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
A chemical compound is classified by a biological taxonomy.
is classified by
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 name of a chemical compound.
Name
Molar mass of a chemical compound.
Molar mass
Molecular volume of a chemical compound.
Molecular volume
Prediction of clogP.
clogP
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
Automatic code of a chemical compound.
Automatic code
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
Standard deviation of the method.
GT TODO.
Lt TODO.
Method result.
methodResults
The identification number of the bioactivity.
Activity ID
Additional information about the bioactivity analysis.
Extra Information
Observation information about the bioactivity analysis.
Observation
Bioactivity Code TODO.
Code
Bioactivity concentration? TODO.
Concentration
positionActivity TODO.
Position activity
A one word description of the observed properties during bioactivity analysis.
Results
The species of which a chemical compound is part of.
Species
The family of which a chemical compound is part of.
Family
The gender of which a chemical compound is part of.
Gender
The Subclass of which a chemical compound is part of.
Subclass
The Class of which a chemical compound is part of.
Class
The entity from which 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 jsut by it's short code.
Isolation state
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
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
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.
Ld 50
The EC50 is the concentration of a drug that gives half-maximal response.
EC 50
The minimum inhibitory concentration (MIC) is the lowest concentration of a chemical, usually a drug, which prevents visible growth of a bacterium or bacteria.
MIC
The minimum fungicidal concentrations(MFC) was defined as the lowest concentration of drug showing no visible growth.
MFC
ED TODO.
DL TODO.
Inhibition TODO.
Inhibition
Unique identifiers of a chemical compound like smiles and inchikeys.
Unique identifiers
The biological taxonomy of a chemical compound.
Taxonomy
Information on where and from what the chemical compound has been isolated.
Isolation