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.

Classes

Acridine Alkaloid Or Acridonec 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
Alkaloidsc

Aminoacidc back to ToC or Class ToC

IRI: http://nubbe.db/Aminoacid

is defined by
http://nubbe.db/

A Aminoacid.

has super-classes
aminoacids and peptidec

Aminoacid or Peptidec 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 Compoundc

Anthocyanidinc back to ToC or Class ToC

IRI: http://nubbe.db/Anthocyanidin

is defined by
http://nubbe.db/

A Anthocyanidin.

has super-classes
Flavonoidc

Aromatic Acidc back to ToC or Class ToC

IRI: http://nubbe.db/AromaticAcid

is defined by
http://nubbe.db/

A Aromatic Acid.

has super-classes
Aromatic Derivativec

Aromatic Derivativec back to ToC or Class ToC

IRI: http://nubbe.db/AromaticDerivative

is defined by
http://nubbe.db/

A Aromatic Derivative.

has super-classes
Chemical Compoundc
has sub-classes
Aromatic Acidc, Benzofuranoidc, Benzophenone Derivativec, Chromanec, Chromanonec, Chromenec, Chromonec, Coumarinc, Stilbenec, Styryl Pyronec, Xanthonec

Aromatic Polyketidec back to ToC or Class ToC

IRI: http://nubbe.db/AromaticPolyketide

is defined by
http://nubbe.db/

A Aromatic Polyketide.

has super-classes
Polyketidesc

Benzofuranoidc back to ToC or Class ToC

IRI: http://nubbe.db/Benzofuranoid

is defined by
http://nubbe.db/

A Benzofuranoid.

has super-classes
Aromatic Derivativec

Benzophenone Derivativec back to ToC or Class ToC

IRI: http://nubbe.db/BenzophenoneDerivative

is defined by
http://nubbe.db/

A Benzophenone Derivative.

has super-classes
Aromatic Derivativec

Biflavonoidc back to ToC or Class ToC

IRI: http://nubbe.db/Biflavonoid

is defined by
http://nubbe.db/

A Biflavonoid.

has super-classes
Flavonoidc

Carbohydratec back to ToC or Class ToC

IRI: http://nubbe.db/Carbohydrates

is defined by
http://nubbe.db/

A Carbohydrate.

has super-classes
Chemical Compoundc

Chalconesc back to ToC or Class ToC

IRI: http://nubbe.db/Chalcones

is defined by
http://nubbe.db/

A Chalcones.

has super-classes
Chemical Compoundc

Chemical Substancec back to ToC or Class ToC

IRI: http://nubbe.db/ChemicalSubstance

is defined by
http://nubbe.db/

A Chemical Substance.

has super-classes
thingc
has sub-classes
Chemical Compoundc

Chromanec back to ToC or Class ToC

IRI: http://nubbe.db/Chromane

is defined by
http://nubbe.db/

A Chromane.

has super-classes
Aromatic Derivativec

Chromanonec back to ToC or Class ToC

IRI: http://nubbe.db/Chromanone

is defined by
http://nubbe.db/

A Chromanone.

has super-classes
Aromatic Derivativec

Chromenec back to ToC or Class ToC

IRI: http://nubbe.db/Chromene

is defined by
http://nubbe.db/

A Chromene.

has super-classes
Aromatic Derivativec

Chromonec back to ToC or Class ToC

IRI: http://nubbe.db/Chromone

is defined by
http://nubbe.db/

A Chromone.

has super-classes
Aromatic Derivativec

Coumarinc back to ToC or Class ToC

IRI: http://nubbe.db/Coumarin

is defined by
http://nubbe.db/

A Coumarin.

has super-classes
Aromatic Derivativec

Diterpenoidc back to ToC or Class ToC

IRI: http://nubbe.db/Diterpenoid

is defined by
http://nubbe.db/

A Diterpenoid.

has super-classes
Terpenec

Flavanolc back to ToC or Class ToC

IRI: http://nubbe.db/Flavanol

is defined by
http://nubbe.db/

A Flavanol.

has super-classes
Flavonoidc

Flavanonec back to ToC or Class ToC

IRI: http://nubbe.db/Flavanone

is defined by
http://nubbe.db/

A Flavanone.

has super-classes
Flavonoidc

Flavonec back to ToC or Class ToC

IRI: http://nubbe.db/Flavone

is defined by
http://nubbe.db/

A Flavone.

has super-classes
Flavonoidc

Flavonoidc back to ToC or Class ToC

IRI: http://nubbe.db/Flavonoid

is defined by
http://nubbe.db/

A Flavonoid.

has super-classes
Chemical Compoundc
has sub-classes
Anthocyanidinc, Biflavonoidc, Flavanolc, Flavanonec, Flavonec, Flavonolc, Isoflavonoidc

