NuBBE: The NuBBE DB Ontology

IRI:: http://nubbe.db/

Current version:: 11.2021-SNAPSHOT

Authors:: https://aksw.org/EdgardMarx

Publisher:: NUBBE

Other visualisation:: Ontology source; WebVOWL

Abstract

The NuBBE biochemical knowledge graph vocabulary.

Table of Content

Classes

Acridine Alkaloid Or Acridone^c back to ToC or Class ToC

IRI: http://nubbe.db/AcridineAlkaloidOrAcridone

is defined by: http://nubbe.db/

A Acridine Alkaloid Or Acridone.

has super-classes: Alkaloids^c

Alkaloids^c back to ToC or Class ToC

IRI: http://nubbe.db/Alkaloid

is defined by: http://nubbe.db/

A Alkaloids.

has super-classes: Chemical Compound^c
has sub-classes: Acridine Alkaloid Or Acridone^c, Imidazole Alkaloid^c, Indole Alkaloid^c, Piperidine Alkaloid^c, Pyridine Alkaloid^c, Pyrrolidine Alkaloid^c, Quinazoline Alkaloid^c, Quinoline Alkaloid^c, Tetrahydroisoquinoline Alkaloid^c

Aminoacid^c back to ToC or Class ToC

IRI: http://nubbe.db/Aminoacid

is defined by: http://nubbe.db/

A Aminoacid.

has super-classes: aminoacids and peptide^c

Aminoacid or Peptide^c back to ToC or Class ToC

IRI: http://nubbe.db/AminoacidORPeptide

is defined by: http://nubbe.db/

A Aminoacid or Peptide.

has super-classes: Chemical Compound^c

Anthocyanidin^c back to ToC or Class ToC

IRI: http://nubbe.db/Anthocyanidin

is defined by: http://nubbe.db/

A Anthocyanidin.

has super-classes: Flavonoid^c

Aromatic Acid^c back to ToC or Class ToC

IRI: http://nubbe.db/AromaticAcid

is defined by: http://nubbe.db/

A Aromatic Acid.

has super-classes: Aromatic Derivative^c

Aromatic Derivative^c back to ToC or Class ToC

IRI: http://nubbe.db/AromaticDerivative

is defined by: http://nubbe.db/

A Aromatic Derivative.

has super-classes: Chemical Compound^c
has sub-classes: Aromatic Acid^c, Benzofuranoid^c, Benzophenone Derivative^c, Chromane^c, Chromanone^c, Chromene^c, Chromone^c, Coumarin^c, Stilbene^c, Styryl Pyrone^c, Xanthone^c

Aromatic Polyketide^c back to ToC or Class ToC

IRI: http://nubbe.db/AromaticPolyketide

is defined by: http://nubbe.db/

A Aromatic Polyketide.

has super-classes: Polyketides^c

Benzofuranoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Benzofuranoid

is defined by: http://nubbe.db/

A Benzofuranoid.

has super-classes: Aromatic Derivative^c

Benzophenone Derivative^c back to ToC or Class ToC

IRI: http://nubbe.db/BenzophenoneDerivative

is defined by: http://nubbe.db/

A Benzophenone Derivative.

has super-classes: Aromatic Derivative^c

Biflavonoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Biflavonoid

is defined by: http://nubbe.db/

A Biflavonoid.

has super-classes: Flavonoid^c

Carbohydrate^c back to ToC or Class ToC

IRI: http://nubbe.db/Carbohydrates

is defined by: http://nubbe.db/

A Carbohydrate.

has super-classes: Chemical Compound^c

Chalcones^c back to ToC or Class ToC

IRI: http://nubbe.db/Chalcones

is defined by: http://nubbe.db/

A Chalcones.

has super-classes: Chemical Compound^c

Chemical Compound^c back to ToC or Class ToC

IRI: http://nubbe.db/ChemicalCompound

is defined by: http://nubbe.db/

A Chemical Compound.

