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nubbe: The data model for nubbeDB Knowledge Graph

Latest version:
http://nubbekg.aksw.org/ontology#
Revision:
SNAPSHOT
Authors:
Edgard Marx, Stefan Schmidt-Dichte, Istvan J. Mocsy
Download serialization:
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License:
https://creativecommons.org/licenses/by-nc-nd/4.0/
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Cite as:
Edgard Marx, Stefan Schmidt-Dichte, Istvan J. Mocsy. nubbe: The data model for nubbeDB Knowledge Graph. Revision: SNAPSHOT.
Ontology Specification Draft

Abstract

The nubbe Ontology contains the data model of nubbeDB Knowledge Graph. It facilitates the knowledge graph data manipulation and consumption through concepts such as natural products, molecules, and their respective properties.

Introduction back to ToC

This is a place holder text for the introduction. The introduction should briefly describe the ontology, its motivation, state of the art and goals.

Namespace declarations

Table 1: Namespaces used in the document
nubbe<http://nubbekg.aksw.org/ontology#>
owl<http://www.w3.org/2002/07/owl>
rdf<http://www.w3.org/1999/02/22-rdf-syntax-ns>
terms<http://purl.org/dc/terms>
xml<http://www.w3.org/XML/1998/namespace>
xsd<http://www.w3.org/2001/XMLSchema>
rdfs<http://www.w3.org/2000/01/rdf-schema>
vann<http://purl.org/vocab/vann>

nubbe: The data model for nubbeDB Knowledge Graph: Overview back to ToC

This ontology has the following classes and properties.

Classes

Object Properties

Data Properties

nubbe: The data model for nubbeDB Knowledge Graph: Description back to ToC

This is a placeholder text for the description of your ontology. The description should include an explanation and a diagram explaining how the classes are related, examples of usage, etc.

Cross-reference for nubbe: The data model for nubbeDB Knowledge Graph classes, object properties and data properties back to ToC

This section provides details for each class and property defined by nubbe: The data model for nubbeDB Knowledge Graph.

Classes

Bioactivityc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#Bioactivity

A description of the observed properties during bioactivity analysis.
is in range of
revealed op

Bioactivity analysisc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#BioactivityAnalysis

Bioactivity analysis data of a chemical compound.
is in domain of
EC50 dp, ED50 dp, IC12 dp, IC50 dp, LD50 dp, MFC dp, MIC dp, revealed op
is in range of
was subjected to op

Cityc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#City

The city in which the chemical compound has been extracted.
has super-classes
Isolation site c

Compoundc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#Compound

A chemical compound.
is in domain of
Common name dp, Molecular formula dp, SMILES dp, has descriptors op, is identified by op, part of class op, part of species op, part of subclass op, was discovered at op, was isolated from op, was mentioned in op, was subjected to op

Constitutional descriptorsc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#ConstitutionalDescriptors

Constitutional descriptors of a chemical compound.
has super-classes
Descriptors c
is in domain of
Lipinski rule of 5 failures dp, logP Coefficient dp

Descriptorsc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#Descriptors

Descriptors chemical compound.
has sub-classes
Constitutional descriptors c, Electronic descriptors c, Molecular descriptors c, Topological descriptors c
is in range of
has descriptors op

Electronic descriptorsc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#ElectronicDescriptors

Electronic descriptors of a chemical compound.
has super-classes
Descriptors c
is in domain of
hydrogen bond acceptor count dp, hydrogen bond donor count dp

Isolation sitec back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#IsolationSite

Information on where and from what entity the chemical compound has been isolated.
has sub-classes
City c, State c
is in range of
was discovered at op

Isolation typec back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#IsolationType

Explains in what way the chemical compound has been extracted.
is in range of
was isolated from op

Metabolic classc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#MetabolicClass

The metabolic class of which a chemical compound is part of.
is in range of
part of class op

Metabolic subclassc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#MetabolicSubclass

The metabolic subclass of which a chemical compound is part of.
is in range of
part of subclass op

Molecular descriptorsc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#MolecularDescriptors

Molecular descriptors of a chemical compound.
has super-classes
Descriptors c
is in domain of
Molecular volume dp, Molecular weight dp, Monoisotopic mass dp, nRotB dp

