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:
- License:
- Visualization:
- Cite as:
- Edgard Marx, Stefan Schmidt-Dichte, Istvan J. Mocsy. nubbe: The data model for nubbeDB Knowledge Graph. Revision: SNAPSHOT.
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
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
- Bioactivity
- Bioactivity analysis
- City
- Compound
- Constitutional descriptors
- Descriptors
- Electronic descriptors
- Isolation site
- Isolation type
- Metabolic class
- Metabolic subclass
- Molecular descriptors
- Publication
- Publication type
- Species
- State
- Topological descriptors
- Unique identifiers
Object Properties
- has descriptors
- is identified by
- part of class
- part of species
- part of subclass
- revealed
- was discovered at
- was isolated from
- was mentioned in
- was published as
- was subjected to
Data Properties
- Common name
- EC50
- ED50
- hydrogen bond acceptor count
- hydrogen bond donor count
- IC12
- IC50
- inchi
- inchikey
- IUPAC Name
- LD50
- Lipinski rule of 5 failures
- logP Coefficient
- MFC
- MIC
- Molecular formula
- Molecular volume
- Molecular weight
- Monoisotopic mass
- nRotB
- NUBBE ID
- Publication agency
- Publication ID
- Publication page numbers
- Publication title
- Publication volume
- Publication year
- Publications citation extra information
- Publications events
- Publications local publishments
- Publications periodic magazine
- Publications process
- Publications publisher
- SMILES
- Sub-Pub ID
- TPSA
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
- Bioactivity
- Bioactivity analysis
- City
- Compound
- Constitutional descriptors
- Descriptors
- Electronic descriptors
- Isolation site
- Isolation type
- Metabolic class
- Metabolic subclass
- Molecular descriptors
- Publication
- Publication type
- Species
- State
- Topological descriptors
- Unique identifiers
Bioactivityc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#Bioactivity
- is in range of
- revealed op
Bioactivity analysisc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#BioactivityAnalysis
Cityc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#City
- has super-classes
- Isolation site c
Compoundc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#Compound
- is in domain of
- Common name dp, Molecular formula dp, SMILES dp, has descriptors op, is identified by op, part of class op, part of species op, part of subclass op, was discovered at op, was isolated from op, was mentioned in op, was subjected to op
Constitutional descriptorsc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#ConstitutionalDescriptors
- 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
- 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
- has super-classes
- Descriptors c
- is in domain of
- hydrogen bond acceptor count dp, hydrogen bond donor count dp
Isolation sitec back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#IsolationSite
- has sub-classes
- City c, State c
- is in range of
- was discovered at op
Isolation typec back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#IsolationType
- is in range of
- was isolated from op
Metabolic classc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#MetabolicClass
- is in range of
- part of class op
Metabolic subclassc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#MetabolicSubclass
- is in range of
- part of subclass op
Molecular descriptorsc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#MolecularDescriptors
- has super-classes
- Descriptors c
- is in domain of
- 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
- is in domain of
- Publication ID dp, Publication agency dp, Publication page numbers dp, Publication title dp, Publication volume dp, Publication year dp, Publications citation extra information dp, Publications events dp, Publications local publishments dp, Publications periodic magazine dp, Publications process dp, Publications publisher dp, Sub-Pub ID dp, was published as op
- is in range of
- was mentioned in op
Publication typec back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#PublicationType
- is in range of
- was published as op
Speciesc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#Species
- is in range of
- part of species op
Statec back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#State
- has super-classes
- Isolation site c
Topological descriptorsc back to ToC or Class ToC
IRI: http://nubbekg.aksw.org/ontology#TopologicalDescriptors
- 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
- is in domain of
- IUPAC Name dp, NUBBE ID dp, inchi dp, inchikey dp
- is in range of
- is identified by op
Object Properties
- has descriptors
- is identified by
- part of class
- part of species
- part of subclass
- revealed
- was discovered at
- was isolated from
- was mentioned in
- was published as
- was subjected to
has descriptorsop back to ToC or Object Property ToC
IRI: http://nubbekg.aksw.org/ontology#hasDescriptors
- 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
- has domain
- Compound c
- has range
- Unique identifiers c
part of classop back to ToC or Object Property ToC
IRI: http://nubbekg.aksw.org/ontology#partOfClass
- 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
part of subclassop back to ToC or Object Property ToC
IRI: http://nubbekg.aksw.org/ontology#partOfSubclass
- has domain
- Compound c
- has range
- Metabolic subclass c
revealedop back to ToC or Object Property ToC
IRI: http://nubbekg.aksw.org/ontology#revealed
- has domain
- Bioactivity analysis c
- has range
- Bioactivity c
was discovered atop back to ToC or Object Property ToC
IRI: http://nubbekg.aksw.org/ontology#wasDiscoveredAt
- has domain
- Compound c
- has range
- Isolation site c
was isolated fromop back to ToC or Object Property ToC
IRI: http://nubbekg.aksw.org/ontology#wasIsolatedFrom
- has domain
- Compound c
- has range