has super-classes: Chemical Substance^c
has sub-classes: Alkaloids^c, Aminoacid or Peptide^c, Aromatic Derivative^c, Carbohydrate^c, Chalcones^c, Flavonoid^c, Lignoid^c, Lipid^c, Phenylpropanoids^c, Polyketides^c, Terpene^c
is in domain of: biological activity^dp, code^dp, collection site^dp, collection specie^dp, collection type^dp, doi^dp, logP coeficient^dp, molecular mass^dp, molecular volume^dp, monoisotropic mass^dp, number of H-bond acceptors^dp, number of H-bond donors^dp, number of Lipiski violations^dp, number of rotable bonds^dp, smile^dp, topological polar surface area (TPSA)^dp

Chemical Substance^c back to ToC or Class ToC

IRI: http://nubbe.db/ChemicalSubstance

is defined by: http://nubbe.db/

A Chemical Substance.

has super-classes: thing^c
has sub-classes: Chemical Compound^c

Chromane^c back to ToC or Class ToC

IRI: http://nubbe.db/Chromane

is defined by: http://nubbe.db/

A Chromane.

has super-classes: Aromatic Derivative^c

Chromanone^c back to ToC or Class ToC

IRI: http://nubbe.db/Chromanone

is defined by: http://nubbe.db/

A Chromanone.

has super-classes: Aromatic Derivative^c

Chromene^c back to ToC or Class ToC

IRI: http://nubbe.db/Chromene

is defined by: http://nubbe.db/

A Chromene.

has super-classes: Aromatic Derivative^c

Chromone^c back to ToC or Class ToC

IRI: http://nubbe.db/Chromone

is defined by: http://nubbe.db/

A Chromone.

has super-classes: Aromatic Derivative^c

Coumarin^c back to ToC or Class ToC

IRI: http://nubbe.db/Coumarin

is defined by: http://nubbe.db/

A Coumarin.

has super-classes: Aromatic Derivative^c

Diterpenoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Diterpenoid

is defined by: http://nubbe.db/

A Diterpenoid.

has super-classes: Terpene^c

Flavanol^c back to ToC or Class ToC

IRI: http://nubbe.db/Flavanol

is defined by: http://nubbe.db/

A Flavanol.

has super-classes: Flavonoid^c

Flavanone^c back to ToC or Class ToC

IRI: http://nubbe.db/Flavanone

is defined by: http://nubbe.db/

A Flavanone.

has super-classes: Flavonoid^c

Flavone^c back to ToC or Class ToC

IRI: http://nubbe.db/Flavone

is defined by: http://nubbe.db/

A Flavone.

has super-classes: Flavonoid^c

Flavonoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Flavonoid

is defined by: http://nubbe.db/

A Flavonoid.

has super-classes: Chemical Compound^c
has sub-classes: Anthocyanidin^c, Biflavonoid^c, Flavanol^c, Flavanone^c, Flavone^c, Flavonol^c, Isoflavonoid^c

Flavonol^c back to ToC or Class ToC

IRI: http://nubbe.db/Flavonol

is defined by: http://nubbe.db/

A Flavonol.

has super-classes: Flavonoid^c

Hemiterpenoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Hemiterpenoid

is defined by: http://nubbe.db/

A Hemiterpenoid.

has super-classes: Terpene^c

Hydrolysable Tannin^c back to ToC or Class ToC

IRI: http://nubbe.db/HydrolysableTannin

is defined by: http://nubbe.db/

A Hydrolysable Tannin.

has super-classes: tanins^c

Imidazole Alkaloid^c back to ToC or Class ToC

IRI: http://nubbe.db/ImidazoleAlkaloid

is defined by: http://nubbe.db/

A Imidazole Alkaloid.

has super-classes: Alkaloids^c

Indole Alkaloid^c back to ToC or Class ToC

IRI: http://nubbe.db/IndoleAlkaloid

is defined by: http://nubbe.db/

A Indole Alkaloid.

has super-classes: Alkaloids^c

Iridoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Iridoid

is defined by: http://nubbe.db/

A Iridoid.

has super-classes: Terpene^c

Isoflavonoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Isoflavonoid

is defined by: http://nubbe.db/

A Isoflavonoid.

has super-classes: Flavonoid^c

Lignoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Lignoid

is defined by: http://nubbe.db/

A Lignoid.

