal’s impact and quality relative to other journals in their field
Journal ranking
types of databases based on level of curation
- Archival or primary databases
- Derived or curated database
- Direct submission by researchers
- usually experimental data
Archival or primary databases
Contain experimental data in Archival/Primary databases
- DNA & protein sequences (with annotation)
- Nucleic acid & protein structures (with annotation)
- Protein expression patterns
What is included in Derived/Curated databases
- Sequence motifs
- Mutations & variants in DNA or protein
- Classification/relationships
Types of databases based on level of scope
- Nucleotide
- Protein
- Protein structure
- Genomes and Maps
- Systems/Pathways
- Organism-centered
Provides a comprehensive, high quality and freely-acessible resource of protein sequence and functional information
Protein sequence database: UniProt
Two sections of UniProt
- UniProtKB/Swiss-prot
- UniProtKB/TrEMBL
What is the organism-centered database for Homo sapiens?
UCSC Genome Browser – https://genome.ucsc.edu
What is the organism-centered database for Arabidopsis?
TAIR (The Arabidopsis Information Resource)
What is the organism-centered database for Drosophila?
FlyBase
