EMBiology
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
[edit]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
[edit]EmBiology Data sources include:[3]
- 7.2 million PubMed abstracts
- 430,000 from Clinicaltrials.gov
- 7.2 million Full-text articles from 936 Elsevier journals and 939 non-Elsevier journals
Biological Concepts
[edit]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
[edit]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
- ^ a b "Elsevier launches EmBiology to deliver the unparalleled insights into biological activities that accelerate drug discovery". elsevier.com. Retrieved 2023-09-18.
- ^ Description of EMBiology "Ovid and Elsevier announce exclusive partnership..." (Online). Ovid Technologies, Inc. 2005. Retrieved 2011-01-30. Press release
- ^ "Biological data structured for insights | EmBiology | Elsevier". beta.elsevier.com. Retrieved 2023-09-18.
- ^ "What biological concepts are included in EmBiology? – EmBiology Support Center". service.elsevier.com. Retrieved 2023-09-18.
- ^ "What biological relationships are extracted in EmBiology? – EmBiology Support Center". service.elsevier.com. Retrieved 2023-09-18.