has super-classes: Chemical Compound^c

Linear Polyketide^c back to ToC or Class ToC

IRI: http://nubbe.db/LinearPolyketide

is defined by: http://nubbe.db/

A Linear Polyketide.

has super-classes: Polyketides^c

Lipid^c back to ToC or Class ToC

IRI: http://nubbe.db/Lipid

is defined by: http://nubbe.db/

A Lipid.

has super-classes: Chemical Compound^c

Meroterpenoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Meroterpenoid

is defined by: http://nubbe.db/

A Meroterpenoid.

has super-classes: Terpene^c

Monoterpenoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Monoterpenoid

is defined by: http://nubbe.db/

A Monoterpenoid.

has super-classes: Terpene^c

Peptide^c back to ToC or Class ToC

IRI: http://nubbe.db/Peptide

is defined by: http://nubbe.db/

A Peptide.

has super-classes: aminoacids and peptide^c

Phenylpropanoids^c back to ToC or Class ToC

IRI: http://nubbe.db/Phenylpropanoid

is defined by: http://nubbe.db/

A Phenylpropanoids.

has super-classes: Chemical Compound^c

Piperidine Alkaloid^c back to ToC or Class ToC

IRI: http://nubbe.db/PiperidineAlkaloid

is defined by: http://nubbe.db/

A Piperidine Alkaloid.

has super-classes: Alkaloids^c

Polyketides^c back to ToC or Class ToC

IRI: http://nubbe.db/Polyketide

is defined by: http://nubbe.db/

A Polyketides.

has super-classes: Chemical Compound^c
has sub-classes: Aromatic Polyketide^c, Linear Polyketide^c

Pyridine Alkaloid^c back to ToC or Class ToC

IRI: http://nubbe.db/PyridineAlkaloid

is defined by: http://nubbe.db/

A Pyridine Alkaloid.

has super-classes: Alkaloids^c

Pyrrolidine Alkaloid^c back to ToC or Class ToC

IRI: http://nubbe.db/PyrrolidineAlkaloid

is defined by: http://nubbe.db/

A Pyrrolidine Alkaloid.

has super-classes: Alkaloids^c

Quinazoline Alkaloid^c back to ToC or Class ToC

IRI: http://nubbe.db/QuinazolineAlkaloid

is defined by: http://nubbe.db/

A Quinazoline Alkaloid.

has super-classes: Alkaloids^c

Quinoline Alkaloid^c back to ToC or Class ToC

IRI: http://nubbe.db/QuinolineAlkaloid

is defined by: http://nubbe.db/

A Quinoline Alkaloid.

has super-classes: Alkaloids^c

Quinolizidine Alkaloid^c back to ToC or Class ToC

IRI: http://nubbe.db/QuinolizidineAlkaloid

is defined by: http://nubbe.db/

A Quinolizidine Alkaloid.

has super-classes: alkaloids^c

Sesquiterpenoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Sesquiterpenoid

is defined by: http://nubbe.db/

A Sesquiterpenoid.

has super-classes: Terpene^c

Steroids^c back to ToC or Class ToC

IRI: http://nubbe.db/Steroid

is defined by: http://nubbe.db/

A Steroids.

has super-classes: Terpene^c

Stilbene^c back to ToC or Class ToC

IRI: http://nubbe.db/Stilbene

is defined by: http://nubbe.db/

A Stilbene.

has super-classes: Aromatic Derivative^c

Styryl Pyrone^c back to ToC or Class ToC

IRI: http://nubbe.db/StyrylPyrone

is defined by: http://nubbe.db/

A Styryl Pyrone.

has super-classes: Aromatic Derivative^c

Terpene^c back to ToC or Class ToC

IRI: http://nubbe.db/Terpene

is defined by: http://nubbe.db/

A Terpene.

has super-classes: Chemical Compound^c
has sub-classes: Diterpenoid^c, Hemiterpenoid^c, Iridoid^c, Meroterpenoid^c, Monoterpenoid^c, Sesquiterpenoid^c, Steroids^c, Triterpenoid^c

Tetrahydroisoquinoline Alkaloid^c back to ToC or Class ToC

IRI: http://nubbe.db/TetrahydroisoquinolineAlkaloid

is defined by: http://nubbe.db/

A Tetrahydroisoquinoline Alkaloid.

