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.
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] .
EmBiology Data sources include [3] :
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 |
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
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