- Isolation type c
was mentioned inop back to ToC or Object Property ToC
IRI: http://nubbekg.aksw.org/ontology#wasMentionedIn
- has domain
- Compound c
- has range
- Publication c
was published asop back to ToC or Object Property ToC
IRI: http://nubbekg.aksw.org/ontology#wasPublishedAs
- has domain
- Publication c
- has range
- Publication type c
was subjected toop back to ToC or Object Property ToC
IRI: http://nubbekg.aksw.org/ontology#wasSubjectedTo
- has domain
- Compound c
- has range
- Bioactivity analysis c
Data Properties
- Common name
- EC50
- ED50
- hydrogen bond acceptor count
- hydrogen bond donor count
- IC12
- IC50
- inchi
- inchikey
- IUPAC Name
- LD50
- Lipinski rule of 5 failures
- logP Coefficient
- MFC
- MIC
- Molecular formula
- Molecular volume
- Molecular weight
- Monoisotopic mass
- nRotB
- NUBBE ID
- Publication agency
- Publication ID
- Publication page numbers
- Publication title
- Publication volume
- Publication year
- Publications citation extra information
- Publications events
- Publications local publishments
- Publications periodic magazine
- Publications process
- Publications publisher
- SMILES
- Sub-Pub ID
- TPSA
Common namedp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#commonName
EC50dp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#EC50
- has domain
- Bioactivity analysis c
- has range
- double
ED50dp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#ED50
- has domain
- Bioactivity analysis c
- has range
- double
hydrogen bond acceptor countdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#hBondAcceptorCount
- 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
- has domain
- Electronic descriptors c
- has range
- int
IC12dp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#IC12
- has domain
- Bioactivity analysis c
- has range
- double
IC50dp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#IC50
- has domain
- Bioactivity analysis c
- has range
- double
inchidp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#inchi
- has domain
- Unique identifiers c
- has range
- string
inchikeydp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#inchikey
- has domain
- Unique identifiers c
- has range
- string
IUPAC Namedp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#iupacName
- has domain
- Unique identifiers c
- has range
- string
LD50dp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#LD50
- has domain
- Bioactivity analysis c
- has range
- double
Lipinski rule of 5 failuresdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#lipinskiRuleOf5Failures
- has domain
- Constitutional descriptors c
- has range
- int
logP Coefficientdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#logpCoefficient
- has domain
- Constitutional descriptors c
- has range
- float
MFCdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#MFC
- has domain
- Bioactivity analysis c
- has range
- double
MICdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#MIC
- has domain
- Bioactivity analysis c
- has range
- double
Molecular formuladp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#molecularFormula
Molecular volumedp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#molecularVolume
- has domain
- Molecular descriptors c
- has range
- float
Molecular weightdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#molecularWeight
- has domain
- Molecular descriptors c
- has range
- float
Monoisotopic massdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#monoisotopicMass
- has domain
- Molecular descriptors c
- has range
- float
nRotBdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#nrotb
- has domain
- Molecular descriptors c
- has range
- float
NUBBE IDdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#nubbeId
- has domain
- Unique identifiers c
- has range
- string
Publication agencydp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationAgency
- has domain
- Publication c
- has range
- string
Publication IDdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationId
- has domain
- Publication c
- has range
- int
Publication page numbersdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationPages
- has domain
- Publication c
- has range
- string
Publication titledp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationTitle
- has domain
- Publication c
- has range
- string
Publication volumedp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationVolume
- has domain
- Publication c
- has range
- string
Publication yeardp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationYear
- has domain
- Publication c
- has range
- int
Publications citation extra informationdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationCitationExtra
- has domain
- Publication c
- has range
- string
Publications eventsdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationEvent
- has domain
- Publication c
- has range
- string
Publications local publishmentsdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationLocal
- has domain
- Publication c
- has range
- string
Publications periodic magazinedp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationPeriodic
- has domain
- Publication c
- has range
- string
Publications processdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationProcess
- has domain
- Publication c
- has range
- string
Publications publisherdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#publicationPublisher
- has domain
- Publication c
- has range
- string
SMILESdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#smiles
Sub-Pub IDdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#subpubId
- has domain
- Publication c
- has range
- int
TPSAdp back to ToC or Data Property ToC
IRI: http://nubbekg.aksw.org/ontology#tpsa
- has domain
- Topological descriptors c
- has range
- float
Legend back to ToC
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.