Use of Database in Research and Bioinformatics

This set of vocabulary flashcards covers key definitions, databases, and omics fields within the scope of bioinformatics and research databases as presented in the lecture.

Bioinformatics

A scientific discipline that encompasses all aspects of biological information acquisition, processing, storage, distribution, analysis and interpretation.

In silico

Biological hypothesis testing performed on a computer, distinct from in vivo (whole organisms) or in vitro (cells/test tubes) methods.

GeneCards

A searchable, integrated database of human genes that provides comprehensive, updated, and user-friendly information on all known and predicted genes.

PubChem

A database used for chemical information search, providing data such as molecular formula (MF), molecular weight (MW), IUPAC Name, and SMILES strings.

RCSB PDB

The Protein Data Bank; a resource providing access to experimentally-determined 3D structures and Computed Structure Models (CSM) from AlphaFold DB and ModelArchive.

UniProt

A comprehensive, high-quality resource of protein sequence and functional information consisting of UniProtKB, UniRef, and UniParc.

Swiss-Prot

A section of UniProtKB containing manually annotated and reviewed records with information extracted from literature and curator-evaluated computational analysis.

TrEMBL

A section of UniProtKB containing automatically annotated records that are not reviewed and await full manual annotation.

UniParc

A comprehensive and non-redundant database that contains most of the publicly available protein sequences in the world.

PubMed

A resource comprising more than 24 million citations for biomedical literature from MEDLINE, life science journals, and online books.

BLAST

Basic Local Alignment Search Tool; used to search for homologous genes, predict protein function, and analyze evolutionary relationships.

Genomics

The study of the genome, often utilizing high-throughput experimentation methods.

Transcriptomics

The study of the transcriptome using instrumentation such as micro-arrays.

Proteomics

The study of the proteome using instrumentation such as Mass Spectroscopy (MS).

Metabolomics

The study of metabolites using instrumentation such as Mass Spectroscopy (MS) and Nuclear Magnetic Resonance (NMR).