Adverse Outcome Pathway (AOP)
An analytical construct that describes a sequential chain of causally linked events at different levels of biological organization that lead to an adverse effect.
Big Data
A popular term used to describe the exponentially growing size and availability of data, with three V’s: volume, velocity (of flow), and variety (complexity) requiring specialized methods to manage.
Causal Network Model
The representation of a system as objects and the causal (or directed) relationships between them.
Chromatin Immunoprecipitation (ChIP)
A method for identifying genomic DNA sequences bound by proteins, such as transcription factor binding sites.
Classifier
An algorithm or mathematical expression that enables the grouping objects according to a common feature or features.
Deep Learning Methods
Machine learning methods that represent observed data as factors and factor interactions organized in multiple layers. Artificial neural networks are one example.
Epigenomics
The study of the epigenome, or the complete set of epigenetic or chemical modifications to the DNA in a cell or sample.
Expression Quantitative Trait Loci (eQTL)
Genomic regions (loci) that regulate the expression levels of mRNAs.
Factor Analysis
A mathematical procedure applied to a data set that reduces the number of variables into a smaller set of factors that together account for the original variables.
Feedback Loop
A process by which system outputs can influence inputs to the system and either dampen or amplify the response.
Gene Ontology
A bioinformatics initiative (GO) to represent gene attributes (function, localization) using a controlled vocabulary (GO terms).
Gene Regulatory Network
A collection of genes and/or gene products that are connected by relationships.
Gene Set Analysis
A method of analyzing a subset of genes in a transcriptomics study.
Knowledgebase
Repository of summarized information on biological activity data, useful for facilitating the building of predictive models.
Genomics
The study of the genome, or the entire DNA sequence in a cell or sample.
Good Laboratory Practice (GLP)
A quality system of management controls for research laboratories to ensure the consistency, reliability, and integrity of pharmaceutical studies.
Graphical Network Model
The representation of a system as a series of objects and their relationships (physical, mathematical, or association) as nodes and connections (edges).
Logic-based Models
The representation of a system as objects and the relationships between them as logic statements.
Machine Learning
The use of computer algorithms to generate rules based on input data.
Mechanism of Action
The biochemical interaction through which a drug produces a pharmacologic effect.
Metabolomics
The study of the metabolome, or the complete set of small molecule metabolites in a cell or sample.
Natural Language Processing
A discipline in artificial intelligence focused on computational techniques for analyzing and representing text.
Network Medicine
The study of medicine and disease from a network perspective.
Network Pharmacology
Mapping of drug-target networks onto biological networks.
Omics
Informal reference to studies in biology on the collective quantitation and characterization of biological molecules including DNA (genomics), RNA (transcriptomics), proteins (proteomics), metabolites (metabolomics), etc.
Ontology
The formal specification of knowledge as a set of concepts and the relationships between concepts.
Principal Component Analysis (PCA)
A mathematical procedure to reduce the number of (possibly correlated) variables into a smaller number of uncorrelated variables called principal components.
Phenotypic Drug Discovery
The use of biological systems for primary drug screening; target agnostic.
Proteomics
The study of the proteome, or the set of all protein species in a cell or sample.
Read Across
A technique that applies data for a particular property or effect from one agent (chemical) to a similar untested agent, often used in safety assessment.
Regression Analysis
A statistical technique for estimating the relationships among variables, for example, the relationship between a dependent variable and one or more independent variables.
RNA-Seq
A technique for sequencing and quantifying all the RNA species in a sample.
Semantic Analysis
Method for representing knowledge in a format that is suitable for data mining and machine learning.
Support Vector Machines
Supervised learning models or machine learning tasks with associated learning algorithms that analyze data and recognize patterns, used for classification and regression analysis.
Systems Biology
The study of a biological system by comprehensive analysis of components and their interactions, and integration of this information into predictive models.
Transcriptomics
The study of the transcriptome, or the set of all of the RNA species in a biological system.