BioAssay Ontology
type: Ontology
license: https://creativecommons.org/licenses/by-sa/4.0/
version info: 2.7.2
label: BAO
comment: Created by: Hande Küçük McGinty, Janice Kranz, Joseph Ostrow, Alex Clark, Yu Lin, Saminda Abeyruwan, Uma Vempati, Kunie Sakurai, Vance Lemmon, Ubbo Visser, John Turner, Stephan Schurer*
comment: Contact: Stephan Schurer stephan dot schurer at gmail dot com
date: 8 Jul 2021

computational method
type: Class
IAO_0000115: Method based on the application of information technology to chemistry and biology.

bioinformatics method
type: Class
IAO_0000115: Method based on application of information technology to the field of molecular biology.
subclass of: computational method

computational expression analysis
type: Class
subclass of: bioinformatics method

computational analysis of gene expression
type: Class
IAO_0000115: Computational methods used for analysis of microarrays, expressed cDNA sequence tag (EST) sequencing, serial analysis of gene expression (SAGE) tag sequencing, massively parallel signature sequencing (MPSS), or various applications of multiplexed in-situ hybridization.
subclass of: computational expression analysis

computational analysis of protein expression
type: Class
IAO_0000115: Computational methods involved in analysis of protein microarrays and high throughput (HT) mass spectrometry (MS).
subclass of: computational expression analysis

computational phylogenetic analysis
type: Class
IAO_0000115: Computational methods involved in construction and interpretation of phylogenetic trees, which are used to classify the evolutionary relationships between homologous genes represented in the genomes of divergent species.
subclass of: bioinformatics method

Mesquite phylogenetic analysis
type: Class
IAO_0000115: Software for evolutionary biology, designed to help biologists analyze comparative data about organisms. Its emphasis is on phylogenetic analysis, but some of its modules concern population genetics, while others do non-phylogenetic multivariate analysis.
subclass of: computational phylogenetic analysis

SplitsTree phylogenetic analysis
type: Class
IAO_0000115: Program for inferring phylogenetic trees or, more generally, phylogenetic networks from various types of data such as a sequence alignment, a distance matrix or a set of trees.
subclass of: computational phylogenetic analysis

Treefinder phylogenetic analysis
type: Class
IAO_0000115: is a free computer program for the likelihood-based reconstruction of phylogenetic trees from molecular sequences.
subclass of: computational phylogenetic analysis

phylogenetic analysis using parsimony
type: Class
subclass of: computational phylogenetic analysis

phylogeny inference package
type: Class
IAO_0000115: A free Computational phylogenetics package of programs for inferring evolutionary trees (phylogenies).
subclass of: computational phylogenetic analysis

sequence alignment
type: Class
IAO_0000115: Computational methods used to arrange the sequences of DNA, RNA, or protein to identify regions of similarity that may be a consequence of functional, structural, or evolutionary relationships between the sequences.
subclass of: bioinformatics method

sequence alignment by method
type: Class
subclass of: sequence alignment

global sequence alignment
type: Class
IAO_0000115: Global alignments, which attempt to align every residue in every sequence, are most useful when the sequences in the query set are similar and of roughly equal size.
subclass of: sequence alignment by method

AVID sequence alignment
type: Class
IAO_0000115: Pairwise global alignment with whole genomes.
subclass of: global sequence alignment

DIALIGN sequence alignment
type: Class
subclass of: global sequence alignment
subclass of: multiple sequence alignment

local sequence alignment
type: Class
IAO_0000115: Local alignments are more useful for dissimilar sequences that are suspected to contain regions of similarity or similar sequence motifs within their larger sequence context.
subclass of: sequence alignment by method

FASTA local sequence alignment
type: Class
IAO_0000115: Local search with fast k-tuple heuristic, slower but more sensitive than BLAST.
subclass of: local sequence alignment

basic local alignment search tool
type: Class
IAO_0000115: Local search with fast k-tuple heuristic.
subclass of: local sequence alignment

progressive system alignment
type: Class
subclass of: sequence alignment by method

Clustal sequence alignment
type: Class
IAO_0000115: Multiple sequence alignment computer program.
subclass of: multiple sequence alignment
subclass of: progressive system alignment

