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: The entity a chemical compound has been extracted from is classified by a biological taxonomy.

has structure information
type: ObjectProperty
domain: Compound
range: Classyfire
comment: A chemical compound has a structural classification.

was discovered at
type: ObjectProperty
domain: Compound
range: Isolation site
comment: A compound was discovered in a distinct isolation site.

was subjected to
type: ObjectProperty
domain: Compound
range: Bioactivity analysis
comment: A chemical compound was subjected to bioactivity analysis.

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.

is located in
type: ObjectProperty
domain: Isolation site
range: City
range: State
comment: An isolation-site is located in a distinct city and state.

part of species
type: ObjectProperty
domain: Taxonomy
range: Species
comment: A compound is part of a species of life.

revealed
type: ObjectProperty
domain: Bioactivity analysis
range: Bioactivity
comment: Bioactivity analysis revealed a specific bioactivity behaviour.

used Matter
type: ObjectProperty
domain: Bioactivity analysis
range: Matter type
comment: For bioactivity analysis a specific matter type was used.

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

Molecular weight
type: DatatypeProperty
domain: Molecular descriptors
range: float
comment: Molecular weight of a chemical compound.

Monoisotopic mass
type: DatatypeProperty
domain: Molecular descriptors
range: float
comment: Monoisotopic mass of a chemical compound.

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

logP Coefficient
type: DatatypeProperty
domain: Constitutional descriptors
range: float
comment: Prediction of the logP Coefficient.

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.

NUBBE ID
type: DatatypeProperty
domain: Unique identifiers
range: string
comment: The numeric identifier a chemical compound has in the NubbeDB database.

SMILES
type: DatatypeProperty
domain: Compound
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.

structure superclass
type: DatatypeProperty
domain: Classyfire
range: string
comment: The superclass of which a chemical compound is part of.

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

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

structure Kingdom
type: DatatypeProperty
domain: Classyfire
range: string
comment: The kingdom of which a chemical compound is part of.

Isolation type
type: DatatypeProperty
domain: Isolation site
range: string
comment: Explains in what way the chemical compound has been extracted.

IC50
type: DatatypeProperty
domain: Bioactivity
range: double
comment: The concentration of a drug or inhibitor needed to inhibit a biological process or response by 50%.

IC12
type: DatatypeProperty
domain: Bioactivity
range: double
comment: The concentration of a drug or inhibitor needed to inhibit a biological process or response by 12,5%.

LD50
type: DatatypeProperty
domain: Bioactivity
range: double
comment: The amount of a material, given all at once, which causes the death of 50% of a group of test animals.

EC50
type: DatatypeProperty
domain: Bioactivity
range: double
comment: The effective concentration of a drug that gives half-maximal response.

MIC
type: DatatypeProperty
domain: Bioactivity
range: double
comment: The minimum inhibitory concentration is the lowest concentration of a chemical, usually a drug, which prevents visible growth of a bacterium or bacteria.

MFC
type: DatatypeProperty
domain: Bioactivity
range: double
comment: The minimum fungicidal concentrations was defined as the lowest concentration of drug showing no visible growth.

ED50
type: DatatypeProperty
domain: Bioactivity
range: double
comment: The effective dose of a drug that gives half-maximal response.

Scientific name
type: DatatypeProperty
domain: Species
range: string
comment: The given scientific name of a taxonomic species.

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 analysis
type: Class
comment: Bioactivity analysis 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.

Unique identifiers
type: Class
comment: Unique identifiers of a chemical compound like IUPAC-name and inchikey.

Classyfire
type: Class
comment: The structural classification of a chemical compound, containing kingdom, superclass, class and subclass information.

Taxonomy
type: Class
comment: The biological taxonomy of the entity a chemical compound has been extracted from.

Species
type: Class
comment: The species of which a biological entity is part of.

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

City
type: Class
subclass of: Location
comment: The city in which the chemical compound has been extracted.

State
type: Class
subclass of: Location
comment: The state in which the chemical compound has been extracted, usually just by it's short code.

Location
type: Class
comment: Parent location class, includes city and statecode.

Bioactivity
type: Class
comment: A description of the observed properties during bioactivity analysis.

Matter type
type: Class
comment: The type of matter the actual bioactivity testing is performed on.