Flavonolc back to ToC or Class ToC

IRI: http://nubbe.db/Flavonol

is defined by
http://nubbe.db/

A Flavonol.

has super-classes
Flavonoidc

Hemiterpenoidc back to ToC or Class ToC

IRI: http://nubbe.db/Hemiterpenoid

is defined by
http://nubbe.db/

A Hemiterpenoid.

has super-classes
Terpenec

Hydrolysable Tanninc back to ToC or Class ToC

IRI: http://nubbe.db/HydrolysableTannin

is defined by
http://nubbe.db/

A Hydrolysable Tannin.

has super-classes
taninsc

Imidazole Alkaloidc back to ToC or Class ToC

IRI: http://nubbe.db/ImidazoleAlkaloid

is defined by
http://nubbe.db/

A Imidazole Alkaloid.

has super-classes
Alkaloidsc

Indole Alkaloidc back to ToC or Class ToC

IRI: http://nubbe.db/IndoleAlkaloid

is defined by
http://nubbe.db/

A Indole Alkaloid.

has super-classes
Alkaloidsc

Iridoidc back to ToC or Class ToC

IRI: http://nubbe.db/Iridoid

is defined by
http://nubbe.db/

A Iridoid.

has super-classes
Terpenec

Isoflavonoidc back to ToC or Class ToC

IRI: http://nubbe.db/Isoflavonoid

is defined by
http://nubbe.db/

A Isoflavonoid.

has super-classes
Flavonoidc

Lignoidc back to ToC or Class ToC

IRI: http://nubbe.db/Lignoid

is defined by
http://nubbe.db/

A Lignoid.

has super-classes
Chemical Compoundc

Linear Polyketidec back to ToC or Class ToC

IRI: http://nubbe.db/LinearPolyketide

is defined by
http://nubbe.db/

A Linear Polyketide.

has super-classes
Polyketidesc

Lipidc back to ToC or Class ToC

IRI: http://nubbe.db/Lipid

is defined by
http://nubbe.db/

A Lipid.

has super-classes
Chemical Compoundc

Meroterpenoidc back to ToC or Class ToC

IRI: http://nubbe.db/Meroterpenoid

is defined by
http://nubbe.db/

A Meroterpenoid.

has super-classes
Terpenec

Monoterpenoidc back to ToC or Class ToC

IRI: http://nubbe.db/Monoterpenoid

is defined by
http://nubbe.db/

A Monoterpenoid.

has super-classes
Terpenec

Peptidec back to ToC or Class ToC

IRI: http://nubbe.db/Peptide

is defined by
http://nubbe.db/

A Peptide.

has super-classes
aminoacids and peptidec

Phenylpropanoidsc back to ToC or Class ToC

IRI: http://nubbe.db/Phenylpropanoid

is defined by
http://nubbe.db/

A Phenylpropanoids.

has super-classes
Chemical Compoundc

Piperidine Alkaloidc back to ToC or Class ToC

IRI: http://nubbe.db/PiperidineAlkaloid

is defined by
http://nubbe.db/

A Piperidine Alkaloid.

has super-classes
Alkaloidsc

Polyketidesc back to ToC or Class ToC

IRI: http://nubbe.db/Polyketide

is defined by
http://nubbe.db/

A Polyketides.

has super-classes
Chemical Compoundc
has sub-classes
Aromatic Polyketidec, Linear Polyketidec

Pyridine Alkaloidc back to ToC or Class ToC

IRI: http://nubbe.db/PyridineAlkaloid

is defined by
http://nubbe.db/

A Pyridine Alkaloid.

has super-classes
Alkaloidsc

Pyrrolidine Alkaloidc back to ToC or Class ToC

IRI: http://nubbe.db/PyrrolidineAlkaloid

is defined by
http://nubbe.db/

A Pyrrolidine Alkaloid.

has super-classes
Alkaloidsc

Quinazoline Alkaloidc back to ToC or Class ToC

IRI: http://nubbe.db/QuinazolineAlkaloid

is defined by
http://nubbe.db/

A Quinazoline Alkaloid.

has super-classes
Alkaloidsc

Quinoline Alkaloidc back to ToC or Class ToC

IRI: http://nubbe.db/QuinolineAlkaloid

is defined by
http://nubbe.db/

A Quinoline Alkaloid.

has super-classes
Alkaloidsc

Quinolizidine Alkaloidc back to ToC or Class ToC

IRI: http://nubbe.db/QuinolizidineAlkaloid

is defined by
http://nubbe.db/

A Quinolizidine Alkaloid.

has super-classes
alkaloidsc

Sesquiterpenoidc back to ToC or Class ToC

IRI: http://nubbe.db/Sesquiterpenoid

is defined by
http://nubbe.db/

A Sesquiterpenoid.

has super-classes
Terpenec

Steroidsc back to ToC or Class ToC

IRI: http://nubbe.db/Steroid

is defined by
http://nubbe.db/

A Steroids.

