language en

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:
JSON-LD RDF/XML N-Triples TTL
License:
http://insertlicenseURIhere.org
Visualization:
Visualize with WebVowl
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

Annotation 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

Analysisc back to ToC or Class ToC

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

A bioanalysis of a ?.
is in domain of
about specimen op, discovered op, has bioassay op, reference op

Assayc back to ToC or Class ToC

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

A bioassay of an analysis.
is in domain of
bioactivity op, generates op
is in range of
has bioassay op

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
bioactivity op

Bioactivity quantificationc back to ToC or Class ToC

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

Bioactivity quantification of a bioactivity.
is in domain of
EC50 dp, ED50 dp, IC50 dp, LD50 dp, MIC dp
is in range of
generates 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
Location c
is in domain of
located in op

Compoundc back to ToC or Class ToC

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

A chemical compound.
is in domain of
Common name dp, SMILES dp, has descriptors op, is identified by op, part of metabolic class op
is in range of
discovered 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

Locationc back to ToC or Class ToC

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

Location where a specimen was found.
has sub-classes
City c, State c
is in range of
was discovered in 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.
has super-classes
Metabolic class c
has sub-classes
Metabolic class c
is in range of
part of metabolic class 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 formula dp, 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.
has super-classes
Reference c
is in domain of
Periodic magazine dp, Publication doi dp, Publication page numbers dp, Publication title dp, Publication volume dp, Publication year dp, Publisher dp, Summary dp

Referencec back to ToC or Class ToC

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

A reference.
has sub-classes
Publication c
is in range of
reference 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

Specimenc back to ToC or Class ToC

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

A specimen, like a part of a plant or microorganism, that contains natural chemical compounds.
is in domain of
part of species op, sample type dp, was discovered in op
is in range of
about specimen 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
Location c
is in range of
located in op

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

about specimenop back to ToC or Object Property ToC

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

A bioanalysis has information on specimen.
has domain
Analysis c
has range
Specimen c

bioactivityop back to ToC or Object Property ToC

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

A bioassay revealed a specific bioactivity.
has domain
Assay c
has range
Bioactivity c

discoveredop back to ToC or Object Property ToC

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

A bioanalysis is about one or more natural chemical compounds.
has domain
Analysis c
has range
Compound c

generatesop back to ToC or Object Property ToC

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

A bioassay generates specific bioactivity quantifications.
has domain
Assay c
has range
Bioactivity quantification c

has bioassayop back to ToC or Object Property ToC

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

A bioanalysis has a bioassay.
has domain
Analysis c
has range
Assay c

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

located inop back to ToC or Object Property ToC

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

A city is located within a state.
has domain
City c
has range
State c

part of metabolic classop back to ToC or Object Property ToC

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

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 specimen is part of a species of life.
has domain
Specimen c
has range
Species c

referenceop back to ToC or Object Property ToC

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

A analysis was referenced in a certain reference medium.
has domain
Analysis c
has range
Reference c

was discovered inop back to ToC or Object Property ToC

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

A specimen was discovered in a certain location.
has domain
Specimen c
has range
Location 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 quantification 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 quantification 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

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 quantification 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 quantification 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

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 quantification 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
Molecular descriptors 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

Periodic magazinedp back to ToC or Data Property ToC

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

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

Publication doidp back to ToC or Data Property ToC

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

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

Publication page numbersdp back to ToC or Data Property ToC

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

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#title

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

Publication volumedp back to ToC or Data Property ToC

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

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

Publisherdp back to ToC or Data Property ToC

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

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

sample typedp back to ToC or Data Property ToC

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

The type of specimen sample, wether it has been taking from a plant, microorganism or animal.
has domain
Specimen 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

Summarydp back to ToC or Data Property ToC

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

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

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

Annotation Properties

creatorap back to ToC or Annotation Property ToC

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

descriptionap back to ToC or Annotation Property ToC

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

preferred namespace prefixap back to ToC or Annotation Property ToC

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

preferred namespace uriap back to ToC or Annotation Property ToC

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

rightsap back to ToC or Annotation Property ToC

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

titleap back to ToC or Annotation Property ToC

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

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.