Lecture 2C: Databases

Question 1

• large, organized body of persistent data
• designed to update, query, retrieve components of the data stored within the system
• may be private or public

Answer 1

Databases

Question 2

What is the main purpose of databases? (2)

Answer 2

• Storage
• Retrieval of data

Question 3

What are the three key operations in databases? (3)

Answer 3

• entry
• value
• query

Question 4

Two main types of databeses (2)

Answer 4

• Bibliographic
• Molecular biology DB

Question 5

What are examples of bibliographic databases? (2)

Answer 5

• journal/articles
• books

Question 6

Molecular biology databases can be classified based on what two factors? (2)

Answer 6

• level of curation
• level of scope

Question 7

Index, store and for access of scientific literature

Answer 7

Bibliographic databases

Question 8

What are the two models of bibliographic databases? (2)

Answer 8

• Closed access model
• Open access model

Question 9

Models of Bibliographic databases

publishers hold copyright

Answer 9

Closed access model

Question 10

Models of Bibliographic databases

content must be available on the internet and is free to access/no cost (especially for publicly-funded research — NIH and some European funding agencies)

Answer 10

Open access model

Question 11

Bibliographic databases

When did the open access model start becoming common?

Answer 11

mid-2000s

Question 12

Bibliographic databases

Where are open access journals indexed?

Answer 12

Directory of Open Access Journals (http://www.doaj.org)

Question 13

Give examples of bibliographic databases for journals/articles. (3)

Answer 13

• PubMed
• Google Scholar
• ResearchGate

Question 14

Give examples of bibliographic databases for books. (2)

Answer 14

• EBSCO (E-books)
• NCBI (National Center for Biotechnology Information) Books

Question 15

Useful metrics in bliographic databases (2)

Answer 15

• impact factor
• journal ranking

Question 16

Frequency that a typical article from a certain journal is cited given a particular year or period

Answer 16

Impact factor

Question 17

What does a higher Impact Factor indicate?

Answer 17

The journal is more prestigious/better to publish in

Question 18

Provides an indication of an academic journal’s impact and quality relative to other journals in their field

Answer 18

Journal ranking

Question 19

Give an example of a tool for Journal Ranking. (2)

Answer 19

• Scimago
• Scopus Journal Analyzer

Question 20

What are the two types of molecular biology databases based on curation? (2)

Answer 20

• Archival or primary databases
• Derived or curated databases

Question 21

What are the types of molecular biology databases based on scope? (6)

Answer 21

• Nucleotide
• Protein
• Protein Structure
• Genomes and Maps
• System/Pathway
• Organism-centered

Question 22

Databases that are direct submission by researchers; usually experimental data

Answer 22

Archival or primary databases

Question 23

What types of data are included in archival databases? (3)

Answer 23

• DNA and protein sequences (with annotation)
• nucleic acid and protein structures (with annotation)
• protein expression patterns

Question 24

Databases that contain information collected from the archival databanks and from the analysis of their contents

Answer 24

derived or curated databases

Question 25

What types of data are included in derived or curated databases? (3)

Answer 25

- sequence motifs - mutations and variants in DNA or protein - classification or relationships

Question 26

Give examples of nucleotide databases. (3)

Answer 26

- GenBank - EMBL-EBI (European Molecular Biology Laboratory-European Bioinformatics Institute) - DDJB (DNA Data Bank of Japan)

Question 27

Give examples of protein databases. (2)

Answer 27

- Swiss-Prot - PIR-International

Question 28

Give examples of protein structure databases. (2)

Answer 28

- PDB (Protein Data Bank) - MMDB (Molecular Modeling DataBase)

Question 29

Give an example of genomes and maps database. (1)

Answer 29

Entrez Genomes

Question 30

Give an example of systems/pathways database (1)

Answer 30

KEGG (Kyoto Encyclopedia of Genes and Genomes)

Question 31

A comprehensive, high-quality and freely accessible resource of protein sequence and functional information.

Answer 31

UniProt

Question 32

What are the two sections of UniProt? (2)

Answer 32

- UniProtKB/Swiss-Prot - UniProtKB/TrEMBL

Question 33

Give the organism-centered database for *Homo sapiens*.

Answer 33

https://genome.ucsc.edu

Question 34

Give the organism-centered database for Arabidopsis.

Answer 34

The Arabidopsis Information Resource (TAIR)

Question 35

Give the organism-centered database for Drosophila.

Answer 35

FlyBase

Question 36

Give the organism-centered database for Nematodes.

Answer 36

WormBase

Question 37

Give the organism-centered database for Saccharomyces.

Answer 37

Yeast Genome Database

Question 38

Give the organism-centered database for Plants.

Answer 38

Gramene

Question 39

Give the organism-centered database for Corn.

Answer 39

MaizeGDB

Question 40

Name two organism-centered databases for plants aside from Gramene and MaizeGDB. (2)

Answer 40

- Tree Fruit Genome Database - Ornamental Plant Database

Question 41

Give the organism-centered database for marine species.

Answer 41

World Register of Marine Species (WoRMS)

Question 42

What type of databases are included for microbes?

Answer 42

Microbial Genome Databases