EmBiology (formerly EMBiology) is a web-based Software as a service tool from Elsevier in which researchers can view biological relationships between entities, such as genes, proteins, and cells.[1]
Launched in 2023, EmBiology queries a Biological Knowledge Graph with 1.4 million entities connected by 15.7 million relationships.[1] It uses a Sankey diagram to visualize search findings, and displays "snippets" of text from relevant scientific literature.
Previous Version
EmBiology was originally launched as EMBiology in 2005 as a life science bibliographic database in a partnership with Ovid Technologies as a smaller version of Embase.[2]
Content Coverage
EmBiology Data sources include:[3]
- 7.2 million Full-text articles from 936 Elsevier journals and 939 non-Elsevier journals
Biological Concepts
The following biological concepts are included in EmBiology:[4]
| Concept
|
Description
|
| Drugs & chemicals
|
Naturally occurring metabolites, small molecules found in cell, drugs (incl. small molecules & biologics)
|
| Diseases
|
Health conditions and disease terms
|
| Proteins
|
Represents both genes and the gene products, including proteins and miRNAs
|
| Functional classes
|
Proteins classes based on biological function
|
| Protein complexes
|
One or more polypeptides that form a complex via physical interactions
|
| Genetic variant
|
Variants searchable by SNPID and text
|
| Cells
|
Mammalian cell types & cell lines
|
| Cell Process
|
Biological processes (e.g., apoptosis, inflammation)
|
| Organs
|
Mammalian organ types
|
| Tissues
|
Mammalian tissue types
|
| Viruses
|
An agent that causes infectious diseases
|
| Clinical parameter
|
Measured parameters of the human body used in clinical practice
|
| Treatment
|
Non-chemical treatments and environmental conditions
|
| Cell object
|
Organelles, cell structural components
|
Biological Relationships
The following biological relationships are included in EmBiology[5]
| Relation
|
Description
|
Example
|
| Expression
|
Changes protein abundance by affecting levels of transcript or protein stability
|
MDM2 has a negative "Expression" relationship with TP53
|
| miRNA Effect
|
Inhibitory effect of an miRNA on its mRNA target
|
miR-30 has a negative "miRNAEffect" relationship with TP53
|
| Promoter Binding
|
Binds to the promoter of a gene
|
FOXC1 has a positive "PromoterBinding" relationship with MMP7
|
| Regulation
|
Changes activity by an unknown mechanism (may be direct or indirect)
|
SOCS3 has a positive "Regulation" relationship with diabetes mellitus
|
| Direct Regulation
|
Influences activity by direct physical interaction
|
BRCA1 has a "DirectRegulation" relationship with BARD1
|
| Binding
|
Direct physical interaction between two molecules
|
FANCD2 has a "Binding" relationship with BRCA1
|
| Protein Modification
|
Changes the modification of the target molecule, usually by direct interaction
|
SRC has a "ProtModification" relationship with GRB2
|
| Biomarker
|
Identification of proteins/complexes/functional classes/metabolites that are prognostic or diagnostic biomarkers for a disease
|
Lung cancer has a "Biomarker" relationship with IL6
|
| Genetic Change
|
Genetic changes such as gene deletions, amplifications, mutations or epigenetic changes
|
Lung cancer has a "GeneticChange" relationship with ALK
|
| Quantitative Change
|
Changes in abundance/activity/expression of a gene/protein/small molecule in a disease state
|
Breast cancer has a positive "QuantitativeChange" relationship with AGK
|
| State Change
|
Changes in a protein's post-translational modification status or alternative splicing events
|
Breast cancer has a "StateChange" relationship with estrogen receptor
|
| Functional Assoc.
|
Between a disease and a cellular process or another disease
|
Chronic pancreatitis has a "FunctionalAssociation" relationship with pancreatic cancer
|
| Chemical Reaction
|
Either enzyme catalysed or spontaneous chemical reaction
|
CYP3A has a "ChemicalReaction" relationship with ticagrelor
|
| Molecular Synthesis
|
Changes the concentration of the target
|
CYP3A has a "MolSynthesis" relationship with midazolam
|
| Molecular Transport
|
Changes the localization of the target
|
Tamoxifen has a positive "MolTransport" relationship with MAPK3
|
| Clinical Trial
|
Clinical trials conducted for a drug against a disease (from CT.gov)
|
Tamoxifen has a positive "Clinical Trial" relationship with breast cancer
|
| Cell Expression
|
Expression of proteins within or on the surface of a cell
|
Hepatocyte has a "CellExpression" relationship with EGFR
|
References