has super-classes: Alkaloids^c

Triterpenoid^c back to ToC or Class ToC

IRI: http://nubbe.db/Triterpenoid

is defined by: http://nubbe.db/

A Triterpenoid.

has super-classes: Terpene^c

Xanthone^c back to ToC or Class ToC

IRI: http://nubbe.db/Xanthone

is defined by: http://nubbe.db/

A Xanthone.

has super-classes: Aromatic Derivative^c

Β-Lactam^c back to ToC or Class ToC

IRI: http://nubbe.db/Β-Lactam

is defined by: http://nubbe.db/

A Β-Lactam.

has super-classes: aminoacids and peptide^c

Data Properties

biological activity^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/biologicalActivity

is defined by: http://nubbe.db/

The value of the mapping.

has domain: Chemical Compound^c
has range: string

code^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/code

is defined by: http://nubbe.db/

The NUBBE unique identifier code of the Chemical Compound.

has domain: Chemical Compound^c
has range: integer

collection site^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/collectionSite

is defined by: http://nubbe.db/

The name of the site where the sample was collected.

has domain: Chemical Compound^c
has range: string

collection specie^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/collectionSpecie

is defined by: http://nubbe.db/

The name living specie where the molecule is reported to be found.

has domain: Chemical Compound^c
has range: string

collection type^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/collectionType

is defined by: http://nubbe.db/

The type of the collection.

has domain: Chemical Compound^c
has range: string

doi^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/doi

is defined by: http://nubbe.db/

The doi of the document from which the information was extracted.

has domain: Chemical Compound^c
has range: string

logP coeficient^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/clogP

is defined by: http://nubbe.db/

The logP value of a compound, which is the logarithm of its partition coefficient between n-octanol and water log(c_octanol/c_water).

has domain: Chemical Compound^c
has range: double

molecular mass^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/molecularMass

is defined by: http://nubbe.db/

The mass of the molecule.

has domain: Chemical Compound^c
has range: double

molecular volume^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/molecularVolume

is defined by: http://nubbe.db/

The volume occupied by one mole of it at a given temperature and pressure.

has domain: Chemical Compound^c
has range: double

monoisotropic mass^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/monoisotropicMass

is defined by: http://nubbe.db/

The monoisotropic mass of the molecule.

has domain: Chemical Compound^c
has range: double

number of H-bond acceptors^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/numberOfH-bondAcceptors

is defined by: http://nubbe.db/

The value (numerical or not) of a mesurement.

has domain: Chemical Compound^c
has range: int

number of H-bond donors^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/numberOfH-bondDonors

is defined by: http://nubbe.db/

The value (numerical or not) of a mesurement.

has domain: Chemical Compound^c
has range: int

number of Lipiski violations^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/numberOfLipinskiViolations

is defined by: http://nubbe.db/

Number of violations of Lipinski's rule of five, also known as Pfizer's rule of five or simply the rule of five (RO5), is a rule of thumb to evaluate druglikeness or determine if a chemical compound with a certain pharmacological or biological activity has chemical properties and physical properties that would make it a likely orally active drug in humans.

has domain: Chemical Compound^c
has range: int

number of rotable bonds^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/numberOfRotableBonds

is defined by: http://nubbe.db/

A rotatable bond is defined as any single non-ring bond, attached to a non-terminal, non-hydrogen atom.

has domain: Chemical Compound^c
has range: int

smile^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/smile

is defined by: http://nubbe.db/

The SMILE representation of the Chemical Compound.

has domain: Chemical Compound^c
has range: string

topological polar surface area (TPSA)^dp back to ToC or Data Property ToC

IRI: http://nubbe.db/property/tpsa

is defined by: http://nubbe.db/

The topological polar surface area (TPSA) of a molecule is defined as the surface sum over all polar atoms or molecules, primarily oxygen and nitrogen, also including their attached hydrogen atoms.

has domain: Chemical Compound^c
has range: double

Named Individuals

edgard marxⁿⁱ back to ToC or Named Individual ToC

IRI: https://aksw.org/EdgardMarx

belongs to: agent^c; person^c