Publicationc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#Publication

A publication in which a chemical compound was mentioned in.
is in domain of
Publication ID dp, Publication agency dp, Publication page numbers dp, Publication title dp, Publication volume dp, Publication year dp, Publications citation extra information dp, Publications events dp, Publications local publishments dp, Publications periodic magazine dp, Publications process dp, Publications publisher dp, Sub-Pub ID dp, was published as op
is in range of
was mentioned in op

Publication typec back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#PublicationType

The type of the publication medium.
is in range of
was published as op

Speciesc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#Species

The species of which a biological entity is part of.
is in range of
part of species op

Statec back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#State

The state in which the chemical compound has been extracted, usually just by it's short code.
has super-classes
Isolation site c

Topological descriptorsc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#TopologicalDescriptors

Topological descriptors of a chemical compound.
has super-classes
Descriptors c
is in domain of
TPSA dp

Unique identifiersc back to ToC or Class ToC

IRI: http://nubbekg.aksw.org/ontology#UniqueIdentifiers

Unique identifiers of a chemical compound like IUPAC-name and inchikey.
is in domain of
IUPAC Name dp, NUBBE ID dp, inchi dp, inchikey dp
is in range of
is identified by op

Object Properties

has descriptorsop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#hasDescriptors

A chemical compound has various descriptors.
has domain
Compound c
has range
Descriptors c

is identified byop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#isIdentifiedBy

A chemical compound is identified by it's unique identifiers.
has domain
Compound c
has range
Unique identifiers c

part of classop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#partOfClass

A compound is part of a metabolic class.
has domain
Compound c
has range
Metabolic class c

part of speciesop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#partOfSpecies

A compound is part of a species of life.
has domain
Compound c
has range
Species c

part of subclassop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#partOfSubclass

A compound is part of a metabolic subclass.
has domain
Compound c
has range
Metabolic subclass c

revealedop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#revealed

Bioactivity analysis revealed a specific bioactivity behaviour.
has domain
Bioactivity analysis c
has range
Bioactivity c

was discovered atop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#wasDiscoveredAt

A compound was discovered in a distinct isolation site.
has domain
Compound c
has range
Isolation site c

was isolated fromop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#wasIsolatedFrom

A compound was isolated from a specific host.
has domain
Compound c
has range
Isolation type c

was mentioned inop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#wasMentionedIn

A chemical compound was mentioned in a publication.
has domain
Compound c
has range
Publication c

was published asop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#wasPublishedAs

A publication was published as a certain medium type.
has domain
Publication c
has range
Publication type c

was subjected toop back to ToC or Object Property ToC

IRI: http://nubbekg.aksw.org/ontology#wasSubjectedTo

A chemical compound was subjected to bioactivity analysis.
has domain
Compound c
has range
Bioactivity analysis c

Data Properties

Common namedp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#commonName

Given common name of a chemical compound.
has domain
Compound c
has range
string

EC50dp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#EC50

The effective concentration of a drug that gives half-maximal response.
has domain
Bioactivity analysis c
has range
double

ED50dp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#ED50

The effective dose of a drug that gives half-maximal response.
has domain
Bioactivity analysis c
has range
double

hydrogen bond acceptor countdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#hBondAcceptorCount

Acceptor count is the sum of the acceptor atoms. An acceptor atom always has a lone electron pair/lone electron pairs that is capable of establishing a H bond.
has domain
Electronic descriptors c
has range
int

hydrogen bond donor countdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#hBondDonorCount

Donor count is the sum of the atoms in the molecule which have H donor property.
has domain
Electronic descriptors c
has range
int

IC12dp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#IC12

The concentration of a drug or inhibitor needed to inhibit a biological process or response by 12,5%.
has domain
Bioactivity analysis c
has range
double

IC50dp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#IC50

The concentration of a drug or inhibitor needed to inhibit a biological process or response by 50%.
has domain
Bioactivity analysis c
has range
double

inchidp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#inchi

International Chemical Identifier.
has domain
Unique identifiers c
has range
string

inchikeydp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#inchikey

International Chemical Identifier key.
has domain
Unique identifiers c
has range
string

