LibGuides: Biomedical Informatics: Selecting Databases & Finding Articles

Selected Databases

National Center for Biotechnology Information (NCBI)
Biomedical and genomic data and tools for discovering, exploring, storing, and analyzing knowledge about molecular biology, biochemistry, and genetics.
NCBI - Develop
A variety of resources that allow developers to access and manipulate NCBI data in their applications: APIs, code libraries, data formats.

PubMed This link opens in a new window
One component of the NCBI resources, PubMed is a database of citations and abstracts for biomedical literature from MEDLINE and additional life science journals. Covers over 5,700 journals in the biomedical and health sciences. Connect to PubMed via the Library link for fully integration with UC-eLinks, to open full-text articles, determine location of print journals, and request articles through Interlibrary Loan.

Broad Institute
Data produced and analytical software tools developed by The Broad Institute are openly shared with the entire scientific community. Data is arranged by organism/species, with links to relevant tools and project information; software tools allow for analysis of genome-related datasets.
ExPASy
ExPASy, Swiss Institute of Bioinformatics [SIB] Bioinformatics Resource Portal, provides access to scientific databases and software tools in different areas of life sciences including proteomics, genomics, phylogeny, systems biology, population genetics, transcriptomics etc.
EMBL-EBI part of the European Molecular Biology Laboratory
The home for big data in biology
We help scientists exploit complex information to make discoveries that benefit humankind.
Find tools and resources or deposit data.

GeneNetwork a group of linked data sets and tools used to study complex networks of genes, molecules, and higher order gene function and phenotypes. Users are welcome to enter their own private data directly into GeneNetwork to exploit the full range of analytic tools and to map modulators.

GOLD
(Genomes Online Database) - An online resource for comprehensive access to information regarding complete and ongoing genome projects, as well as metagenomes and metadata, around the world.
J. Craig Venter Institute
Links to various software, mathematical tools, and databases to assemble and analyze genomic data.
KEGG: Kyoto Encyclopedia of Genes and Genomes
KEGG is a database resource for understanding high-level functions and utilities of the biological system, such as the cell, the organism and the ecosystem, from molecular-level information, especially large-scale molecular datasets generated by genome sequencing and other high-throughput experimental technologies.
NCI Center for Bioinformatics
National Cancer Institute Center for Biomedical Informatics and Information Technology (NCI CBIIT) offers open-source infrastructure components for use in developing databases and software tools.
PharmGKB
The Pharmacogenomics Knowledge Base focuses on collecting, encoding, and disseminating knowledge about the impact of human genetic variations on drug response. They curate primary genotype and phenotype data, annotate gene variants and gene-drug-disease relationships via literature review, and summarize important PGx genes and drug pathways.
RCSB Protein Data Bank
RCSB Protein Data Bank provides information about 3D shapes of proteins, nucleic acids, and complex assemblies. Provides a variety of tools and resources for research and education in molecular biology, structural biology, computational biology and beyond.

Organism-Specific Databases

FlyBase
A database of Drosophila genes and genomes.
Mouse Genome Informatics
MGI is the international database resource for the laboratory mouse, providing integrated genetic, genomic, and biological data to facilitate the study of human health and disease.
WormBase
Biology and genome of C. elegans
Zfin - the zebrafish information network
ZFIN - the zebrafish model organism database. Includes genetic, genomic & developmental information and definitive reference data sets of zebrafish research information.

Get Full Text Articles

The full text of an article within a database is provided in multiple formats. Look for:

An HTML link
PDF link
Link to Get it at UC

The Get it at UC link will provide you options for how to access the full text of the article. If there are no online links available, this means you need to request the item through Interlibrary Loan if a print version is not available at UC San Diego. The Library will deliver the full text of an article to you free of charge. When requesting you will need your Library ID number.

Your library card/account number begins with "21822" and can be found on the back of your UCSD ID card or within the UCSD app. Enter the 14-digit number without spaces.