ClustalW sequence alignment
type: Class
subclass of: Clustal sequence alignment

ClustalX sequence alignment
type: Class
subclass of: Clustal sequence alignment

MAVID sequence alignment
type: Class
IAO_0000115: is a multiple sequence alignment program suitable for the alignment of large numbers of DNA sequences.
subclass of: progressive system alignment

sequence alignment by type
type: Class
subclass of: sequence alignment

multiple sequence alignment
type: Class
IAO_0000115: Multiple sequence alignment is an extension of pairwise alignment to incorporate more than two sequences at a time.
subclass of: sequence alignment by type

pairwise sequence alignment
type: Class
IAO_0000115: Pairwise sequence alignment methods are used to find the best-matching piecewise (local) or global alignments of two query sequences.
subclass of: sequence alignment by type

JAligner sequence alignment
type: Class
IAO_0000115: is an open source Java implementation of the Smith-Waterman algorithm with Gotoh's improvement for biological local pairwise sequence alignment using the affine gap penalty model.
subclass of: pairwise sequence alignment

cheminformatics method
type: Class
IAO_0000115: Methods using of computer and informational techniques for problems in the field of chemistry
subclass of: computational method

conformational search
type: Class
IAO_0000115: Consists of the exploration of energetically favorable spatial arrangements (shapes) of a molecule (conformations).
subclass of: cheminformatics method

distance geometry conformational search
type: Class
subclass of: conformational search

random conformational search
type: Class
subclass of: conformational search

cartesian conformational search
type: Class
subclass of: random conformational search

dihedral conformational search
type: Class
subclass of: random conformational search

systematic conformational search
type: Class
subclass of: conformational search

database filtering
type: Class
subclass of: cheminformatics method

Lipinski rule of 5 filtering
type: Class
IAO_0000115: Set of criteria for predicting the oral bioavailability of a compound on the basis of simple molecular features (molecular weight, CLogP, numbers of hydrogen- bond donors and acceptors).
subclass of: database filtering

library design
type: Class
IAO_0000115: Library design enables access to the large number of drug- like molecules that could theoretically be made and can serve several purposes: for example, to generate a maximally diverse virtual library for lead generation, a biased library aimed at a specific target or target family, or a lead optimization library.
subclass of: cheminformatics method

structure database search
type: Class
subclass of: cheminformatics method

exact match structure search
type: Class
subclass of: structure database search

structure similarity search
type: Class
subclass of: structure database search

2D structure similarity search
type: Class
subclass of: structure similarity search
subclass of: scaffold hopping

MACCS key
type: Class
subclass of: 2D structure similarity search

circular fingerprint search
type: Class
subclass of: 2D structure similarity search

3D structure similarity search
type: Class
subclass of: structure similarity search
subclass of: scaffold hopping

shape fingerprint search
type: Class
subclass of: 3D structure similarity search

rapid overlay of chemical structures
type: Class
subclass of: shape fingerprint search

topomer search
type: Class
subclass of: 3D structure similarity search

substructure search
type: Class
subclass of: structure database search

structure generation
type: Class
subclass of: cheminformatics method

data based structure generation
type: Class
subclass of: structure generation

CORINA structure generation
type: Class
subclass of: data based structure generation

de novo structure design
type: Class
IAO_0000115: The design of bioactive compounds by incremental construction of a ligand model within a model of the receptor or enzyme active site, the structure of which is known from X-ray or NMR data.
subclass of: structure generation

GROW structure design
type: Class
subclass of: de novo structure design

Groupbuild structure design
type: Class
subclass of: de novo structure design

LEGEND structure design
type: Class
subclass of: de novo structure design

LUDI structure design
type: Class
subclass of: de novo structure design

SPROUT structure design
type: Class
subclass of: de novo structure design

fragment based structure generation
type: Class
subclass of: structure generation

Chem-X structure generation
type: Class
subclass of: fragment based structure generation

rule based structure generation
type: Class
subclass of: structure generation

CONCORD structure generation
type: Class
subclass of: rule based structure generation

computer simulation method
type: Class
subclass of: computational method

computer simulation method by force field
type: Class
IAO_0000115: A set of functions and parametrization used in molecular mechanics calculations.
subclass of: computer simulation method

classical force field simulation
type: Class
subclass of: computer simulation method by force field

AMBER force field simulation
type: Class
subclass of: classical force field simulation

CHARMM force field simulation
type: Class
subclass of: classical force field simulation
subclass of: force field based scoring function

GROMOS force field simulation
type: Class
subclass of: classical force field simulation

polarizable force field simulation
type: Class
subclass of: computer simulation method by force field

second generation force field simulation
type: Class
subclass of: computer simulation method by force field