has super-classes
Terpenec

Stilbenec back to ToC or Class ToC

IRI: http://nubbe.db/Stilbene

is defined by
http://nubbe.db/

A Stilbene.

has super-classes
Aromatic Derivativec

Styryl Pyronec back to ToC or Class ToC

IRI: http://nubbe.db/StyrylPyrone

is defined by
http://nubbe.db/

A Styryl Pyrone.

has super-classes
Aromatic Derivativec

Terpenec back to ToC or Class ToC

IRI: http://nubbe.db/Terpene

is defined by
http://nubbe.db/

A Terpene.

has super-classes
Chemical Compoundc
has sub-classes
Diterpenoidc, Hemiterpenoidc, Iridoidc, Meroterpenoidc, Monoterpenoidc, Sesquiterpenoidc, Steroidsc, Triterpenoidc

Tetrahydroisoquinoline Alkaloidc back to ToC or Class ToC

IRI: http://nubbe.db/TetrahydroisoquinolineAlkaloid

is defined by
http://nubbe.db/

A Tetrahydroisoquinoline Alkaloid.

has super-classes
Alkaloidsc

Triterpenoidc back to ToC or Class ToC

IRI: http://nubbe.db/Triterpenoid

is defined by
http://nubbe.db/

A Triterpenoid.

has super-classes
Terpenec

Xanthonec back to ToC or Class ToC

IRI: http://nubbe.db/Xanthone

is defined by
http://nubbe.db/

A Xanthone.

has super-classes
Aromatic Derivativec

Β-Lactamc 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 peptidec

Data Properties

biological activitydp 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 Compoundc
has range
string

codedp 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 Compoundc
has range
integer

collection sitedp 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 Compoundc
has range
string

collection speciedp 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 Compoundc
has range
string

collection typedp 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 Compoundc
has range
string

doidp 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 Compoundc
has range
string

logP coeficientdp 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 Compoundc
has range
double

molecular massdp 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 Compoundc
has range
double

molecular volumedp 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 Compoundc
has range
double

monoisotropic massdp 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 Compoundc
has range
double

number of H-bond acceptorsdp 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 Compoundc
has range
int

number of H-bond donorsdp 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 Compoundc
has range
int

number of Lipiski violationsdp 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 Compoundc
has range
int

number of rotable bondsdp 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 Compoundc
has range
int

smiledp 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 Compoundc
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 Compoundc
has range
double

Named Individuals

edgard marxni back to ToC or Named Individual ToC

IRI: https://aksw.org/EdgardMarx

belongs to
agentc
personc

NUBBE: The NUBBE DB Ontologyni back to ToC or Named Individual ToC

IRI: http://nubbe.db/

belongs to
vocabularyc

Annotation Properties

creatorap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/creator

is defined by
http://purl.org/dc/terms/

descriptionap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/description

is defined by
http://purl.org/dc/terms/

issuedap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/issued

is defined by
http://purl.org/dc/terms/

licenseap back to ToC or Annotation Property ToC

IRI: http://creativecommons.org/ns#license

is defined by
http://creativecommons.org/ns

modifiedap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/modified

is defined by
http://purl.org/dc/terms/

nameap back to ToC or Annotation Property ToC

IRI: http://xmlns.com/foaf/0.1/name

preferred namespace prefixap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocab/vann/preferredNamespacePrefix

is defined by
http://purl.org/vocab/vann/

preferred namespace uriap back to ToC or Annotation Property ToC

IRI: http://purl.org/vocab/vann/preferredNamespaceUri

is defined by
http://purl.org/vocab/vann/

publisherap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/publisher

is defined by
http://purl.org/dc/terms/

rightsap back to ToC or Annotation Property ToC

IRI: http://purl.org/dc/terms/rights

is defined by
http://purl.org/dc/terms/

vocabularyap back to ToC or Annotation Property ToC

IRI: http://rdfs.org/ns/void#vocabulary

Namespace Declarations back to ToC

default namespace
http://nubbe.db/
aksw-org
https://aksw.org/
creativecommons-org
http://creativecommons.org/
dct
http://purl.org/dc/terms/
foaf
http://xmlns.com/foaf/0.1/
ns
http://creativecommons.org/ns#
nubbeclass
http://nubbe.db/class/
nubbeprop
http://nubbe.db/property/
owl
http://www.w3.org/2002/07/owl#
rdf
http://www.w3.org/1999/02/22-rdf-syntax-ns#
rdfs
http://www.w3.org/2000/01/rdf-schema#
vann
http://purl.org/vocab/vann/
voaf
http://purl.org/vocommons/voaf#
void
http://rdfs.org/ns/void#
xsd
http://www.w3.org/2001/XMLSchema#

This HTML document was obtained by processing the OWL ontology source code through LODE, Live OWL Documentation Environment, developed by Silvio Peroni.