Edgard Marx, Stefan Schmidt-Dichte, Istvan J. Mocsy
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.
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nubbe: The data model for nubbeDB Knowledge Graph
A chemical compound has various descriptors.
has descriptors
The entity a chemical compound has been extracted from is classified by a biological taxonomy.
is classified by
A chemical compound has a structural classification.
has structure information
A chemical compound has data about it's isolation site and origin.
has isolation data
A chemical compound has bioactivity data.
has bioactivity data
A chemical compound is identified by it's unique identifiers.
is identified by
A chemical compound was mentioned in a publication.
was mentioned in
Given common name of a chemical compound.
Common name
Molecular weight of a chemical compound.
Molecular weight
Monoisotopic mass of a chemical compound.
Monoisotopic mass
Molecular volume of a chemical compound.
Molecular volume
Prediction of the logP Coefficient.
logP Coefficient
Calculation of topological polar surface area based on fragment contributions (TPSA) (Ertl, P. et. al.. J.Med. Chem.. 2000. 43).
TPSA
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.
Lipinski rule of 5 failures
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 acceptor count
Donor count is the sum of the atoms in the molecule which have H donor property.
hydrogen bond donor count
Number of rotatable bonds of a chemical compound.
nRotB
The numeric identifier a chemical compound has in the NubbeDB database.
NUBBE ID
Simplified Molecular Input Line Entry Specification.
SMILES
Name within the International Union of Pure and Applied Chemistry.
IUPAC Name
International Chemical Identifier.
inchi
International Chemical Identifier key.
inchikey
Molecular formula of a chemical compound.
Molecular formula
The sub-publication Id of a compounds publication.
Sub-Pub ID
The publication Id of a compounds publication.
Publication ID
The type of a compounds publication.
Publication type
The title of a compounds publication.
Publication title
The digital object identifier of a compounds publication.
Publication DOI
The year of the publication was published.
Publication year
The volume in which the publication was published.
Publication volume
The page numbers of the mediium the publication was published.
Publication page numbers
The agency which published the publication.
Publication agency
The periodic magazine in which the publication appeared.
Publications periodic magazine
The Process TODO in which the publication appeared.
Publications process
The local publication medium in which the publication appeared.
Publications local publishments
The publisher of a publication.
Publications publisher
Any event where the publication has been a topic.
Publications events
Extra informations on citations of the publication.
Publications citation extra information
A one word description of the observed properties during bioactivity analysis.
Observation
The species of which a biological entity is part of.
Species
The genus of which a biological entity is part of.
Genus
The family of which a biological entity is part of.
Family
The order of which a biological entity is part of.
Order
The class of which a biological entity is part of.
Class
The phylum of which a biological entity is part of.
Phylum
The kingdom of which a biological entity is part of.
Kingdom
The domain of which a biological entity is part of.
Domain
The superclass of which a chemical compound is part of.
structure superclass
The subclass of which a chemical compound is part of.
structure Subclass
The class of which a chemical compound is part of.
structure Class
The kingdom of which a chemical compound is part of.
structure Kingdom
Explains in what way the chemical compound has been extracted.
Isolation type
The city in which the chemical compound has been extracted.
Isolation city
The state in which the chemical compound has been extracted, usually just by it's short code.
Isolation state
The concentration of a drug or inhibitor needed to inhibit a biological process or response by 50%.
IC50
The concentration of a drug or inhibitor needed to inhibit a biological process or response by 12,5%.
IC12
The amount of a material, given all at once, which causes the death of 50% of a group of test animals.
LD50
The effective concentration of a drug that gives half-maximal response.
EC50
The minimum inhibitory concentration is the lowest concentration of a chemical, usually a drug, which prevents visible growth of a bacterium or bacteria.
MIC
The minimum fungicidal concentrations was defined as the lowest concentration of drug showing no visible growth.
MFC
The effective dose of a drug that gives half-maximal response.
ED50
The type of matter the actual bioactivity testing is performed on.
tested as
A chemical compound.
Compound
Descriptors chemical compound.
Descriptors
A publication in which a chemical compound was mentioned in.
Publication
Bioactivity data of a chemical compound.
Bioactivity data
Electronic descriptors of a chemical compound.
Electronic descriptors
Constitutional descriptors of a chemical compound.
Constitutional descriptors
Topological descriptors of a chemical compound.
Topological descriptors
Molecular descriptors of a chemical compound.
Molecular descriptors
Unique identifiers of a chemical compound like IUPAC-name and inchikey.
Unique identifiers
The structural classification of a chemical compound, containing kingdom, superclass, class and subclass information.
Classyfire
The biological taxonomy of the entity a chemical compound has been extracted from.
Taxonomy
Information on where and from what entity the chemical compound has been isolated.
Isolation