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

  1. 1 2 "Elsevier launches EmBiology to deliver the unparalleled insights into biological activities that accelerate drug discovery". elsevier.com. Retrieved 2023-09-18.
  2. ↑ Description of EMBiology "Ovid and Elsevier announce exclusive partnership..." (Online). Ovid Technologies, Inc. 2005. Retrieved 2011-01-30. Press release
  3. ↑ "Biological data structured for insights | EmBiology | Elsevier". beta.elsevier.com. Retrieved 2023-09-18.
  4. ↑ "What biological concepts are included in EmBiology? – EmBiology Support Center". service.elsevier.com. Retrieved 2023-09-18.
  5. ↑ "What biological relationships are extracted in EmBiology? – EmBiology Support Center". service.elsevier.com. Retrieved 2023-09-18.
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