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Bioinformatics > Theory for bioinformatics > Flashcards

Theory for bioinformatics Flashcards

1
Q

What are databases

A

It is a collection of information stored in a computer medium that can be easily accessed and manipulated.

It is an electronic filling system.

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2
Q

What is a biological database

A

Collection of biological data

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3
Q

What are the uses of database?

A

Handle, share and manage large volumes of biological data.

Store
Maintain
Enter
Search 
Sort
Retrieve and Analyze
Present or Display
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4
Q

What are the 3 general functions of databases?

A

Support large-scale analysis efforts
Make data access easy and updated
Use knowledge from various fields of biology and medicine.

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5
Q

Fields

A

A particular data about a person or thing stored in a database. Usually, it is the column of the table.

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6
Q

Field type/attribute

A

The properties of a data of a particular field such as strings, numeric, date etc

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7
Q

Record and entries

A

A set of fields within a table that are relevant to a specific entity.

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8
Q

Primary key

A

Unique identifier of a record or a field unique to the record.

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9
Q

Secondary key

A

A field used to link up a table with other tables in a database.

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10
Q

Relational database

A

A complex database with many tables and linked by different secondary keys.

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11
Q

Choose the primary key in a relational database

A

Choose a key that has items that are not duplicated.

A primary key can also be a secondary key if it links up another key

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12
Q

What are bibliographic databases?

A

They contain scientific literature

Examples: Pubmed and ScienceDirect

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13
Q

What are taxonomic databases?

A

They contain classification
Examples: Integration taxonomic information system itis.gov, Biodiversity information standards tdwg.org and ncbi taxonomy.

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14
Q

What are nucleic acid databases?

A

They contain DNA information

Examples: NDB, EMBL-Bank, GenBank, DDBJ

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15
Q

What are genomic databases?

A

They contain genome level information

Examples: Ensembl Genome Browser, UCSC Genome Browser, WormBase, AceDB, Comprehensive Microbial Resource and FlyBase

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16
Q

What are protein databases

A

They contain protein information

17
Q

What are protein families, domains and functional sites databases

A

They contain classification of proteins and identifying domains information.

18
Q

What are enzymes/metabolic pathways database

A

They contain information on metabolic pathways information.

19
Q

Binding site and promoters of genes databases

A

Genes are regulated by promoters that can turn on or off a gene, regulate how much a gene product is made, usually found ‘upstream’ of a gene

DBTBS, EPD, PromEC, TRANSFAC

20
Q

Examples of protein databases

A

InterPro: Protein families and domains
EXprot: proteins with experimentally verified functions
Protein Information Resource (PIR)
SWISS-PROT/TrEMBL curated protein sequence

21
Q

Examples of protein motifs and domains databases

A

Proteins have conserved regions(motifs) which may have functional significance
These databases store protein families, motifs and structural domains.

BLOCKS (multiple alignments of conserved regions)
CDD
eMOTIF
Pfam
PRINTS
ProDom
PROSITE
ProtoMAP
22
Q

Protein structure databases

A

Proteins take on a 3-D structure

3-D data for some proteins is available due to techniques such as NMR and X-ray crystallography.

ASTRAL
PDB
SCOP
MMDB

23
Q

Disease databases

A

ONIM
OMIA
HGMD
Tumor Gene Family databases

24
Q

Many databases are actually interconnected with each other

A

Yep

25
Q

Entrez from NCBI

A

It is a search and retrieval system that links to nucleotide, protein and literature information.

26
Q

SRS from EBI

A

It is a search and retrieval system that links 168 databases for searching through a single database.

27
Q

3 types of databases

A

Primary databases - experimental results
Secondary databases - analysis of experimental results
Composite databases - aggregate of many databases. -> Links to other data items
-> Combination of data
-> Consolidation of data.

28
Q

Where do information in primary databases come from?

A
  • > Original biological data such as protein or nucleic acid
  • > From experiments
  • > From literature and patents
  • > Primary sequence data
  • > Literature databases
29
Q

Describe secondary databases

A
  • > Curated and annotated
  • > Add value to primary database
  • > List structural/functional motifs
30
Q

Describe composite databases

A
  • > Links to other data items
  • > Combination of data
  • > Consolidation of data
31
Q

Examples of primary databases

A

Nucleic acid

  • EMBL
  • GenBank
  • DDBJ

Protein

  • SWISS-PROT
  • TREMBL
  • PIR
32
Q

Common database search methods

A

Keyword matching, sequence similarity, motif searching and class searching

33
Q

Problems with using biological databases

A 
Incomplete information
Data spread over multiple databases
Redundant information
Various errors 
Sometimes incorrect links
Constant change
34
Q

Retrieval system

A

Help retrieve rich information from multiple databases

Bioinformatics (10 decks)

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