nubbe: The data model for nubbeDB Knowledge Graph
type: Ontology
creator: Edgard Marx, Stefan Schmidt-Dichte, Istvan J. Mocsy
description: 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.
rights: Copyright © 2023 ChemNet
preferred namespace prefix: nubbe
version info: SNAPSHOT

has descriptors
type: ObjectProperty
domain: Compound
range: Descriptors
comment: A chemical compound has various descriptors.

is classified by
type: ObjectProperty
domain: Compound
range: Taxonomy
comment: A chemical compound is classified by a biological taxonomy.

has isolation data
type: ObjectProperty
domain: Compound
range: Isolation
comment: A chemical compound has data about it's isolation site and origin.

has bioactivity data
type: ObjectProperty
domain: Compound
range: Bioactivity data
comment: A chemical compound has bioactivity data.

is identified by
type: ObjectProperty
domain: Compound
range: Unique identifiers
comment: A chemical compound is identified by it's unique identifiers.

was mentioned in
type: ObjectProperty
domain: Compound
range: Publication
comment: A chemical compound was mentioned in a publication.

Name
type: DatatypeProperty
domain: Compound
range: string
comment: Given name of a chemical compound.

Molar mass
type: DatatypeProperty
domain: Descriptors
range: float
comment: Molar mass of a chemical compound.

Molecular volume
type: DatatypeProperty
domain: Descriptors
range: float
comment: Molecular volume of a chemical compound.

clogP
type: DatatypeProperty
domain: Constitutional descriptors
range: float
comment: Prediction of clogP.

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

Lipinski rule of 5 failures
type: DatatypeProperty
domain: Constitutional descriptors
range: int
comment: 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.

hydrogen bond acceptor count
type: DatatypeProperty
domain: Electronic descriptors
range: int
comment: 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.

hydrogen bond donor count
type: DatatypeProperty
domain: Electronic descriptors
range: int
comment: Donor count is the sum of the atoms in the molecule which have H donor property.

nRotB
type: DatatypeProperty
domain: Molecular descriptors
range: float
comment: Number of rotatable bonds of a chemical compound.

Automatic code
type: DatatypeProperty
domain: Compound
range: string
comment: Automatic code of a chemical compound.

smiles
type: DatatypeProperty
domain: Unique identifiers
range: string
comment: Simplified Molecular Input Line Entry Specification.

IUPAC Name
type: DatatypeProperty
domain: Unique identifiers
range: string
comment: Name within the International Union of Pure and Applied Chemistry.

inchi
type: DatatypeProperty
domain: Unique identifiers
range: string
comment: International Chemical Identifier.

inchikey
type: DatatypeProperty
domain: Unique identifiers
range: string
comment: International Chemical Identifier key.

Molecular formula
type: DatatypeProperty
domain: Compound
range: string
comment: Molecular formula of a chemical compound.

Sub-Pub ID
type: DatatypeProperty
domain: Publication
range: int
comment: The sub-publication Id of a compounds publication.

Publication ID
type: DatatypeProperty
domain: Publication
range: int
comment: The publication Id of a compounds publication.

Publication type
type: DatatypeProperty
domain: Publication
range: string
comment: The type of a compounds publication.

Publication title
type: DatatypeProperty
domain: Publication
range: string
comment: The title of a compounds publication.

Publication DOI
type: DatatypeProperty
domain: Publication
range: string
comment: The digital object identifier of a compounds publication.

Publication year
type: DatatypeProperty
domain: Publication
range: int
comment: The year of the publication was published.

Publication volume
type: DatatypeProperty
domain: Publication
range: string
comment: The volume in which the publication was published.

Publication page numbers
type: DatatypeProperty
domain: Publication
range: string
comment: The page numbers of the mediium the publication was published.

Publication agency
type: DatatypeProperty
domain: Publication
range: string
comment: The agency which published the publication.

Publications periodic magazine
type: DatatypeProperty
domain: Publication
range: string
comment: The periodic magazine in which the publication appeared.

Publications process
type: DatatypeProperty
domain: Publication
range: string
comment: The Process TODO in which the publication appeared.

Publications local publishments
type: DatatypeProperty
domain: Publication
range: string
comment: The local publication medium in which the publication appeared.

Publications publisher
type: DatatypeProperty
domain: Publication
range: string
comment: The publisher of a publication.

Publications events
type: DatatypeProperty
domain: Publication
range: string
comment: Any event where the publication has been a topic.

Publications citation extra information
type: DatatypeProperty
domain: Publication
range: string
comment: Extra informations on citations of the publication.

SD
type: DatatypeProperty
domain: IC50
domain: IC12
domain: Ld 50
domain: EC 50
domain: MIC
domain: MFC
domain: ED
domain: DL
domain: Inhibition
range: float
comment: Standard deviation of the method.

