EMBiology

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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] .

Contents

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] :

Biological Concepts

The following biological concepts are included in EmBiology [4] :

ConceptDescription
Drugs & chemicalsNaturally occurring metabolites, small molecules found in cell, drugs (incl. small molecules & biologics)
DiseasesHealth conditions and disease terms
ProteinsRepresents both genes and the gene products, including proteins and miRNAs
Functional classesProteins classes based on biological function
Protein complexesOne or more polypeptides that form a complex via physical interactions
Genetic variantVariants searchable by SNPID and text
CellsMammalian cell types & cell lines
Cell ProcessBiological processes (e.g., apoptosis, inflammation)
OrgansMammalian organ types
TissuesMammalian tissue types
VirusesAn agent that causes infectious diseases
Clinical parameterMeasured parameters of the human body used in clinical practice
TreatmentNon-chemical treatments and environmental conditions
Cell objectOrganelles, cell structural components

Biological Relationships

The following biological relationships are included in EmBiology [5]

RelationDescriptionExample
ExpressionChanges protein abundance by affecting levels of transcript or protein stabilityMDM2 has a negative "Expression" relationship with TP53
miRNA EffectInhibitory effect of an miRNA on its mRNA targetmiR-30 has a negative "miRNAEffect" relationship with TP53
Promoter BindingBinds to the promoter of a geneFOXC1 has a positive "PromoterBinding" relationship with MMP7
RegulationChanges activity by an unknown mechanism (may be direct or indirect)SOCS3 has a positive "Regulation" relationship with diabetes mellitus
Direct RegulationInfluences activity by direct physical interactionBRCA1 has a "DirectRegulation" relationship with BARD1
BindingDirect physical interaction between two moleculesFANCD2 has a "Binding" relationship with BRCA1
Protein ModificationChanges the modification of the target molecule, usually by direct interactionSRC has a "ProtModification" relationship with GRB2
BiomarkerIdentification of proteins/complexes/functional classes/metabolites that are prognostic or diagnostic biomarkers for a diseaseLung cancer has a "Biomarker" relationship with IL6
Genetic ChangeGenetic changes such as gene deletions, amplifications, mutations or epigenetic changesLung cancer has a "GeneticChange" relationship with ALK
Quantitative ChangeChanges in abundance/activity/expression of a gene/protein/small molecule in a disease stateBreast cancer has a positive "QuantitativeChange" relationship with AGK
State ChangeChanges in a protein’s post-translational modification status or alternative splicing eventsBreast cancer has a "StateChange" relationship with estrogen receptor
Functional Assoc.Between a disease and a cellular process or another diseaseChronic pancreatitis has a "FunctionalAssociation" relationship with pancreatic cancer
Chemical ReactionEither enzyme catalysed or spontaneous chemical reactionCYP3A has a "ChemicalReaction" relationship with ticagrelor
Molecular SynthesisChanges the concentration of the targetCYP3A has a "MolSynthesis" relationship with midazolam
Molecular TransportChanges the localization of the targetTamoxifen has a positive "MolTransport" relationship with MAPK3
Clinical TrialClinical trials conducted for a drug against a disease (from CT.gov)Tamoxifen has a positive “Clinical Trial" relationship with breast cancer
Cell ExpressionExpression of proteins within or on the surface of a cellHepatocyte 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". www.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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