CFF force field simulation
type: Class
subclass of: second generation force field simulation

MM4 force field simulation
type: Class
subclass of: second generation force field simulation

MMFF force field simulation
type: Class
subclass of: second generation force field simulation

global minimum search
type: Class
subclass of: computer simulation method

genetic algorithm search
type: Class
subclass of: global minimum search

simulated annealing
type: Class
IAO_0000115: a simulations procedure, in which the system is allowed to equilibrate at high temperatures, and then cooled down slowly to remove kinetic energy and to permit trajectories to settle into local minimum energy conformations.
subclass of: global minimum search

local minimum search
type: Class
subclass of: computer simulation method

energy minimization method
type: Class
subclass of: local minimum search

Newton-Raphson method
type: Class
subclass of: energy minimization method

conjugate gradient method
type: Class
subclass of: energy minimization method

steepest descent method
type: Class
subclass of: energy minimization method

molecular dynamics simulation
type: Class
IAO_0000115: A simulation procedure consisting of the computation of the motion of atoms in a molecule or of individual atoms or molecules in solids, liquids and gases, according to Newton's laws of motion. The forces acting on the atoms, required to simulate their motions, are generally calculated using molecular mechanics force fields.
subclass of: computer simulation method

constraint molecular dynamics simulation
type: Class
subclass of: molecular dynamics simulation

stochastic simulation
type: Class
subclass of: computer simulation method

Monte Carlo simulation
type: Class
subclass of: stochastic simulation

quantum chemistry computational method
type: Class
subclass of: computational method

ab initio quantum chemistry computational method
type: Class
IAO_0000115: Methods of quantum mechanical calculations independent of any experiment other than the determination of fundamental constants. The methods are based on the use of the full Schr
subclass of: quantum chemistry computational method

Hartree-Fock method
type: Class
subclass of: ab initio quantum chemistry computational method

restricted open-shell Hartree-Fock
type: Class
subclass of: Hartree-Fock method

unrestricted Hartree-Fock
type: Class
subclass of: Hartree-Fock method

post Hartree-Fock method
type: Class
subclass of: ab initio quantum chemistry computational method

configuration interaction method
type: Class
subclass of: post Hartree-Fock method

coupled cluster method
type: Class
subclass of: post Hartree-Fock method

quadratic configuration interaction method
type: Class
subclass of: post Hartree-Fock method

semi-empirical quantum chemistry computational method
type: Class
IAO_0000115: Use parameters derived from experimental data to simplify computations.
subclass of: quantum chemistry computational method

pi-electron computational method
type: Class
subclass of: semi-empirical quantum chemistry computational method

Pariser Parr Pople method
type: Class
subclass of: pi-electron computational method

valence electron computational method
type: Class
subclass of: semi-empirical quantum chemistry computational method

Zerner's intermediate neglect of differential overlap
type: Class
subclass of: valence electron computational method

austin model 1
type: Class
subclass of: valence electron computational method

intermediate neglect of differential overlap
type: Class
subclass of: valence electron computational method

modified neglect of differential overlap
type: Class
subclass of: valence electron computational method

parameterized model number 3
type: Class
subclass of: valence electron computational method

statistical method
type: Class
subclass of: computational method

experimental design method
type: Class
subclass of: statistical method

completely randomized design
type: Class
subclass of: experimental design method

fractional factorial design
type: Class
subclass of: experimental design method

full factorial design
type: Class
subclass of: experimental design method

randomized block design
type: Class
subclass of: experimental design method

statistical classification method
type: Class
subclass of: statistical method

decision tree
type: Class
subclass of: statistical classification method

hierarchial clustering
type: Class
subclass of: statistical classification method

k means clustering
type: Class
subclass of: statistical classification method

neural network model
type: Class
subclass of: statistical classification method

principal component analysis
type: Class
subclass of: statistical classification method

systems biology method
type: Class
subclass of: computational method

pathway analysis
type: Class
subclass of: systems biology method

pathway analysis by knowledge base
type: Class
subclass of: pathway analysis

automatic pathway analysis
type: Class
subclass of: pathway analysis by knowledge base

natural language processing
type: Class
subclass of: automatic pathway analysis

Ariadne Pathway Studio
type: Class
subclass of: natural language processing

pathway analysis by method
type: Class
subclass of: pathway analysis

gene list enrichment analysis
type: Class
subclass of: pathway analysis by method