IUPAC Namedp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#iupacName

Name within the International Union of Pure and Applied Chemistry.
has domain
Unique identifiers c
has range
string

LD50dp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#LD50

The amount of a material, given all at once, which causes the death of 50% of a group of test animals.
has domain
Bioactivity analysis c
has range
double

Lipinski rule of 5 failuresdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#lipinskiRuleOf5Failures

Number of failures in the Lipinski rule of five. The Rule of Five is a rule of thumb for the oral bioavailability of a chemical compound.
has domain
Constitutional descriptors c
has range
int

logP Coefficientdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#logpCoefficient

Prediction of the logP Coefficient.
has domain
Constitutional descriptors c
has range
float

MFCdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#MFC

The minimum fungicidal concentrations was defined as the lowest concentration of drug showing no visible growth.
has domain
Bioactivity analysis c
has range
double

MICdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#MIC

The minimum inhibitory concentration is the lowest concentration of a chemical, usually a drug, which prevents visible growth of a bacterium or bacteria.
has domain
Bioactivity analysis c
has range
double

Molecular formuladp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#molecularFormula

Molecular formula of a chemical compound.
has domain
Compound c
has range
string

Molecular volumedp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#molecularVolume

Molecular volume of a chemical compound.
has domain
Molecular descriptors c
has range
float

Molecular weightdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#molecularWeight

Molecular weight of a chemical compound.
has domain
Molecular descriptors c
has range
float

Monoisotopic massdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#monoisotopicMass

Monoisotopic mass of a chemical compound.
has domain
Molecular descriptors c
has range
float

nRotBdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#nrotb

Number of rotatable bonds of a chemical compound.
has domain
Molecular descriptors c
has range
float

NUBBE IDdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#nubbeId

The numeric identifier a chemical compound has in the NubbeDB database.
has domain
Unique identifiers c
has range
string

Publication agencydp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationAgency

The agency which published the publication.
has domain
Publication c
has range
string

Publication IDdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationId

The publication Id of a compounds publication.
has domain
Publication c
has range
int

Publication page numbersdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationPages

The page numbers of the mediium the publication was published.
has domain
Publication c
has range
string

Publication titledp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationTitle

The title of a compounds publication.
has domain
Publication c
has range
string

Publication volumedp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationVolume

The volume in which the publication was published.
has domain
Publication c
has range
string

Publication yeardp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationYear

The year of the publication was published.
has domain
Publication c
has range
int

Publications citation extra informationdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationCitationExtra

Extra informations on citations of the publication.
has domain
Publication c
has range
string

Publications eventsdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationEvent

Any event where the publication has been a topic.
has domain
Publication c
has range
string

Publications local publishmentsdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationLocal

The local publication medium in which the publication appeared.
has domain
Publication c
has range
string

Publications periodic magazinedp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationPeriodic

The periodic magazine in which the publication appeared.
has domain
Publication c
has range
string

Publications processdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationProcess

The Process TODO in which the publication appeared.
has domain
Publication c
has range
string

Publications publisherdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#publicationPublisher

The publisher of a publication.
has domain
Publication c
has range
string

SMILESdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#smiles

Simplified Molecular Input Line Entry Specification.
has domain
Compound c
has range
string

Sub-Pub IDdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#subpubId

The sub-publication Id of a compounds publication.
has domain
Publication c
has range
int

TPSAdp back to ToC or Data Property ToC

IRI: http://nubbekg.aksw.org/ontology#tpsa

Calculation of topological polar surface area based on fragment contributions (TPSA) (Ertl, P. et. al.. J.Med. Chem.. 2000. 43).
has domain
Topological descriptors c
has range
float

Legend back to ToC

c: Classes
op: Object Properties
dp: Data Properties

References back to ToC

Add your references here. It is recommended to have them as a list.

Acknowledgments back to ToC

The authors would like to thank Silvio Peroni for developing LODE, a Live OWL Documentation Environment, which is used for representing the Cross Referencing Section of this document and Daniel Garijo for developing Widoco, the program used to create the template used in this documentation.