GT
type: DatatypeProperty
domain: IC50
domain: IC12
domain: Ld 50
domain: EC 50
domain: MIC
domain: MFC
domain: ED
domain: DL
domain: Inhibition
range: boolean
comment: GT TODO.

LT
type: DatatypeProperty
domain: IC50
domain: IC12
domain: Ld 50
domain: EC 50
domain: MIC
domain: MFC
domain: ED
domain: DL
domain: Inhibition
range: boolean
comment: Lt TODO.

methodResults
type: DatatypeProperty
domain: IC50
domain: IC12
domain: Ld 50
domain: EC 50
domain: MIC
domain: MFC
domain: ED
domain: DL
domain: Inhibition
range: float
comment: Method result.

Activity ID
type: DatatypeProperty
domain: Bioactivity data
range: int
comment: The identification number of the bioactivity.

Extra Information
type: DatatypeProperty
domain: Bioactivity data
range: string
comment: Additional information about the bioactivity analysis.

Observation
type: DatatypeProperty
domain: Bioactivity data
range: string
comment: Observation information about the bioactivity analysis.

Code
type: DatatypeProperty
domain: Bioactivity data
range: int
comment: Bioactivity Code TODO.

Concentration
type: DatatypeProperty
domain: Bioactivity data
range: string
comment: Bioactivity concentration? TODO.

Position activity
type: DatatypeProperty
domain: Bioactivity data
range: int
comment: positionActivity TODO.

Results
type: DatatypeProperty
domain: Bioactivity data
range: string
comment: A one word description of the observed properties during bioactivity analysis.

Species
type: DatatypeProperty
domain: Taxonomy
range: string
comment: The species of which a chemical compound is part of.

Family
type: DatatypeProperty
domain: Taxonomy
range: string
comment: The family of which a chemical compound is part of.

Gender
type: DatatypeProperty
domain: Taxonomy
range: string
comment: The gender of which a chemical compound is part of.

Subclass
type: DatatypeProperty
domain: Taxonomy
range: string
comment: The Subclass of which a chemical compound is part of.

Class
type: DatatypeProperty
domain: Taxonomy
range: string
comment: The Class of which a chemical compound is part of.

Isolation type
type: DatatypeProperty
domain: Isolation
range: string
comment: The entity from which the chemical compound has been extracted.

Isolation city
type: DatatypeProperty
domain: Isolation
range: string
comment: The city in which the chemical compound has been extracted.

Isolation state
type: DatatypeProperty
domain: Isolation
range: string
comment: The state in which the chemical compound has been extracted, usually jsut by it's short code.

Compound
type: Class
comment: A chemical compound.

Descriptors
type: Class
comment: Descriptors chemical compound.

Publication
type: Class
comment: A publication in which a chemical compound was mentioned in.

Bioactivity data
type: Class
comment: Bioactivity data of a chemical compound.

Electronic descriptors
type: Class
subclass of: Descriptors
comment: Electronic descriptors of a chemical compound.

Constitutional descriptors
type: Class
subclass of: Descriptors
comment: Constitutional descriptors of a chemical compound.

Topological descriptors
type: Class
subclass of: Descriptors
comment: Topological descriptors of a chemical compound.

Molecular descriptors
type: Class
subclass of: Descriptors
comment: Molecular descriptors of a chemical compound.

IC50
type: Class
subclass of: Bioactivity data
comment: The concentration of a drug or inhibitor needed to inhibit a biological process or response by 50%.

IC12
type: Class
subclass of: Bioactivity data
comment: The concentration of a drug or inhibitor needed to inhibit a biological process or response by 12,5%.

Ld 50
type: Class
subclass of: Bioactivity data
comment: LD50 is the amount of a material, given all at once, which causes the death of 50% (one half) of a group of test animals.

EC 50
type: Class
subclass of: Bioactivity data
comment: The EC50 is the concentration of a drug that gives half-maximal response.

MIC
type: Class
subclass of: Bioactivity data
comment: The minimum inhibitory concentration (MIC) is the lowest concentration of a chemical, usually a drug, which prevents visible growth of a bacterium or bacteria.

MFC
type: Class
subclass of: Bioactivity data
comment: The minimum fungicidal concentrations(MFC) was defined as the lowest concentration of drug showing no visible growth.

ED
type: Class
subclass of: Bioactivity data
comment: ED TODO.

DL
type: Class
subclass of: Bioactivity data
comment: DL TODO.

Inhibition
type: Class
subclass of: Bioactivity data
comment: Inhibition TODO.

Unique identifiers
type: Class
comment: Unique identifiers of a chemical compound like smiles and inchikeys.

Taxonomy
type: Class
comment: The biological taxonomy of a chemical compound.

Isolation
type: Class
comment: Information on where and from what the chemical compound has been isolated.