GOstat enrichment analysis
type: Class
subclass of: gene list enrichment analysis

GSEA-P enrichment analysis
type: Class
subclass of: gene list enrichment analysis

GeneTrail enrichment analysis
type: Class
subclass of: gene list enrichment analysis

Onto-Express enrichment analysis
type: Class
subclass of: gene list enrichment analysis

integrated pathway analysis
type: Class
subclass of: pathway analysis by method

MetaDiscovery pathway analysis
type: Class
subclass of: integrated pathway analysis

network analysis
type: Class
subclass of: pathway analysis by method

Cytoscape network analysis
type: Class
subclass of: network analysis

target family knowledge analysis
type: Class
subclass of: systems biology method

virtual screening
type: Class
IAO_0000115: Selection of compounds by evaluating their desirability in a computational model.
subclass of: computational method

ligand based virtual screening
type: Class
subclass of: virtual screening

ligand based pharmacophore model
type: Class
IAO_0000115: The ligand-based ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target structure and to trigger (or to block) its biological response.
subclass of: ligand based virtual screening

Catalyst modeling
type: Class
subclass of: ligand based pharmacophore model

DISCOtech modeling
type: Class
subclass of: ligand based pharmacophore model

distance comparison modeling
type: Class
subclass of: ligand based pharmacophore model

genetic algorithm similary program
type: Class
subclass of: ligand based pharmacophore model

scaffold hopping
type: Class
subclass of: ligand based virtual screening

structure based virtual screening
type: Class
subclass of: virtual screening

molecular docking
type: Class
IAO_0000115: Method which predicts the preferred orientation of one molecule to a second when bound to each other to form a stable complex.
subclass of: structure based virtual screening

molecular docking by method
type: Class
subclass of: molecular docking

Monte Carlo minimization method
type: Class
subclass of: molecular docking by method

internal coordinate mechanics method
type: Class
subclass of: Monte Carlo minimization method

Monte Carlo simulated annealing
type: Class
subclass of: molecular docking by method

AutoDock docking method
type: Class
subclass of: Monte Carlo simulated annealing

descriptor matching method
type: Class
subclass of: molecular docking by method

ADAM docking method
type: Class
subclass of: descriptor matching method

DOCK docking method
type: Class
subclass of: descriptor matching method

SLIDE docking method
type: Class
subclass of: descriptor matching method

genetic algorithm method
type: Class
subclass of: molecular docking by method

AutoDock3 docking method
type: Class
subclass of: genetic algorithm method

DARWIN docking method
type: Class
subclass of: genetic algorithm method

GOLD docking method
type: Class
subclass of: genetic algorithm method

incremental construction method
type: Class
subclass of: molecular docking by method

DOCK4 docking method
type: Class
subclass of: incremental construction method

FlexX docking method
type: Class
subclass of: incremental construction method

Hummerhead docking method
type: Class
subclass of: incremental construction method

tabu docking method
type: Class
subclass of: molecular docking by method

SFdock docking method
type: Class
subclass of: tabu docking method

molecular docking by scoring function
type: Class
subclass of: molecular docking

empirical scoring function
type: Class
subclass of: molecular docking by scoring function

AutoDock3 scoring function
type: Class
subclass of: empirical scoring function

FLOG scoring function
type: Class
subclass of: empirical scoring function

GOLD scoring function
type: Class
subclass of: empirical scoring function

force field based scoring function
type: Class
subclass of: molecular docking by scoring function

AMBER polarizable
type: Class
subclass of: polarizable force field simulation

CHARMM polarizable
type: Class
subclass of: polarizable force field simulation

knowledge based scoring function
type: Class
subclass of: molecular docking by scoring function

DrugScore scoring function
type: Class
subclass of: knowledge based scoring function

potentials of mean force scoring function
type: Class
subclass of: knowledge based scoring function

receptor based pharmacophore search
type: Class
IAO_0000115: The receptor-based ensemble of steric and electronic features that is necessary to ensure the optimal supramolecular interactions with a specific biological target structure and to trigger (or to block) its biological response.
subclass of: structure based virtual screening

CoMFA pharmacophore search
type: Class
subclass of: receptor based pharmacophore search

GRID pharmacophore search
type: Class
subclass of: receptor based pharmacophore search

SPROUT pharmacophore search
type: Class
subclass of: receptor based pharmacophore search