Biological Sciences: Web Resources

The preprint server for biology.

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The term ‘molecular entity’ refers to any constitutionally or isotopically distinct atom, molecule, ion, ion pair, radical, radical ion, complex, conformer, etc., identifiable as a separately distinguishable entity. The molecular entities in question are either products of nature or synthetic products used to intervene in the processes of living organisms.

Contains part of an electronic structure collection donated by Tudor Oprea. This set originates from a compilation of ~4.5 million compounds commercially available in August 2002.

The DrugBank database is a unique bioinformatics and cheminformatics resource that combines detailed drug (i.e. chemical, pharmacological and pharmaceutical) data with comprehensive drug target (i.e. sequence, structure, and pathway) information. The database contains 8261 drug entries including 2021 FDA-approved small molecule drugs, 233 FDA-approved biotech (protein/peptide) drugs, 94 nutraceuticals and over 6000 experimental drugs. Additionally, 4338 non-redundant protein (i.e. drug target/enzyme/transporter/carrier) sequences are linked to these drug entries. Each DrugCard entry contains more than 200 data fields with half of the information being devoted to drug/chemical data and the other half devoted to drug target or protein data.

This resource is powered by the Protein Data Bank archive-information about the 3D shapes of proteins, nucleic acids, and complex assemblies that helps students and researchers understand all aspects of biomedicine and agriculture, from protein synthesis to health and disease.

BindingDB is a public, web-accessible database of measured binding affinities, focusing chiefly on the interactions of protein considered to be drug-targets with small, drug-like molecules. BindingDB contains 1,357,744 binding data, for 7,140 protein targets and 605,839 small molecules.

ClinicalTrials.gov is a registry and results database of publicly and privately supported clinical studies of human participants conducted around the world.

Open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, excluding biopolymers.

KEGG PATHWAY is a collection of manually drawn pathway maps representing our knowledge on the molecular interaction, reaction and relation networks for:
1. Metabolism 
Global/overview Carbohydrate Energy Lipid Nucleotide Amino acid Other amino Glycan 
Cofactor/vitamin Terpenoid/PK Other secondary metabolite Xenobiotics Chemical structure 
2. Genetic Information Processing 
3. Environmental Information Processing 
4. Cellular Processes 
5. Organismal Systems 
6. Human Diseases 
7. Drug Development

KEGG PATHWAY is a reference database for Pathway Mapping.

A TOXNET DATABASE

PubChem integrated chemical hazard and related occupational disease information for more than 12,000 chemicals from Haz-Map® (https://haz-map.com/). This integration added chemical property information, adverse effects, occupational disease from hazardous agents, use information, and more.  Haz-Map® is an occupational health database designed for health and safety professionals and for consumers seeking information about the adverse effects of workplace exposures to chemical and biological agents. The main links in Haz-Map® are between chemicals and occupational diseases. These links have been established using current scientific evidence. 

iDigBio is the national resource for digitized information about vouchered natural history collections within the context established by the NIBA community strategic plan and is supported through funds from the NSF ADBC program. As such, iDigBio serves as the coordinating center for the national digitization effort; fosters partnerships and innovations; facilitates the determination and dissemination of digitization practices and workflows; establishes integration and interconnectivity among the data generated by collection digitization projects; and promotes the uses of biological/paleontological collections data by the scientific community and stakeholders including government agencies, educational institutions, non-governmental organizations (NGOs), and other national and international entities to benefit science and society through enhanced research and outreach activities. iDigBio provides these services to all stakeholders with clarity, simplicity, transparency, intuitive methodology, and intuitive design.

The Genotype-Tissue Expression (GTEx) project aims to provide to the scientific community a resource with which to study human gene expression and regulation and its relationship to genetic variation. This project will collect and analyze multiple human tissues from donors who are also densely genotyped, to assess genetic variation within their genomes. By analyzing global RNA expression within individual tissues and treating the expression levels of genes as quantitative traits, variations in gene expression that are highly correlated with genetic variation can be identified as expression quantitative trait loci, or eQTLs.